Contacts of the helix formed by residues 12 - 23 (chain B) in PDB entry 3GSS
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 GLY 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B TYR* 3.7 8.7 - - - -
10B VAL* 3.6 3.5 - - - +
11B ARG* 1.3 76.0 - - - +
13B ARG* 1.3 60.2 + - - -
14B CYS 3.2 2.4 + - - -
15B ALA* 3.5 12.3 + - - +
16B ALA 5.0 0.3 + - - -
100B ARG* 3.9 16.0 + - - -
157B ASP* 4.1 1.2 - - - +
203B ILE* 2.8 24.1 + - - +
204B ASN* 5.1 5.4 - - - -
211B EAA 6.1 0.4 - - - -
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B TYR* 3.0 17.7 + - - +
12B GLY* 1.3 70.4 - - - -
14B CYS* 1.3 61.5 + - - +
15B ALA 3.6 0.4 - - - -
16B ALA* 5.1 4.2 + - - +
17B LEU* 3.9 7.8 + - - +
53B PRO* 4.4 6.7 - - + -
65B SER* 3.2 41.0 + - - -
66B ASN* 5.1 0.2 - - - -
69B LEU* 6.1 0.9 - - - +
97B GLU* 2.9 40.9 + - - -
100B ARG* 3.7 23.1 - - - +
101B CYS* 3.7 13.1 - - - -
104B ILE* 3.5 32.0 - - + +
210B GSH 3.4 50.8 + - - +
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Residues in contact with CYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.1 11.4 - - - -
7B TYR* 3.5 25.1 - - + -
11B ARG 2.9 4.0 + - - +
13B ARG* 1.3 76.3 - - - +
15B ALA* 1.3 65.4 + - - +
16B ALA 3.4 2.2 - - - -
17B LEU* 3.4 16.5 - - + +
18B ARG* 3.0 53.1 + - + +
53B PRO* 3.3 37.0 - - - -
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ARG* 3.1 27.7 + - + -
12B GLY 3.5 10.2 + - - +
14B CYS* 1.3 76.7 - - - +
16B ALA* 1.3 57.3 + - - +
18B ARG* 3.3 10.1 + - - +
19B MET* 2.9 35.4 + - - +
157B ASP* 3.2 26.9 - - - +
192B PHE* 4.9 0.5 - - - -
198B TYR* 4.8 12.1 - - + -
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 5.0 0.6 + - - -
13B ARG 5.1 3.5 + - - +
14B CYS 3.4 0.6 - - - -
15B ALA* 1.3 78.3 - - - +
17B LEU* 1.3 58.3 + - - +
19B MET* 3.2 15.9 + - - +
20B LEU* 2.9 27.2 + - - +
69B LEU* 4.2 11.4 - - + -
100B ARG* 4.7 2.0 - - - +
153B TYR* 3.6 7.4 - - - +
154B ASN* 3.6 43.3 - - + +
157B ASP* 4.3 6.7 + - + -
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.2 29.2 - - + -
13B ARG 3.9 19.0 + - - +
14B CYS* 3.4 22.6 - - + +
16B ALA* 1.3 78.1 - - - +
18B ARG* 1.3 62.8 + - + +
20B LEU* 3.3 5.3 + - - +
21B LEU* 2.9 40.0 + - + +
55B PHE* 4.6 1.8 - - + -
65B SER* 4.4 7.9 - - - +
68B ILE* 3.7 46.7 - - + -
69B LEU* 3.7 21.4 - - + +
72B LEU* 4.4 5.6 - - + -
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 3.9 10.0 - - + +
7B TYR* 4.0 14.1 - - - +
8B PHE 4.5 3.6 + - - -
9B PRO* 6.0 0.2 - - - +
10B VAL 3.1 23.6 + - - -
11B ARG* 3.8 9.3 + - - +
14B CYS* 3.0 41.9 + - - +
15B ALA* 3.6 6.5 - - - +
17B LEU* 1.3 82.5 - - + +
19B MET* 1.3 60.4 + - - +
21B LEU* 3.3 2.8 + - - -
22B ALA* 2.8 31.7 + - - +
28B TRP* 3.6 17.0 - - + +
30B GLU* 2.7 42.3 + - - +
192B PHE* 3.7 23.3 - - + -
197B GLU* 5.9 1.1 - - - -
198B TYR* 6.5 0.2 - - - -
201B LEU* 3.7 20.8 - - - +
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Residues in contact with MET 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA 2.9 16.6 + - - +
16B ALA* 3.5 11.0 - - - +
18B ARG* 1.3 75.4 - - - +
20B LEU* 1.3 54.4 + - - +
22B ALA* 3.8 0.3 - - - +
23B ASP* 2.8 38.1 + - - +
153B TYR* 3.1 36.8 - - + +
156B LEU* 4.0 21.3 - - + -
157B ASP* 3.6 28.7 - - + +
160B LEU* 4.4 7.2 - - - -
189B LEU* 3.8 15.6 - - + +
192B PHE* 4.0 20.8 - - + -
193B LEU* 4.0 20.9 - - + -
198B TYR* 5.0 3.8 - - + -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 2.9 13.4 + - - +
17B LEU 3.3 8.7 - - - +
19B MET* 1.3 77.2 - - - +
21B LEU* 1.3 62.6 + - - +
23B ASP* 3.7 0.5 - - - -
24B GLN* 2.9 35.9 + - + +
69B LEU* 4.2 12.3 - - + -
72B LEU* 3.9 33.9 - - + -
73B GLY 4.8 0.2 - - - +
76B LEU* 3.9 13.9 - - + -
78B LEU* 3.7 25.1 - - + -
150B PHE* 3.8 28.3 - - + -
153B TYR* 3.7 29.3 - - + -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B TYR* 3.8 21.3 - - + -
5B VAL* 4.6 0.2 - - + -
17B LEU* 2.9 30.7 + - + +
18B ARG* 3.7 1.6 - - - +
20B LEU* 1.3 78.4 - - + +
22B ALA* 1.3 61.5 + - - +
24B GLN 3.2 2.1 + - - -
25B GLY 3.2 3.5 + - - -
26B GLN* 2.9 50.0 + - + +
28B TRP* 3.5 47.3 - - + -
55B PHE* 4.3 20.9 - - + -
72B LEU* 4.0 22.7 - - + -
76B LEU* 5.0 0.4 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG 2.8 21.2 + - - +
19B MET 3.8 2.9 - - - +
21B LEU* 1.3 72.2 - - - +
23B ASP* 1.3 57.7 + - - +
25B GLY* 2.9 20.8 + - - -
26B GLN 4.8 0.7 - - - -
28B TRP* 3.5 6.0 - - + -
188B LYS* 3.6 13.6 - - - +
189B LEU* 5.5 0.4 - - - -
192B PHE* 3.6 33.2 - - + -
212B MES 3.3 27.8 + - - +
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Residues in contact with ASP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B MET 2.8 22.4 + - - +
20B LEU 3.9 0.2 - - - +
22B ALA* 1.3 73.2 - - - +
24B GLN* 1.3 61.9 + - - +
25B GLY 3.3 0.2 - - - -
153B TYR* 2.7 33.4 + - + +
186B ARG* 2.8 42.1 + - - +
188B LYS* 3.5 22.7 + - - +
189B LEU* 3.5 30.2 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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