Contacts of the helix formed by residues 28 - 70 (chain T) in PDB entry 1PP9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 28 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R ASP* 3.0 47.4 + - - -
24T ARG* 4.1 13.6 + - - +
26T PHE 3.3 2.2 + - - -
27T PRO* 1.3 73.9 - - - +
29T TYR* 1.3 65.8 + - - +
30T PHE 3.4 2.2 - - - -
31T SER* 3.0 27.1 - - - +
32T LYS* 2.9 45.8 + - + +
33T GLY 3.4 3.8 + - - -
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Residues in contact with TYR 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220Q TYR* 2.9 38.6 + + - -
224Q ARG* 3.7 18.2 - - - +
3003Q CDL 3.4 53.7 - - + +
26T PHE* 3.5 39.5 + + + +
27T PRO 3.0 5.5 + - - -
28T HIS* 1.3 73.8 - - - +
30T PHE* 1.3 93.0 + + + +
33T GLY* 2.9 27.5 + - - -
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Residues in contact with PHE 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003Q CDL 3.9 14.1 - - + -
29T TYR* 1.3 106.7 - + + +
31T SER* 1.3 68.8 + - - +
32T LYS 3.1 2.5 + - - -
34T ILE* 3.0 41.5 + - + +
35T PRO* 3.7 0.2 - - - +
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Residues in contact with SER 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T HIS* 3.0 44.8 - - - +
30T PHE* 1.3 78.9 - - - +
32T LYS* 1.3 61.4 + - - +
35T PRO* 3.3 18.0 - - - +
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Residues in contact with LYS 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3003Q CDL 5.7 0.2 - - - -
12R ASP* 4.9 6.1 - - - +
27T PRO 5.6 0.2 - - - +
28T HIS* 2.9 42.9 + - + +
31T SER* 1.3 80.1 + - - +
33T GLY* 1.3 65.6 + - - +
35T PRO* 3.2 14.1 - - - +
36T ASN* 3.2 16.6 + - - +
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Residues in contact with GLY 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003Q CDL 4.0 31.3 + - - -
28T HIS 3.4 1.4 + - - -
29T TYR* 2.9 23.5 + - - -
32T LYS* 1.3 76.3 - - - +
34T ILE* 1.3 59.1 + - - +
36T ASN* 3.1 3.5 + - - +
37T VAL* 2.9 32.6 + - - +
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Residues in contact with ILE 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003Q CDL 3.4 26.9 - - + +
30T PHE* 3.0 32.5 - - + +
33T GLY* 1.3 74.7 - - - +
35T PRO* 1.3 70.4 - - + +
37T VAL* 2.9 8.9 + - + +
38T LEU* 2.8 47.6 + - + +
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Residues in contact with PRO 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T PHE 3.7 0.9 - - - +
31T SER 3.3 20.2 - - - +
32T LYS* 3.2 18.2 - - - +
34T ILE* 1.3 94.7 - - + +
36T ASN* 1.3 56.0 + - - +
38T LEU* 3.5 12.1 + - + +
39T ARG* 3.0 27.9 + - - +
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Residues in contact with ASN 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003Q CDL 2.6 30.0 + - - +
71S ARG 4.2 3.2 + - - -
72S GLN* 2.9 25.3 + - - +
73S GLN* 4.4 12.0 - - - +
32T LYS 3.2 10.4 + - - +
33T GLY 3.1 4.6 + - - +
34T ILE 3.1 0.6 - - - -
35T PRO* 1.3 79.5 - - - +
37T VAL* 1.3 59.2 + - - +
39T ARG* 3.2 29.1 + - - +
40T ARG* 3.0 45.6 + - - +
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Residues in contact with VAL 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003Q CDL 3.8 38.6 - - - +
33T GLY 2.9 19.2 + - - +
34T ILE* 2.9 10.3 + - + +
36T ASN* 1.3 73.6 - - - +
38T LEU* 1.3 63.7 + - + +
40T ARG* 3.3 8.4 + - - +
41T THR* 2.7 44.7 + - - +
3004T CDL 3.9 31.9 - - + +
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Residues in contact with LEU 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T ILE* 2.8 38.9 + - + +
35T PRO* 3.7 9.0 - - + +
37T VAL* 1.3 82.1 - - + +
39T ARG* 1.3 57.4 + - - +
41T THR* 3.3 7.3 + - + +
42T ARG* 2.9 58.9 + - - +
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Residues in contact with ARG 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3007P PEE 5.3 4.2 + - - -
28S LYS* 6.2 0.2 - - - +
72S GLN 3.1 26.7 + - - -
73S GLN* 4.0 9.9 - - - +
74S ILE* 3.9 42.4 - - - +
35T PRO 3.0 18.1 + - - +
36T ASN* 3.2 18.7 + - - +
38T LEU* 1.3 76.7 - - - +
40T ARG* 1.3 80.0 + - - +
42T ARG* 3.3 9.4 + - - +
43T ALA* 2.9 32.0 + - + +
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Residues in contact with ARG 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3007P PEE 4.4 4.7 - - - +
3003Q CDL 3.2 37.4 + - - -
72S GLN* 3.6 19.0 - - - +
36T ASN* 3.0 35.8 + - - +
37T VAL* 3.7 5.0 - - - +
39T ARG* 1.3 95.0 - - - +
41T THR* 1.3 64.4 + - - +
43T ALA* 3.4 6.8 + - - +
44T CYS* 3.3 23.9 + - - +
3004T CDL 2.8 107.5 + - - +
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Residues in contact with THR 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T VAL* 2.7 29.9 + - - +
38T LEU* 3.6 9.8 - - - +
40T ARG* 1.3 78.4 - - - +
42T ARG* 1.3 59.0 + - + +
44T CYS* 3.5 5.4 - - - -
45T ILE* 3.0 42.3 + - + +
3004T CDL 3.2 36.3 + - + +
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Residues in contact with ARG 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T LEU* 2.9 43.0 + - + +
39T ARG* 3.7 7.3 - - - +
41T THR* 1.3 78.3 - - + +
43T ALA* 1.3 64.7 + - - +
44T CYS 3.2 0.9 + - - -
45T ILE* 3.7 12.9 + - - +
46T LEU* 4.3 11.3 - - - +
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Residues in contact with ALA 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28S LYS* 5.9 5.4 - - - +
39T ARG* 2.9 26.7 + - + +
40T ARG* 3.7 8.3 - - - +
42T ARG* 1.3 77.9 - - - +
44T CYS* 1.3 58.2 + - + +
46T LEU* 5.2 0.9 + - - +
47T ARG* 3.4 24.1 + - - -
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Residues in contact with CYS 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322P GLN* 5.7 1.8 - - - +
3007P PEE 3.8 35.4 - - - -
40T ARG 3.3 14.2 + - - +
41T THR* 3.5 10.5 - - - -
42T ARG 3.2 0.2 - - - -
43T ALA* 1.3 80.7 - - + +
45T ILE* 1.3 61.3 + - - +
46T LEU 3.3 2.9 - - - -
47T ARG* 2.7 35.5 + - + +
48T VAL* 3.0 18.6 + - + -
3004T CDL 4.0 26.2 - - - +
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Residues in contact with ILE 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41T THR* 3.0 31.6 + - + +
42T ARG* 3.7 6.8 + - - +
44T CYS* 1.3 79.1 - - - +
46T LEU* 1.3 83.2 + - + +
48T VAL* 4.5 4.0 - - + +
49T ALA* 2.9 61.7 + - + +
50T PRO* 3.4 0.3 - - - +
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Residues in contact with LEU 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323P CYS* 4.4 7.3 - - - -
42T ARG 4.3 10.7 + - - +
43T ALA 5.2 1.1 + - - +
44T CYS 3.1 1.4 + - - -
45T ILE* 1.3 94.5 - - + +
47T ARG* 1.3 63.9 + - - +
50T PRO* 3.4 27.8 - - + +
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Residues in contact with ARG 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316P MET 4.8 2.0 + - - -
319P PRO* 3.8 23.8 - - + +
322P GLN* 2.9 50.6 + - + +
323P CYS* 4.0 30.3 - - - -
326P TRP* 3.4 20.0 - - + +
23S ALA* 2.9 37.8 + - - +
43T ALA 3.4 25.7 + - - -
44T CYS* 2.7 18.0 + - - +
46T LEU* 1.3 79.7 - - + +
48T VAL* 1.3 62.6 + - + +
50T PRO* 4.3 0.7 - - - -
51T PRO* 4.0 6.6 - - - +
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Residues in contact with VAL 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P TRP* 3.5 32.8 - - + +
3007P PEE 3.3 47.3 - - + +
44T CYS* 3.0 21.3 + - + +
45T ILE* 4.4 4.3 - - + +
47T ARG* 1.3 79.3 - - + +
49T ALA* 1.3 59.0 + - - +
50T PRO 3.7 0.2 - - - -
51T PRO* 3.2 11.8 - - - +
52T PHE* 3.1 35.8 - - + -
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Residues in contact with ALA 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T ILE* 2.9 42.8 + - + +
48T VAL* 1.3 74.8 - - + +
50T PRO* 1.3 68.8 - - + +
52T PHE* 2.9 19.8 + - - +
53T VAL* 3.0 21.7 + - + +
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Residues in contact with PRO 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T ILE 3.4 6.3 - - - +
46T LEU* 3.4 35.4 - - + +
47T ARG 4.3 0.2 - - - -
48T VAL 3.8 0.2 - - - -
49T ALA* 1.3 87.8 - - + +
51T PRO* 1.3 72.8 - - + +
53T VAL* 2.9 12.2 + - + +
54T ALA* 2.8 22.6 + - - +
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Residues in contact with PRO 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323P CYS* 4.1 8.7 - - + +
326P TRP* 3.5 29.6 - - + +
327P ALA* 3.7 27.6 - - + +
330P ALA* 3.5 13.4 - - + +
47T ARG 4.0 4.7 - - - +
48T VAL 3.2 16.8 - - - +
50T PRO* 1.3 95.8 - - + +
52T PHE* 1.3 55.9 + - + +
54T ALA* 3.3 9.9 + - + +
55T PHE 2.9 21.7 + - - -
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Residues in contact with PHE 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P TRP* 3.7 26.2 - + - -
329P VAL* 3.7 28.0 - - + -
330P ALA* 3.9 22.4 - - + -
333P LEU* 4.1 25.8 - - + -
3007P PEE 4.2 16.6 - - + -
48T VAL* 3.1 35.7 - - + -
49T ALA* 2.9 8.6 + - - +
51T PRO* 1.3 74.9 - - + +
53T VAL* 1.3 61.3 + - + +
55T PHE* 3.4 8.8 + + + +
56T TYR* 3.0 26.2 + - - +
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Residues in contact with VAL 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49T ALA* 3.0 25.7 + - + +
50T PRO* 2.9 11.7 + - + +
52T PHE* 1.3 74.6 - - + +
54T ALA* 1.3 60.6 + - - +
56T TYR* 3.0 10.4 + - + +
57T LEU* 2.9 46.3 + - + +
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Residues in contact with ALA 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50T PRO 2.8 11.0 + - - +
51T PRO* 3.3 13.9 - - + +
53T VAL* 1.3 78.1 - - - +
55T PHE* 1.3 56.7 + - - +
57T LEU* 3.1 13.1 + - - +
58T VAL* 2.8 38.1 + - + +
----------------------------------------------------------
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Residues in contact with PHE 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330P ALA* 4.2 9.2 - - + -
333P LEU* 3.8 42.4 - - + -
334P THR* 3.2 41.7 - - + +
337P TRP* 4.2 19.5 - + + -
51T PRO 2.9 13.3 + - - +
52T PHE* 3.5 15.0 - + + +
53T VAL 3.2 0.2 - - - -
54T ALA* 1.3 76.1 - - - +
56T TYR* 1.3 60.3 + + + +
58T VAL* 3.3 6.9 + - + +
59T TYR* 2.7 61.8 + + + +
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Residues in contact with TYR 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52T PHE 3.0 14.0 + - - +
53T VAL* 3.3 12.8 - - + +
55T PHE* 1.3 86.7 - + + +
57T LEU* 1.3 73.4 + - + +
59T TYR* 3.3 10.3 + + - +
60T THR* 2.9 58.8 + - + +
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Residues in contact with LEU 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53T VAL* 2.9 33.8 + - + +
54T ALA* 3.5 11.0 - - - +
56T TYR* 1.3 89.6 - - + +
58T VAL* 1.3 61.3 + - + +
60T THR* 3.2 7.6 + - - +
61T TRP* 2.9 33.6 + - - +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334P THR* 5.1 7.4 - - + +
337P TRP* 3.8 8.8 - - + -
350P ILE* 3.9 35.7 - - + -
54T ALA* 2.8 27.4 + - + +
55T PHE* 3.8 6.7 - - + +
57T LEU* 1.3 72.5 - - + +
59T TYR* 1.3 58.6 + - - +
61T TRP* 4.5 7.1 - - + -
62T GLY* 2.9 28.1 + - - -
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Residues in contact with TYR 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337P TRP* 3.4 52.1 - + - -
55T PHE* 2.7 45.1 + + + +
56T TYR* 3.6 13.7 - + - +
58T VAL* 1.3 73.5 - - - +
60T THR* 1.3 78.7 + - + +
63T THR* 2.9 47.7 + - + +
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Residues in contact with THR 60 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56T TYR* 2.9 59.0 + - + +
57T LEU* 3.2 14.2 + - - +
59T TYR* 1.3 85.5 - - + +
61T TRP* 1.3 65.6 + - - +
63T THR* 3.9 2.9 - - - -
64T GLN* 2.9 38.4 + - - +
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Residues in contact with TRP 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345P HIS* 5.4 2.2 - - - -
346P PRO* 3.9 33.0 - - + -
350P ILE* 4.2 14.4 - - + -
57T LEU 2.9 19.4 + - - +
58T VAL* 3.9 7.0 - - + +
60T THR* 1.3 81.8 + - - +
62T GLY* 1.3 74.6 + - - +
64T GLN* 3.8 6.8 - - + +
65T GLU* 2.9 50.6 + - + +
----------------------------------------------------------
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Residues in contact with GLY 62 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337P TRP* 4.5 2.7 - - - -
346P PRO* 3.7 16.7 - - - +
347P TYR* 3.9 7.1 - - - -
350P ILE* 4.0 8.5 - - - -
58T VAL 2.9 16.7 + - - -
59T TYR 4.1 0.4 - - - -
61T TRP* 1.3 90.3 - - - +
63T THR* 1.3 62.3 + - - +
65T GLU 3.4 0.5 + - - -
66T PHE* 3.0 24.1 + - - +
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Residues in contact with THR 63 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337P TRP* 3.9 7.8 + - - -
347P TYR* 3.7 16.3 + - - +
59T TYR* 2.9 43.6 + - + +
60T THR* 3.9 4.9 - - - -
62T GLY* 1.3 74.4 - - - +
64T GLN* 1.3 63.5 + - + +
66T PHE* 3.2 4.2 + - + +
67T GLU* 2.9 46.0 + - + +
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Residues in contact with GLN 64 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60T THR* 2.9 32.6 + - - +
61T TRP* 3.8 6.1 - - + +
63T THR* 1.3 78.5 - - + +
65T GLU* 1.3 62.7 + - - +
67T GLU* 3.1 9.6 + - - +
68T LYS* 2.9 32.6 + - + +
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Residues in contact with GLU 65 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345P HIS* 3.1 34.0 + - + -
346P PRO* 3.8 12.1 - - + -
61T TRP* 2.9 42.7 + - + +
62T GLY 3.7 4.3 - - - +
64T GLN* 1.3 77.0 - - - +
66T PHE* 1.3 61.7 + - - +
68T LYS* 3.9 15.3 - - - +
69T SER* 3.2 22.8 + - - -
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Residues in contact with PHE 66 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341P GLN* 5.5 2.2 - - - -
342P PRO* 4.0 18.2 - - + -
344P GLU* 3.5 32.1 - - + -
345P HIS 3.5 15.9 - - - -
346P PRO* 4.1 7.2 - - + +
347P TYR* 3.5 33.4 - + + +
62T GLY 3.0 15.2 + - - +
63T THR* 3.3 9.4 - - + +
65T GLU* 1.3 75.4 - - - +
67T GLU* 1.3 78.4 + - - +
69T SER* 2.8 23.3 + - - -
70T LYS* 3.3 46.6 - - + +
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Residues in contact with GLU 67 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T THR* 2.9 32.6 - - + +
64T GLN* 3.1 7.4 + - - +
66T PHE* 1.3 86.7 - - - +
68T LYS* 1.3 69.6 + - - +
70T LYS* 2.8 25.1 + - - +
71T ARG* 3.7 11.4 + - - +
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Residues in contact with LYS 68 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64T GLN* 2.9 22.4 + - + +
65T GLU* 3.9 17.7 - - - +
67T GLU* 1.3 76.2 - - - +
69T SER* 1.3 62.9 + - - +
70T LYS 3.1 1.2 + - - -
71T ARG* 3.2 29.3 + - + +
----------------------------------------------------------
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Residues in contact with SER 69 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345P HIS* 4.3 21.9 + - - -
65T GLU* 3.2 15.1 + - - -
66T PHE* 2.8 18.9 + - - -
67T GLU 3.1 0.8 - - - -
68T LYS* 1.3 78.3 - - - +
70T LYS* 1.3 63.0 + - - +
71T ARG 3.3 2.8 + - - +
73T ASN* 5.4 1.6 - - - +
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Residues in contact with LYS 70 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344P GLU* 4.8 9.2 + - - +
2Q ASP* 4.3 18.6 + - - -
3Q LEU* 4.2 23.8 - - + +
4Q GLU* 4.2 19.8 + - - +
66T PHE* 3.3 52.4 - - + +
67T GLU* 2.8 15.3 + - - +
69T SER* 1.3 80.5 - - - +
71T ARG* 1.3 59.2 + - - +
73T ASN* 4.9 2.8 - - - +
56U GLU* 4.1 4.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il