Contacts of the helix formed by residues 6 - 49 (chain A) in PDB entry 1NH4
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 PRO 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 1.3 65.3 - - - +
8A LYS* 3.3 3.8 - - - +
9A ALA* 3.5 12.3 - - - +
10A ALA* 3.3 18.6 - - + -
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Residues in contact with ALA 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 1.3 70.6 - - - +
8A LYS* 1.3 58.6 + - - +
10A ALA* 2.9 9.6 + - + +
11A PHE* 2.6 38.3 + - + +
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 5.1 1.6 - - + -
7A ALA* 1.3 79.2 - - - +
9A ALA* 1.3 49.6 + - - +
11A PHE* 4.1 4.5 - - - +
12A ASP* 2.7 47.7 + - + +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 3.5 12.6 - - + +
7A ALA 3.1 0.4 - - - -
8A LYS* 1.3 77.7 - - - +
10A ALA* 1.3 54.9 + - - +
12A ASP* 4.3 3.8 - - - -
13A SER* 2.3 47.1 + - - +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO 3.3 11.8 - - - -
7A ALA* 2.9 13.6 + - - +
9A ALA* 1.3 80.6 - - - +
11A PHE* 1.3 58.2 + - - +
13A SER* 3.9 3.3 - - - -
14A LEU* 3.0 30.5 + - - +
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Residues in contact with PHE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 2.6 19.3 + - + +
8A LYS* 4.1 4.0 - - - +
10A ALA* 1.3 71.0 - - - +
12A ASP* 1.3 62.5 + - + +
14A LEU* 3.9 7.4 - - + +
15A GLN* 3.0 51.2 + - + +
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Residues in contact with ASP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 2.7 32.0 + - + +
9A ALA* 4.2 3.1 - - - +
11A PHE* 1.3 75.6 - - + +
13A SER* 1.3 65.0 + - - +
15A GLN* 3.5 15.2 + - - +
16A ALA* 3.1 25.6 + - - +
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Residues in contact with SER 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 2.3 36.1 + - - +
10A ALA* 3.9 4.7 - - - -
12A ASP* 1.3 76.0 - - - +
14A LEU* 1.3 55.0 + - - +
16A ALA* 3.4 5.3 + - - +
17A SER* 2.8 42.9 + - - -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 3.0 20.8 + - - +
11A PHE* 3.9 8.3 - - + +
13A SER* 1.3 74.8 - - - +
15A GLN* 1.3 58.0 + - - +
17A SER* 3.6 8.9 - - - -
18A ALA* 2.7 48.6 + - + +
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Residues in contact with GLN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.0 38.4 + - + +
12A ASP* 3.7 15.8 - - - +
14A LEU* 1.3 79.3 - - - +
16A ALA* 1.3 50.6 + - - +
18A ALA* 4.4 2.8 - - - +
19A THR* 1.8 53.4 + - - +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 3.1 20.6 + - - +
13A SER* 3.6 4.9 - - - +
15A GLN* 1.3 75.8 - - - +
17A SER* 1.3 58.2 + - - +
19A THR* 3.9 4.5 - - - -
20A GLU* 2.4 57.4 + - + +
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 2.8 32.9 + - - -
14A LEU* 3.6 11.2 - - - -
16A ALA* 1.3 72.6 - - - +
18A ALA* 1.3 57.6 + - - +
20A GLU* 4.1 6.4 - - - +
21A MET* 2.9 34.2 + - - +
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 2.7 29.6 + - + +
15A GLN* 4.4 2.5 - - - +
17A SER* 1.3 74.9 - - - +
19A THR* 1.3 57.0 + - - +
21A MET* 4.1 4.6 - - - +
22A ILE* 3.0 29.3 + - - +
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Residues in contact with THR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 1.8 47.1 + - + +
16A ALA* 3.5 5.2 - - - -
18A ALA* 1.3 75.4 - - - +
20A GLU* 1.3 65.9 + - + +
22A ILE* 2.3 38.3 - - + +
23A GLY* 3.4 1.7 + - - -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 2.4 48.2 + - + +
17A SER* 4.1 4.5 - - - +
19A THR* 1.3 75.5 - - + +
21A MET* 1.3 59.2 + - - +
23A GLY* 3.2 11.3 + - - -
24A TYR* 2.9 30.9 + - + -
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Residues in contact with MET 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 2.9 22.5 + - - +
18A ALA* 4.1 5.4 - - - +
20A GLU* 1.3 74.5 - - - +
22A ILE* 1.3 61.4 + - - +
24A TYR* 2.9 47.6 + - + +
25A ALA* 3.2 7.7 + - + +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 3.0 17.6 + - - +
19A THR* 2.3 39.9 - - + +
21A MET* 1.3 77.0 - - - +
23A GLY* 1.3 63.7 + - - +
25A ALA* 3.6 7.8 + - + +
26A TRP* 3.3 21.4 + - + +
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR 4.3 0.9 - - - -
20A GLU* 3.2 8.6 + - - -
21A MET 3.0 0.8 - - - -
22A ILE* 1.3 87.4 - - - +
24A TYR* 1.3 57.4 + - - +
26A TRP* 3.8 6.3 - - - +
27A ALA* 2.8 32.8 + - - +
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 2.9 41.2 + - + -
21A MET* 2.9 33.3 + - + +
23A GLY* 1.3 75.3 - - - +
25A ALA* 1.3 55.6 + - - +
27A ALA* 3.6 5.2 - - + +
28A MET* 2.6 40.9 + - - +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.2 7.8 + - + +
22A ILE* 3.8 11.9 - - + +
24A TYR* 1.3 80.3 - - - +
26A TRP* 1.3 53.3 + - - +
28A MET* 4.4 10.1 - - + -
29A VAL* 2.5 51.5 + - + +
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Residues in contact with TRP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.3 15.1 + - + +
23A GLY* 3.8 6.7 - - - +
25A ALA* 1.3 78.7 - - - +
27A ALA* 1.3 54.4 + - - +
29A VAL* 4.4 6.3 - - + -
30A VAL* 2.3 71.8 + - + +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 2.8 20.2 + - - +
24A TYR* 3.6 6.5 - - - +
26A TRP* 1.3 81.4 - - + +
28A MET* 1.3 54.4 + - - +
30A VAL* 4.0 2.6 - - - +
31A VAL* 2.7 42.2 + - + +
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Residues in contact with MET 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR 2.6 21.6 + - - +
25A ALA* 3.8 8.3 - - + +
27A ALA* 1.3 72.4 - - - +
29A VAL* 1.3 66.2 + - + +
31A VAL* 3.4 2.8 + - - +
32A ILE* 2.6 67.9 + - + +
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 2.5 39.4 + - + +
26A TRP* 4.2 6.1 - - + +
28A MET* 1.3 80.3 - - + +
30A VAL* 1.3 61.4 + - + +
32A ILE* 4.2 6.5 - - + -
33A VAL* 2.6 57.0 + - + +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 2.3 80.8 + - + +
27A ALA* 4.0 4.3 - - - +
29A VAL* 1.3 75.7 - - + +
31A VAL* 1.3 57.8 + - + +
33A VAL* 4.9 1.1 - - - -
34A GLY* 2.6 35.5 + - - +
35A ALA 3.3 0.3 + - - -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 2.7 31.6 + - + +
28A MET* 3.7 4.0 - - - +
30A VAL* 1.3 78.8 - - + +
32A ILE* 1.3 56.9 + - + +
35A ALA* 2.1 56.2 + - + +
36A THR* 2.7 6.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A MET* 2.6 64.6 + - + +
29A VAL* 3.8 5.4 - - + +
31A VAL* 1.3 76.9 - - + +
33A VAL* 1.3 60.9 - - + +
36A THR* 2.0 57.3 + - + +
37A ILE* 3.0 1.1 + - + +
----------------------------------------------------------
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 2.6 42.1 + - + +
30A VAL* 4.5 1.3 - - - +
32A ILE* 1.3 77.0 - - + +
34A GLY* 1.3 59.4 + - - +
37A ILE* 2.2 65.6 + - + +
38A GLY 3.1 0.5 + - - -
----------------------------------------------------------
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 2.6 24.5 + - - +
33A VAL* 1.3 75.0 - - - +
35A ALA* 1.3 54.0 + - - -
38A GLY* 2.4 35.8 + - - -
----------------------------------------------------------
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL 3.3 1.4 + - - -
31A VAL* 2.1 62.2 + - + +
34A GLY* 1.3 66.3 - - - -
36A THR* 1.3 51.1 + - - +
39A ILE* 2.3 56.9 + - + +
----------------------------------------------------------
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 2.7 9.1 + - - +
32A ILE* 2.0 50.5 + - + +
35A ALA* 1.3 72.8 - - - +
37A ILE* 1.3 62.3 + - + +
39A ILE* 4.0 2.8 - - - +
40A LYS* 3.2 23.0 + - - +
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 4.1 1.8 - - + +
33A VAL* 2.2 67.1 + - + +
36A THR* 1.3 79.6 - - + +
38A GLY* 1.3 64.1 + - - +
40A LYS* 3.5 10.2 - - + +
41A LEU* 3.3 32.5 + - + +
----------------------------------------------------------
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL 3.1 2.8 + - - -
34A GLY* 2.4 29.1 + - - -
37A ILE* 1.3 71.8 - - - +
39A ILE* 1.3 64.1 + - - -
41A LEU* 3.2 28.9 + - - +
42A PHE* 3.4 5.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY 3.5 0.2 + - - -
35A ALA* 2.3 44.4 + - + +
36A THR* 4.0 4.0 - - - +
38A GLY* 1.3 73.1 - - - +
40A LYS* 1.3 64.2 + - - +
42A PHE* 2.9 29.9 + - + +
43A LYS* 3.4 18.5 + - + +
----------------------------------------------------------
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR 3.2 15.8 + - - +
37A ILE* 3.5 11.4 - - + +
39A ILE* 1.3 80.2 - - - +
41A LEU* 1.3 64.3 + - + +
43A LYS* 2.9 14.8 + - + +
44A LYS* 2.9 34.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.3 24.9 - - + +
38A GLY* 3.2 16.1 + - - +
40A LYS* 1.3 80.1 - - + +
42A PHE* 1.3 51.3 + - - +
44A LYS* 4.4 14.6 - - + +
45A PHE* 2.4 52.2 + - + +
----------------------------------------------------------
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Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY 3.4 4.9 + - - +
39A ILE* 2.9 23.9 + - + +
41A LEU* 1.3 79.7 - - - +
43A LYS* 1.3 59.0 + - + +
45A PHE* 4.5 2.7 - + - -
46A THR* 2.2 78.0 + - + +
----------------------------------------------------------
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.2 20.4 - - + +
40A LYS* 2.9 13.8 + - + +
42A PHE* 1.3 87.6 - - + +
44A LYS* 1.3 54.2 + - - +
46A THR* 4.5 0.7 - - - -
47A SER* 2.2 47.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 2.9 27.5 + - + +
41A LEU* 3.9 15.5 - - + +
43A LYS* 1.3 78.2 - - - +
45A PHE* 1.3 52.9 + - - +
47A SER* 4.5 0.7 - - - -
48A LYS* 2.2 75.1 + - + +
----------------------------------------------------------
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 2.4 42.5 + - + +
42A PHE* 4.4 1.8 - + - +
44A LYS* 1.3 70.0 - - - +
46A THR* 1.3 63.4 + - - +
48A LYS* 4.5 1.8 - - - -
49A ALA* 2.7 32.0 + - - +
----------------------------------------------------------
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 2.2 75.0 + - + -
43A LYS* 4.5 1.1 - - - -
45A PHE* 1.3 80.8 - - - +
47A SER* 1.3 62.2 + - - +
49A ALA* 3.9 6.1 + - - -
----------------------------------------------------------
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 2.2 37.3 + - - -
44A LYS* 4.5 0.9 - - - -
46A THR* 1.3 74.3 - - - +
48A LYS* 1.3 62.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 2.2 63.1 + - + +
45A PHE* 4.5 1.6 - - - -
47A SER* 1.3 75.8 - - - +
49A ALA* 1.3 55.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 2.7 31.8 + - - +
46A THR 4.2 5.8 - - - -
47A SER 3.4 1.8 - - - -
48A LYS* 1.3 78.1 - - - +
----------------------------------------------------------
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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