Contacts of the helix formed by residues 6 - 31 (chain A) in PDB entry 6VMS
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 SER 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A THR 3.9 0.6 + - - -
5A LEU* 1.3 76.2 - - - +
7A ALA* 1.3 67.8 + - - +
8A GLU 3.3 2.0 - - - -
9A ASP* 3.2 11.9 + - - +
10A LYS* 3.0 23.1 + - - +
167E HIS* 3.0 39.6 + - - -
169E ASN* 4.3 4.1 + - - -
173E TYR* 3.7 28.7 + - - -
233E LEU* 4.9 3.8 - - - +
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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 SER* 1.3 74.4 - - - +
8A GLU* 1.3 62.9 + - - +
10A LYS* 3.2 13.0 + - - +
11A ALA* 3.0 22.7 + - - +
173E TYR* 5.6 0.4 - - - -
232E HIS* 4.0 12.6 - - + +
233E LEU 3.6 22.2 + - - +
234E GLU* 4.6 2.7 - - - -
235E TYR* 3.9 33.5 - - + +
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 3.3 1.8 - - - -
7A ALA* 1.3 76.9 - - - +
9A ASP* 1.3 64.2 + - - +
11A ALA* 3.4 7.9 + - - +
12A ALA* 2.9 27.7 + - - +
101E TYR* 3.6 22.6 - - + +
102E TYR* 5.5 0.2 - - - -
107E PRO* 3.4 11.6 - - - +
173E TYR* 2.7 42.0 - - + +
175E TYR* 2.7 25.1 + - - -
191E ARG* 2.9 27.2 + - - +
232E HIS* 3.3 24.0 + - - +
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Residues in contact with ASP 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.6 18.5 - - + +
6A SER* 3.2 20.5 + - - +
8A GLU* 1.3 83.6 - - - +
10A LYS* 1.3 59.3 + - - +
12A ALA* 3.7 7.6 - - - +
13A VAL* 2.9 36.0 + - + +
68B ARG* 5.7 4.0 + - - -
86B THR* 5.4 8.3 - - + +
88B ASN* 4.6 8.7 + - - +
169E ASN* 4.1 19.5 + - - +
173E TYR* 4.7 3.8 + - - -
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLY 5.2 9.5 - - - +
3A CYS* 4.8 16.7 - - - +
5A LEU* 3.6 37.9 + - + -
6A SER 3.0 16.9 + - - +
7A ALA* 3.5 10.8 - - - +
9A ASP* 1.3 77.0 - - - +
11A ALA* 1.3 55.7 + - - +
13A VAL* 3.3 7.5 + - - +
14A GLU* 2.9 35.4 + - + +
59E TYR* 4.9 14.6 + - - +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA 3.0 13.3 + - - +
8A GLU 3.6 2.7 - - - +
10A LYS* 1.3 76.8 - - - +
12A ALA* 1.3 58.3 + - - +
14A GLU* 3.2 14.7 + - - +
15A ARG* 2.9 26.3 + - - +
50E TYR* 4.5 11.2 - - + +
101E TYR* 3.4 40.4 - - + -
235E TYR* 6.6 0.2 - - + -
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU 2.9 15.4 + - - +
9A ASP* 3.7 9.0 - - - +
10A LYS 3.3 0.4 - - - -
11A ALA* 1.3 76.7 - - - +
13A VAL* 1.3 59.3 + - - +
15A ARG* 3.2 6.5 + - - +
16A SER* 2.8 27.6 + - - -
88B ASN* 4.3 17.7 - - + +
89B LYS 4.7 4.4 - - - +
101E TYR 3.3 20.6 + - - +
102E TYR* 4.0 14.6 - - + -
103E TYR 5.2 1.1 - - - +
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.8 15.3 - - + -
9A ASP* 2.9 23.2 + - + +
10A LYS* 3.6 7.4 - - - +
11A ALA 3.2 0.4 - - - -
12A ALA* 1.3 74.4 - - - +
14A GLU* 1.3 66.8 + - + +
16A SER* 3.1 8.6 + - - -
17A LYS* 2.9 42.5 + - + +
88B ASN* 3.3 25.1 - - - +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 2.9 21.4 + - + +
11A ALA* 3.2 14.3 + - - +
13A VAL* 1.3 76.1 - - + +
15A ARG* 1.3 63.2 + - - +
17A LYS* 3.3 9.5 + - + +
18A MET* 2.9 27.8 + - + +
50E TYR* 5.1 4.2 + - - -
52E SER* 3.7 23.9 + - - -
56E GLY* 4.4 8.1 - - - -
57E THR* 3.6 29.1 + - - +
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 2.9 12.7 + - - +
12A ALA* 3.2 10.3 + - - +
14A GLU* 1.3 77.0 - - - +
16A SER* 1.3 57.1 + - - +
18A MET* 3.2 13.5 + - + +
19A ILE* 2.9 43.7 + - + +
89B LYS 4.6 4.5 - - - +
90B VAL 3.3 18.8 + - - -
91B HIS* 3.6 30.9 + - - -
131B GLY 5.5 1.2 + - - -
31E SER* 3.2 23.2 + - - +
100E ILE* 3.0 36.4 - - - +
101E TYR 4.3 8.3 - - - +
102E TYR* 4.0 21.4 - - - -
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 2.8 12.7 + - - -
13A VAL* 3.1 13.4 + - - -
15A ARG* 1.3 77.0 - - - +
17A LYS* 1.3 58.4 + - - +
19A ILE* 3.3 2.8 + - - +
20A ASP* 2.9 40.3 + - - +
87B THR 4.5 2.3 + - - -
88B ASN* 4.3 8.2 - - - -
89B LYS* 3.6 41.3 + - - +
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 2.9 34.1 + - + +
14A GLU* 3.8 7.0 - - + +
16A SER* 1.3 77.1 - - - +
18A MET* 1.3 62.8 + - - +
20A ASP* 3.3 9.6 + - - +
21A ARG* 2.9 40.8 + - + +
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Residues in contact with MET 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 2.9 17.8 + - + +
15A ARG* 3.4 15.7 - - - +
17A LYS* 1.3 77.4 - - - +
19A ILE* 1.3 62.9 + - + +
21A ARG* 3.3 10.9 + - - +
22A ASN* 3.0 35.8 + - - +
30E SER 4.7 3.4 - - - +
31E SER* 5.8 2.5 - - - -
53E SER* 4.0 17.5 - - - +
54E GLY* 3.5 37.5 - - - +
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 2.9 36.7 + - + +
16A SER* 3.7 5.2 - - - +
18A MET* 1.3 78.4 - - + +
20A ASP* 1.3 58.9 + - - +
22A ASN* 3.2 9.6 + - - +
23A LEU* 2.9 39.6 + - + +
80B ILE* 6.4 0.2 - - + -
89B LYS* 4.0 24.0 - - + +
90B VAL 4.1 20.4 - - - +
91B HIS* 4.6 0.7 - - - +
92B ALA* 3.6 38.8 - - + +
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Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 2.9 26.7 + - - +
17A LYS* 3.3 10.7 + - - +
19A ILE* 1.3 76.2 - - - +
21A ARG* 1.3 57.9 + - + +
23A LEU* 3.4 7.9 + - - +
24A ARG* 2.9 30.3 + - - +
53B GLY* 4.9 3.4 - - - -
89B LYS* 2.8 42.6 + - - +
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 2.9 28.1 + - - +
18A MET* 3.6 10.1 - - - +
19A ILE 3.2 0.2 - - - -
20A ASP* 1.3 78.0 - - + +
22A ASN* 1.3 65.8 + - - +
24A ARG* 3.2 25.8 + - - +
25A GLU* 3.0 33.0 + - + +
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Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 3.0 32.0 + - - +
19A ILE* 3.2 8.5 + - - +
21A ARG* 1.3 78.6 - - - +
23A LEU* 1.3 64.0 + - + +
25A GLU* 3.3 16.7 + - - +
26A ASP* 3.0 31.5 + - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 2.9 34.3 + - + +
20A ASP* 3.7 7.2 - - - +
22A ASN* 1.3 79.0 - - + +
24A ARG* 1.3 58.0 + - - +
26A ASP* 3.2 3.2 + - - +
27A GLY 2.9 23.9 + - - -
53B GLY* 3.9 23.3 - - - +
55B LEU* 3.6 12.3 - - + +
76B ASP* 5.4 2.1 - - - +
78B LYS* 3.5 45.3 - - + +
80B ILE* 3.9 21.1 - - + -
89B LYS* 4.3 9.9 - - - -
92B ALA* 4.4 11.4 - - + -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASP 2.9 18.0 + - - +
21A ARG* 3.7 23.8 + - - +
23A LEU* 1.3 76.9 - - - +
25A GLU* 1.3 64.6 + - - +
27A GLY* 3.3 1.8 + - - +
28A GLU* 2.6 62.2 + - - +
55B LEU* 4.8 8.1 - - + -
146R TYR* 4.2 27.5 + - + +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.0 21.2 + - - +
22A ASN* 3.6 19.1 - - - +
24A ARG* 1.3 83.1 - - - +
26A ASP* 1.3 64.6 - - - +
28A GLU* 3.2 17.8 + - - +
29A LYS* 3.0 36.5 + - - +
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN* 3.0 21.9 + - - +
23A LEU 3.7 2.7 - - - +
25A GLU* 1.3 78.3 - - - +
27A GLY* 1.3 58.0 + - - +
29A LYS* 3.3 15.3 + - - +
30A ALA* 2.9 29.7 + - - +
76B ASP* 5.7 4.0 - - - +
78B LYS* 2.6 36.9 + - - +
94B PRO* 5.6 1.0 - - - +
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 2.9 11.3 + - - -
24A ARG 3.6 1.3 - - - -
25A GLU 3.2 0.2 - - - -
26A ASP* 1.3 74.3 - - - +
28A GLU* 1.3 59.6 + - - +
30A ALA* 3.2 5.7 + - - +
31A ALA* 2.9 33.1 + - - +
55B LEU* 3.4 28.2 - - - +
76B ASP* 5.4 3.1 + - - -
146R TYR* 4.1 10.0 - - - -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.6 51.6 + - - +
25A GLU* 3.2 19.5 + - - +
27A GLY* 1.3 75.3 - - - +
29A LYS* 1.3 64.9 + - + +
31A ALA* 3.6 2.6 + - - +
32A ARG* 3.5 26.3 + - - +
144R THR* 6.0 2.2 - - + +
146R TYR* 3.8 35.0 - - + +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 3.0 28.0 + - - +
26A ASP* 3.8 14.5 + - - +
28A GLU* 1.3 77.9 - - + +
30A ALA* 1.3 64.3 + - - +
32A ARG* 3.2 39.6 + - - +
33A GLU* 3.5 17.6 - - - +
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP 2.9 17.8 + - - +
27A GLY* 3.8 6.7 - - - +
29A LYS* 1.3 76.5 - - - +
31A ALA* 1.3 58.9 + - - +
33A GLU* 2.9 43.4 + - - +
35A LYS* 5.2 10.1 + - - -
197A LYS* 5.5 2.2 - - - +
76B ASP* 4.7 12.3 - - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 2.9 17.4 + - - +
28A GLU 4.1 4.5 - - - +
29A LYS 3.3 0.4 - - - -
30A ALA* 1.3 75.6 - - - +
32A ARG* 1.3 59.3 + - + +
33A GLU 3.2 6.9 + - - +
35A LYS* 6.2 0.9 - - - +
140R MET* 5.7 2.9 - - - +
144R THR* 5.0 17.5 + - + +
146R TYR* 4.1 21.8 - - + +
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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