Contacts of the helix formed by residues 27 - 50 (chain H) in PDB entry 3A0B
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 THR 27 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B PHE* 4.2 6.8 - - - -
219B VAL* 4.7 8.2 - - + +
220B ARG 4.1 6.1 - - - +
222B PRO* 3.1 35.4 - - + +
22H ALA* 5.7 1.1 - - + -
25H TRP 2.6 6.5 + - - -
26H GLY* 1.3 71.5 - - - -
28H THR* 1.3 62.1 + - - +
29H PRO* 3.5 1.8 - - - -
30H LEU* 3.3 18.5 + - - +
31H MET 3.5 2.1 + - - -
1017H CLA 2.7 44.0 + - - +
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Residues in contact with THR 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B PRO* 4.4 0.2 - - - +
225B LEU* 3.2 30.1 - - + +
25H TRP* 3.0 36.5 + - + +
27H THR* 1.3 75.9 - - - +
29H PRO* 1.3 64.2 - - + +
31H MET* 2.6 48.9 + - + +
32H ALA* 3.2 10.3 + - + -
1017H CLA 3.8 4.7 + - - -
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Residues in contact with PRO 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H TRP* 4.4 16.8 - - + -
26H GLY 3.8 14.6 - - - +
27H THR 3.8 0.4 - - - -
28H THR* 1.3 95.9 - - + +
30H LEU* 1.3 62.9 + - - +
31H MET 3.1 0.5 + - - -
32H ALA* 3.6 5.5 + - + +
33H VAL* 3.3 24.1 + - - +
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Residues in contact with LEU 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B PHE* 4.9 8.1 - - + -
27H THR* 3.3 17.3 + - - +
28H THR 2.9 2.8 + - - -
29H PRO* 1.3 78.5 - - - +
31H MET* 1.3 59.2 + - - +
33H VAL* 3.1 25.8 - - + +
34H PHE* 3.4 26.4 - - + -
1017H CLA 3.4 19.5 - - + -
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Residues in contact with MET 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LEU* 4.8 9.0 - - + -
27H THR 3.5 1.6 + - - -
28H THR* 2.6 25.7 + - + +
30H LEU* 1.3 68.1 - - - +
32H ALA* 1.3 57.1 + - + +
33H VAL 2.7 4.8 + - - -
34H PHE* 2.6 31.1 + - - +
35H MET* 3.1 43.0 + - + +
1017H CLA 3.1 96.4 - - + +
1049H BCR 4.0 8.2 - - + +
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Residues in contact with ALA 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008D CLA 4.9 8.1 - - + +
28H THR* 3.2 13.4 + - + +
29H PRO* 4.0 6.7 - - + +
31H MET* 1.3 80.3 - - + +
33H VAL* 1.3 56.1 + - - +
34H PHE 3.4 0.4 - - - -
35H MET* 3.4 32.8 - - + +
36H GLY* 3.4 16.1 + - - -
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Residues in contact with VAL 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H PRO 3.3 13.9 + - - +
30H LEU* 3.1 30.7 - - + +
31H MET 2.7 0.8 + - - -
32H ALA* 1.3 77.0 - - - +
34H PHE* 1.3 66.0 + - + +
35H MET 3.3 0.4 - - - -
36H GLY* 3.8 3.3 + - - +
37H LEU* 2.7 41.2 + - + +
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Residues in contact with PHE 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009B CLA 4.4 31.2 - - + -
30H LEU* 3.4 36.6 - - + -
31H MET* 2.6 17.0 + - - +
33H VAL* 1.3 79.5 - - + +
35H MET* 1.3 57.1 + - - +
36H GLY 3.3 0.2 - - - -
37H LEU* 3.3 11.3 + - + +
38H PHE* 2.9 25.5 + - - +
1017H CLA 3.4 39.0 - - + -
1049H BCR 3.7 36.8 - - + +
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Residues in contact with MET 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008D CLA 3.4 31.4 - - + -
31H MET* 3.1 35.8 + - + +
32H ALA* 3.4 20.6 - - + +
34H PHE* 1.3 75.5 - - - +
36H GLY* 1.3 57.5 + - - +
37H LEU 3.1 0.2 - - - -
38H PHE* 3.8 8.3 - - + -
39H LEU* 2.6 38.8 + - + +
1017H CLA 3.4 32.8 - - + -
1049H BCR 2.9 41.5 - - + -
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Residues in contact with GLY 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008D CLA 5.6 8.7 - - - +
32H ALA 3.4 14.1 + - - -
33H VAL* 3.8 3.9 + - - -
34H PHE 3.3 0.2 - - - -
35H MET* 1.3 80.5 - - - +
37H LEU* 1.3 66.6 + - - +
39H LEU* 4.4 3.1 - - - +
40H VAL* 3.4 21.3 + - - +
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009B CLA 3.9 42.8 - - + -
33H VAL* 2.7 32.1 - - + +
34H PHE* 3.3 15.2 + - + +
35H MET 3.1 0.2 - - - -
36H GLY* 1.3 81.8 - - - +
38H PHE* 1.3 56.8 + - - +
40H VAL* 2.8 24.7 - - + +
41H PHE 3.1 2.4 + - - -
1049H BCR 2.9 31.5 - - + +
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Residues in contact with PHE 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010B CLA 5.1 5.6 - - + -
1011B CLA 2.9 52.3 - - + -
34H PHE 2.9 16.3 + - - +
35H MET* 3.0 11.0 + - + +
37H LEU* 1.3 74.7 - - - +
39H LEU* 1.3 73.7 + - + +
40H VAL 2.9 2.2 - - - -
41H PHE* 2.6 29.8 + + - +
42H LEU* 2.6 59.6 + - + -
1049H BCR 3.0 60.6 - - + -
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Residues in contact with LEU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011B CLA 3.6 24.5 - - + -
1016B CLA 4.3 31.4 - - + -
1008D CLA 5.0 23.8 - - + -
35H MET* 2.6 21.0 + - + +
36H GLY* 4.4 4.0 - - - +
38H PHE* 1.3 79.0 - - + +
40H VAL* 1.3 60.4 + - - +
42H LEU* 4.0 2.9 - - + +
43H LEU* 3.1 21.1 + - + +
1017H CLA 3.5 43.5 - - + -
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Residues in contact with VAL 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008D CLA 5.7 3.4 - - + -
36H GLY 3.4 11.8 + - - +
37H LEU* 2.8 25.8 - - - +
38H PHE 2.9 0.4 - - - -
39H LEU* 1.3 75.2 - - - +
41H PHE* 1.3 70.4 + - - +
43H LEU* 2.8 8.9 + - + +
44H ILE* 2.6 47.0 + - + +
1049H BCR 4.3 14.6 - - + -
19X PHE* 4.4 0.4 - - + -
23X LEU* 3.4 42.6 - - + -
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Residues in contact with PHE 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PHE* 4.1 18.8 - + - -
1009B CLA 4.2 19.3 - - + -
1010B CLA 3.8 46.7 - + + -
37H LEU 3.2 13.2 - - - +
38H PHE* 2.6 22.3 + + - +
40H VAL* 1.3 75.8 - - - +
42H LEU* 1.3 95.2 + - + +
44H ILE* 2.6 35.8 + - + +
45H ILE* 3.3 28.7 - - + +
1049H BCR 3.4 35.2 - - + -
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Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B PHE* 4.0 25.6 - - + -
1010B CLA 4.2 37.1 - - + +
1011B CLA 4.2 9.6 - - + -
38H PHE* 2.6 53.3 + - + +
39H LEU* 4.0 7.0 - - + +
41H PHE* 1.3 98.4 - - + +
43H LEU* 1.3 58.4 + - - +
45H ILE* 3.3 10.9 + - + +
46H LEU* 3.0 27.8 + - - +
1017H CLA 4.6 11.2 - - + -
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016B CLA 3.7 32.3 - - + -
1008D CLA 3.4 42.6 - - + -
39H LEU* 3.1 13.4 + - + +
40H VAL* 2.8 18.2 + - + +
42H LEU* 1.3 77.3 - - - +
44H ILE* 1.3 54.5 + - - -
46H LEU* 3.9 12.1 - - + -
47H GLU* 3.0 55.1 + - + +
1017H CLA 5.1 2.8 - - + +
19X PHE* 3.9 13.5 - - + -
23X LEU* 5.5 0.7 - - + -
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Residues in contact with ILE 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PHE* 5.7 2.5 - - + -
1009B CLA 4.3 21.1 - - + -
40H VAL* 2.6 46.0 + - + +
41H PHE* 2.6 19.2 + - + +
43H LEU* 1.3 72.0 - - - +
45H ILE* 1.3 66.8 + - + +
47H GLU* 3.8 0.4 + - - -
48H ILE* 2.8 33.6 + - + +
53H LEU* 3.1 12.5 - - + +
1049H BCR 4.2 31.9 - - + -
19X PHE* 3.4 36.6 - - + -
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Residues in contact with ILE 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PHE* 3.9 40.6 - - + +
1010B CLA 3.8 43.3 - - + +
41H PHE* 3.3 50.9 - - + +
42H LEU* 3.4 13.9 - - + +
44H ILE* 1.3 75.8 - - + +
46H LEU* 1.3 56.4 + - - +
47H GLU 3.1 1.8 - - - -
48H ILE* 2.7 29.5 + - + +
49H TYR* 2.7 19.9 + - + +
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Residues in contact with LEU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010B CLA 3.0 36.9 - - + +
1016B CLA 3.4 34.1 - - + -
89D LEU* 5.5 5.8 - - + -
42H LEU 3.0 16.0 + - - +
43H LEU* 3.5 11.4 - - + +
45H ILE* 1.3 78.0 - - - +
47H GLU* 1.3 57.6 + - + +
49H TYR* 3.9 1.5 - - + +
50H ASN* 2.9 30.7 + - - +
1017H CLA 3.7 22.4 - - + -
1058H DGD 4.0 36.8 - - + +
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Residues in contact with GLU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LEU* 4.6 12.3 - - + +
91D LEU* 2.7 34.8 - - + +
93D TRP* 4.6 0.3 + - - -
1008D CLA 4.4 9.0 - - - +
43H LEU* 3.0 34.5 + - + +
44H ILE* 4.2 2.5 - - - +
46H LEU* 1.3 78.7 - - + +
48H ILE* 1.3 54.6 + - - +
50H ASN* 4.0 1.8 - - - -
52H THR* 2.7 27.2 + - - +
53H LEU* 2.6 41.4 + - + +
19X PHE* 3.0 35.0 - - - +
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PHE* 4.8 20.9 - - + +
191B ASN* 6.3 0.7 - - - -
192B PRO* 6.3 0.7 - - + -
44H ILE* 2.8 33.2 - - + +
45H ILE* 2.7 25.7 + - + +
47H GLU* 1.3 72.6 - - - +
49H TYR* 1.3 66.7 + - - +
51H SER* 3.3 11.4 + - - -
53H LEU* 3.3 33.5 - - + +
54H ILE* 5.7 0.2 - - - -
55H LEU* 3.4 23.8 - - + -
58H VAL* 4.3 23.1 - - + -
60H VAL* 3.8 19.0 - - + +
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Residues in contact with TYR 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B PRO* 3.1 37.5 - - + +
193B TYR* 4.9 4.9 - + - -
251B VAL* 5.7 0.7 - - + -
254B GLY 6.3 0.4 - - - -
255B THR* 4.2 10.3 - - + +
258B TYR* 4.0 7.3 + - + +
259B GLY 3.1 24.5 + - - -
260B SER* 3.8 8.8 + - - -
1010B CLA 3.2 45.9 + - + -
45H ILE* 2.7 15.0 + - + +
46H LEU* 3.9 3.8 - - + +
48H ILE* 1.3 76.1 - - - +
50H ASN* 1.3 54.2 + - - +
51H SER* 2.6 23.3 + - - -
60H VAL* 4.3 13.7 - - + +
1058H DGD 2.7 52.9 - - + +
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Residues in contact with ASN 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D HIS 3.1 11.6 + - - +
88D SER* 3.0 27.8 + - - +
89D LEU* 2.8 46.0 + - + +
46H LEU 2.9 21.3 + - - +
47H GLU* 4.3 0.4 - - - -
48H ILE 3.4 0.4 - - - -
49H TYR* 1.3 74.8 - - - +
51H SER* 1.3 69.1 + - - +
52H THR* 3.5 8.7 + - - +
1058H DGD 3.5 35.6 + - + +
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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) + - + + + + + -
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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