Contacts of the helix formed by residues 3 - 23 (chain A) in PDB entry 2G7S
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO* 1.3 77.1 - - + +
5A GLN* 3.7 9.1 + - - +
6A SER* 2.7 49.5 + - - -
7A LYS* 3.3 14.2 + - - +
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Residues in contact with PRO 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 1.3 91.6 - - + +
5A GLN* 1.3 63.6 + - - +
7A LYS* 3.0 5.1 + - + -
8A ALA* 3.0 19.1 + - - +
46A HIS* 3.1 24.0 + - + +
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Residues in contact with GLN 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 3.4 9.7 + - - +
4A PRO* 1.3 79.2 - - - +
6A SER* 1.3 58.4 + - - +
8A ALA* 3.3 10.7 + - - +
9A ASP* 2.8 56.2 + - - +
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Residues in contact with SER 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN* 2.7 38.4 + - - -
5A GLN* 1.3 80.5 - - - +
7A LYS* 1.3 63.0 + - - +
9A ASP* 3.4 9.6 + - - +
10A ASP* 2.9 37.1 + - - +
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASN 3.3 14.6 + - - +
4A PRO* 3.0 9.7 + - + +
6A SER* 1.3 84.2 + - - +
8A ALA* 1.3 64.7 + - - +
10A ASP* 3.1 19.7 + - - +
11A ILE* 2.9 31.2 + - + +
36A VAL* 4.6 14.5 + - + -
37A GLY 6.1 0.2 - - - -
38A ILE* 4.0 27.3 - - + +
46A HIS* 3.5 17.0 - - + +
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Residues in contact with ALA 8 (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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4A PRO 3.0 9.3 + - - +
5A GLN* 3.6 17.9 - - - +
7A LYS* 1.3 76.8 - - - +
9A ASP* 1.3 57.0 + - - +
11A ILE* 3.2 6.2 + - - +
12A LEU* 2.9 35.9 + - + +
46A HIS* 3.5 27.9 - - + +
47A PHE* 4.1 13.1 - - + -
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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 GLN* 2.8 47.8 + - - +
6A SER* 3.6 9.0 - - - +
7A LYS 3.3 0.2 - - - -
8A ALA* 1.3 76.3 - - - +
10A ASP* 1.3 59.3 + - - +
12A LEU* 3.2 13.0 + - - +
13A GLN* 2.8 32.3 + - - +
60A GLN* 5.0 7.0 + - - +
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Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 2.9 22.7 + - - +
7A LYS* 3.1 27.3 + - - +
9A ASP* 1.3 78.5 - - - +
11A ILE* 1.3 62.8 + - - +
13A GLN* 3.7 12.1 - - - +
14A CYS* 3.0 26.2 + - - +
36A VAL* 3.6 23.7 - - + +
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 2.9 20.8 + - + +
8A ALA 3.2 5.1 + - - +
10A ASP* 1.3 77.2 - - - +
12A LEU* 1.4 58.9 + - - +
14A CYS* 3.7 1.4 - - - +
15A ALA* 2.9 28.1 + - - +
32A ILE* 4.2 23.1 - - + +
36A VAL* 4.4 8.1 - - + -
38A ILE* 4.3 16.4 - - + -
43A ILE* 4.2 19.5 - - + -
46A HIS* 3.7 37.5 - - + -
47A PHE* 3.7 9.9 - - + -
53A LEU* 3.7 30.3 - - + -
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 2.9 23.6 + - + +
9A ASP* 3.8 10.3 - - - +
11A ILE* 1.4 74.8 - - - +
13A GLN* 1.4 66.4 + - - +
15A ALA* 3.4 3.4 + - - +
16A ARG* 2.9 25.3 + - - +
47A PHE* 3.7 27.4 - - + -
53A LEU* 3.7 29.6 - - + +
56A LYS* 4.0 9.4 - - + +
57A LEU* 3.7 21.5 - - + +
60A GLN* 4.0 33.9 - - - +
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Residues in contact with GLN 13 (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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9A ASP 2.8 21.7 + - - +
10A ASP* 3.7 12.3 - - - +
12A LEU* 1.4 69.6 - - - +
14A CYS* 1.3 66.0 + - - +
16A ARG* 3.0 16.9 + - - +
17A THR* 3.0 20.4 + - - +
60A GLN* 5.2 2.0 + - - -
99A HIS* 5.2 3.0 + - + +
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Residues in contact with CYS 14 (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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10A ASP 3.0 15.8 + - - +
11A ILE* 3.7 3.1 - - - +
13A GLN* 1.3 80.7 - - - +
15A ALA* 1.3 63.4 + - - +
17A THR* 3.1 8.4 + - - -
18A LEU* 2.9 46.5 + - - +
32A ILE* 3.9 17.3 - - + -
35A VAL* 3.6 35.7 - - + -
36A VAL* 3.6 14.1 - - + -
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Residues in contact with ALA 15 (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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11A ILE 2.9 18.1 + - - +
12A LEU 3.8 2.0 - - - +
14A CYS* 1.3 78.4 - - - +
16A ARG* 1.3 59.0 + - - +
18A LEU* 3.3 7.8 + - - +
19A ILE* 2.8 32.9 + - - +
27A PHE* 4.3 16.9 - - + -
32A ILE* 4.3 5.6 - - + -
53A LEU* 3.8 19.3 - - + -
57A LEU* 3.6 19.5 - - + +
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Residues in contact with ARG 16 (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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12A LEU 2.9 15.3 + - - +
13A GLN* 3.0 11.1 + - - +
15A ALA* 1.3 77.4 - - - +
17A THR* 1.3 63.7 + - - +
19A ILE* 3.2 9.6 - - - +
20A ILE* 3.1 26.4 + - + +
57A LEU* 3.7 15.7 + - + +
60A GLN* 3.2 26.7 + - - +
61A TYR* 3.7 31.7 - - - +
64A GLU* 3.0 42.6 + - - -
99A HIS* 3.8 28.8 + - + -
103A VAL* 3.9 26.0 - - + -
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Residues in contact with THR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.0 16.3 + - - +
14A CYS* 3.6 8.9 - - - -
16A ARG* 1.3 77.8 - - - +
18A LEU* 1.3 69.3 + - + +
20A ILE* 3.4 9.7 + - - +
21A ARG* 3.5 21.6 + - - +
98A THR* 4.5 19.6 - - + +
99A HIS* 3.2 24.4 + - - +
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Residues in contact with LEU 18 (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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14A CYS* 2.9 40.0 + - - +
15A ALA 3.9 3.4 - - - +
17A THR* 1.3 82.5 - - + +
19A ILE* 1.3 61.9 + - - +
21A ARG* 2.9 60.6 + - - +
22A GLY 3.5 5.9 + - - -
26A SER* 3.6 6.5 + - - -
27A PHE* 3.7 36.1 - - + -
31A ASP* 3.9 21.5 - - + +
32A ILE* 4.3 4.7 - - + -
35A VAL* 5.1 8.7 - - + -
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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
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15A ALA 2.8 18.6 + - - +
16A ARG* 3.2 21.5 - - - +
18A LEU* 1.3 74.3 - - - +
20A ILE* 1.3 65.5 + - + +
23A GLY* 2.8 50.9 + - - +
24A TYR* 4.0 3.1 - - - +
27A PHE* 3.8 19.0 - - + -
54A VAL* 3.8 32.1 - - + -
57A LEU* 4.2 17.9 - - + -
103A VAL* 4.4 9.6 - - + -
106A LEU* 3.6 6.8 - - - +
107A LEU* 4.0 21.3 - - + -
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Residues in contact with ILE 20 (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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16A ARG* 3.1 23.9 + - + +
17A THR* 3.8 5.6 - - - +
18A LEU 3.2 0.4 - - - -
19A ILE* 1.3 76.4 - - - +
21A ARG* 1.3 58.0 + - + +
61A TYR* 5.8 1.3 - - + -
98A THR 4.8 1.8 - - - +
99A HIS* 3.6 35.0 - - + +
100A PRO* 4.0 16.8 - - + -
101A PHE* 3.6 37.9 - - + +
103A VAL* 3.5 34.3 - - + +
106A LEU* 3.2 8.1 - - - +
171A ARG* 2.8 27.2 + - - +
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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 THR* 3.5 19.5 + - + +
18A LEU* 2.9 60.8 + - - +
20A ILE* 1.3 82.6 - - + +
22A GLY* 1.3 58.2 + - - +
26A SER* 4.7 14.6 + - - -
27A PHE* 5.1 0.6 - - - +
31A ASP* 5.8 3.0 + - - -
98A THR 6.1 0.9 - - - +
106A LEU* 4.5 0.2 - - - -
171A ARG* 3.8 17.9 + - - +
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Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU 3.5 3.8 + - - -
19A ILE 3.4 0.8 + - - -
21A ARG* 1.3 82.8 - - - +
23A GLY* 1.3 58.5 + - - +
25A ASN 4.8 0.7 + - - -
26A SER* 3.1 30.3 + - - -
106A LEU* 4.2 8.5 - - - +
110A GLU* 3.9 6.1 - - - +
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Residues in contact with GLY 23 (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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19A ILE* 2.8 32.4 + - - +
22A GLY* 1.3 70.2 - - - +
24A TYR* 1.3 65.7 + - - +
25A ASN 3.1 2.6 + - - -
26A SER* 2.8 21.7 + - - -
27A PHE* 3.7 8.1 - - - -
106A LEU* 3.7 12.7 - - - +
107A LEU* 4.7 2.2 - - - -
110A GLU* 3.5 13.7 - - - -
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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) + - + + + + + -
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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