Contacts of the helix formed by residues 3 - 29 (chain U) in PDB entry 6GYK
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 ASN 3 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2U SER* 1.3 77.6 - - - +
4U ALA* 1.3 68.4 + - - +
5U GLU* 3.1 25.0 + - - +
6U ALA* 3.4 35.0 + - + +
7U SER* 3.9 9.4 + - - -
273U ASP 5.3 9.6 + - - +
274U TYR* 5.8 6.3 - - + +
275U THR* 4.7 10.7 + - - +
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Residues in contact with ALA 4 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U ASN* 1.3 73.4 + - - +
5U GLU* 1.3 61.2 + - - +
6U ALA 3.2 0.9 - - - -
7U SER* 2.5 26.1 + - - +
8U ARG* 2.9 16.2 + - - +
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Residues in contact with GLU 5 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U ASN* 3.1 19.3 + - - +
4U ALA* 1.3 78.6 - - - +
6U ALA* 1.3 56.5 + - - +
8U ARG* 3.3 7.6 + - + +
9U VAL* 2.9 36.9 + - + +
275U THR* 4.3 14.0 + - - +
55V ASN 3.4 14.2 - - - +
56V THR* 4.0 5.4 - - - -
57V GLN* 3.0 30.1 + - - +
58V SER* 4.8 9.4 + - - -
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Residues in contact with ALA 6 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U ASN* 3.4 26.2 - - + +
4U ALA 3.2 0.6 - - - -
5U GLU* 1.3 79.7 - - - +
7U SER* 1.3 56.5 + - - +
9U VAL* 3.5 5.8 + - - +
10U TYR* 2.9 54.9 + - + +
273U ASP* 5.6 10.1 - - + +
274U TYR* 6.5 0.7 - - - -
275U THR* 5.5 13.0 - - + -
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Residues in contact with SER 7 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U ASN 3.9 5.6 + - - -
4U ALA* 2.5 32.8 + - - +
6U ALA* 1.3 76.4 - - - +
8U ARG* 1.3 59.3 + - - +
10U TYR* 3.3 10.4 + - - +
11U GLU* 2.9 29.7 + - - +
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Residues in contact with ARG 8 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4U ALA 2.9 14.0 + - - +
5U GLU* 3.3 11.2 + - + +
7U SER* 1.3 77.4 + - - +
9U VAL* 1.3 57.6 + - + +
11U GLU* 3.2 44.8 + - - +
12U ILE* 2.9 74.2 + - + +
15U GLU* 5.5 2.2 - - - +
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Residues in contact with VAL 9 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5U GLU* 2.9 28.8 + - + +
6U ALA* 3.8 6.1 - - - +
8U ARG* 1.3 75.8 - - + +
10U TYR* 1.3 66.3 + - + +
12U ILE* 3.3 10.6 + - + +
13U ILE* 2.9 46.2 + - + +
275U THR* 5.7 10.3 - - + +
51V THR* 3.6 28.3 - - + -
52V LEU* 5.6 7.9 - - + -
55V ASN* 4.1 24.5 - - + +
56V THR* 6.1 0.9 - - + -
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Residues in contact with TYR 10 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6U ALA* 2.9 40.0 + - + +
7U SER* 3.6 9.6 - - - +
8U ARG 3.3 0.2 - - - -
9U VAL* 1.3 87.0 - - + +
11U GLU* 1.3 57.9 + - - +
13U ILE* 3.3 6.8 + - + +
14U VAL* 2.9 35.0 + - - +
46U LEU* 3.9 36.8 - - + -
266U VAL* 5.5 5.0 - - - +
273U ASP* 3.7 27.6 + - + +
14V THR* 5.6 1.2 - - - +
15V ILE* 3.6 43.9 + - + +
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Residues in contact with GLU 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7U SER 2.9 16.9 + - - +
8U ARG* 3.2 33.6 + - - +
10U TYR* 1.3 74.3 - - - +
12U ILE* 1.3 60.3 + - - +
14U VAL* 3.3 5.8 + - + +
15U GLU* 2.9 51.7 + - + +
43U GLN* 5.8 3.8 - - - +
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Residues in contact with ILE 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8U ARG* 2.9 58.2 + - + +
9U VAL* 3.7 9.2 - - + +
11U GLU* 1.3 75.9 - - - +
13U ILE* 1.3 58.8 + - + +
15U GLU* 4.2 3.3 - - - +
16U SER* 2.9 39.4 + - - -
47V VAL* 6.0 0.9 - - + -
51V THR* 5.3 13.2 - - + +
55V ASN* 4.8 17.7 - - - +
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Residues in contact with ILE 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9U VAL* 2.9 40.6 + - + +
10U TYR* 3.6 6.5 - - + +
12U ILE* 1.3 75.6 - - + +
14U VAL* 1.3 60.0 + - - +
16U SER* 4.2 0.2 - - - -
17U VAL* 2.9 40.2 + - + +
42U TRP* 4.1 17.5 - - + -
15V ILE* 4.1 27.4 - - + -
44V PHE* 4.6 9.0 - - + -
47V VAL* 3.7 26.5 - - + -
48V VAL* 4.4 18.2 - - + -
51V THR* 4.4 9.6 - - + +
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Residues in contact with VAL 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U TYR 2.9 22.5 + - - +
11U GLU* 3.3 6.5 + - + +
13U ILE* 1.3 75.6 - - + +
15U GLU* 1.3 59.9 + - + +
17U VAL* 3.9 0.5 - - - +
18U VAL* 2.9 35.6 + - + +
39U LYS* 4.0 21.3 - - + -
42U TRP* 3.7 38.1 - - + -
43U GLN* 3.5 37.0 - - + +
46U LEU* 4.7 12.8 - - + -
15V ILE* 6.2 0.9 - - + -
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Residues in contact with GLU 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8U ARG* 5.5 2.2 - - - +
11U GLU* 2.9 39.0 + - + +
12U ILE* 4.2 3.8 - - - +
14U VAL* 1.3 76.5 - - + +
16U SER* 1.3 57.6 + - - +
18U VAL* 3.4 3.6 + - - +
19U ASN* 2.9 47.7 + - - +
39U LYS* 3.3 31.1 + - - +
43U GLN* 4.6 2.1 - - - +
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Residues in contact with SER 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U ILE* 2.9 26.5 + - - -
13U ILE* 4.2 2.9 - - - -
15U GLU* 1.3 77.3 - - - +
17U VAL* 1.3 57.8 + - - +
19U ASN* 3.4 4.7 + - - -
20U GLU* 2.9 53.6 + - - +
47V VAL* 4.2 13.8 - - - +
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Residues in contact with VAL 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U ILE* 2.9 30.7 + - + +
16U SER* 1.3 75.2 - - - +
18U VAL* 1.3 61.2 + - + +
20U GLU 3.9 0.4 - - - +
21U VAL* 2.9 48.4 + - + +
38U LEU* 6.0 4.5 - - + -
42U TRP* 3.6 29.4 - - + -
19V LEU* 5.9 0.4 - - + -
40V VAL* 4.3 16.6 - - + -
43V THR* 4.3 16.4 - - + +
44V PHE* 4.9 9.4 - - + -
47V VAL* 4.3 19.1 - - + -
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Residues in contact with VAL 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U VAL* 2.9 25.5 + - + +
15U GLU* 3.8 6.1 - - - +
17U VAL* 1.3 76.5 - - + +
19U ASN* 1.3 60.6 + - - +
21U VAL* 4.7 0.4 - - - -
22U ARG* 2.9 50.4 + - - +
35U LEU* 3.7 29.6 - - + +
36U GLN* 5.6 3.8 - - - +
38U LEU* 5.5 3.1 - - + -
39U LYS* 4.0 40.8 - - + +
42U TRP* 4.8 8.1 - - + -
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Residues in contact with ASN 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15U GLU* 2.9 32.8 + - - +
16U SER* 3.9 5.3 - - - +
18U VAL* 1.3 82.4 - - - +
20U GLU* 1.3 61.1 + - + +
22U ARG* 3.3 41.1 + - - +
23U GLU* 4.4 2.9 + - - +
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Residues in contact with GLU 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U SER* 2.9 37.4 + - - +
17U VAL 4.2 1.3 - - - +
19U ASN* 1.3 78.5 - - + +
21U VAL* 1.3 61.2 + - - +
22U ARG 3.3 0.4 + - - -
23U GLU* 3.9 13.2 + - - +
24U ASP* 3.7 11.8 - - - +
43V THR* 3.4 29.0 - - + +
46V LYS* 3.9 20.2 + - - -
47V VAL* 4.5 5.4 - - - +
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Residues in contact with VAL 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U VAL* 2.9 34.9 + - + +
18U VAL* 4.1 2.9 - - - +
20U GLU* 1.3 74.8 - - - +
22U ARG* 1.3 66.7 + - - +
23U GLU 3.1 2.7 - - - -
24U ASP* 3.0 15.4 + - + +
25U PHE* 2.9 47.5 + - + +
35U LEU* 4.3 8.1 - - + -
38U LEU* 4.9 3.6 - - + -
36V LEU* 5.2 2.5 - - + -
39V ARG* 5.7 3.1 - - + -
40V VAL* 4.3 26.2 - - + +
43V THR* 4.7 15.9 - - + +
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Residues in contact with ARG 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18U VAL* 2.9 39.7 + - - +
19U ASN* 3.3 44.5 + - - +
20U GLU 3.3 0.4 - - - -
21U VAL* 1.3 77.2 - - - +
23U GLU* 1.3 56.9 + - - +
25U PHE* 3.2 2.9 + - - +
26U GLU* 2.9 44.7 + - - +
32U GLU* 3.1 38.0 + - - +
35U LEU* 3.7 11.9 - - + +
36U GLN* 4.6 7.7 - - - +
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Residues in contact with GLU 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U ASN 4.4 2.3 + - - +
20U GLU 3.9 12.8 + - - +
21U VAL 3.1 0.6 - - - -
22U ARG* 1.3 78.7 - - - +
24U ASP* 1.3 62.9 + - - +
26U GLU* 3.1 11.4 + - - +
27U ASN* 2.9 46.6 + - - +
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Residues in contact with ASP 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U GLU 3.7 14.9 - - - +
21U VAL* 3.0 12.4 + - + +
23U GLU* 1.3 80.5 - - - +
25U PHE* 1.3 62.2 + - - +
27U ASN* 3.8 14.7 + - - +
28U ALA* 3.2 23.2 + - - +
36V LEU* 3.8 28.8 - - + +
39V ARG* 3.7 36.9 + - - +
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Residues in contact with PHE 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U VAL* 2.9 36.1 + - + +
22U ARG* 3.5 12.6 - - + +
23U GLU 3.2 0.2 - - - -
24U ASP* 1.3 77.6 - - - +
26U GLU* 1.3 61.5 + - + +
28U ALA* 3.6 1.3 + - - -
29U GLY* 3.3 16.3 + - - -
30U ILE* 3.5 34.5 + - + +
31U ASP 3.6 15.5 + - - +
32U GLU* 5.6 1.8 - - - +
34U THR* 3.7 19.3 - - + -
35U LEU* 3.7 35.0 - - + -
38U LEU* 4.3 19.7 - - + -
26V LEU* 6.0 2.0 - - + -
32V ILE* 5.6 10.5 - - + -
36V LEU* 3.6 26.0 - - + -
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Residues in contact with GLU 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22U ARG* 2.9 42.6 + - + +
23U GLU* 3.1 7.9 + - - +
25U PHE* 1.3 74.8 - - - +
27U ASN* 1.3 68.3 + - - +
29U GLY* 3.5 11.1 + - - -
32U GLU* 4.4 9.3 - - - +
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Residues in contact with ASN 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U GLU* 2.9 42.9 + - - +
24U ASP* 3.8 15.5 + - - +
25U PHE 3.3 0.2 - - - -
26U GLU* 1.3 80.8 - - - +
28U ALA* 1.3 60.2 + - - +
29U GLY* 4.6 0.2 - - - -
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Residues in contact with ALA 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24U ASP 3.2 17.7 + - - +
25U PHE* 4.1 4.0 - - - +
26U GLU 3.3 0.4 - - - -
27U ASN* 1.3 78.3 - - - +
29U GLY* 1.3 63.1 + - - +
30U ILE* 4.6 10.5 - - + -
33V GLU* 4.6 18.1 - - + +
36V LEU* 5.2 8.7 - - + -
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Residues in contact with GLY 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U PHE 3.3 7.1 + - - -
26U GLU* 3.5 9.6 + - - -
27U ASN 3.3 3.4 - - - -
28U ALA* 1.3 80.4 - - - +
30U ILE* 1.3 64.6 + - - +
33V GLU* 5.2 0.7 - - - -
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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