Contacts of the helix formed by residues 12 - 23 (chain A) in PDB entry 10GS
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A TYR* 3.6 9.4 - - - -
10A VAL* 3.6 4.1 - - - +
11A ARG* 1.3 80.2 - - - +
13A ARG* 1.3 61.6 + - - -
14A CYS 3.3 2.1 + - - -
15A ALA* 3.6 12.1 + - - +
100A ARG* 4.3 13.7 + - - -
157A ASP* 4.3 1.0 - - - +
203A ILE* 2.9 20.1 + - - +
204A ASN* 5.0 6.1 - - - -
210A VWW 5.8 2.2 - - - -
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Residues in contact with ARG 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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7A TYR* 3.1 15.5 + - - +
12A GLY* 1.3 72.2 - - - -
14A CYS* 1.3 60.6 + - - +
15A ALA 3.6 0.2 - - - -
16A ALA* 5.1 3.9 + - - +
17A LEU* 3.8 7.1 + - - +
53A PRO* 4.5 7.2 - - + -
65A SER* 3.3 33.1 + - - -
66A ASN* 4.2 0.8 - - - +
97A GLU* 3.0 40.6 + - - -
100A ARG* 3.9 21.1 - - - +
101A CYS* 4.1 8.7 - - - -
104A ILE* 3.4 33.4 - - + +
210A VWW 3.3 65.2 + - - +
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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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5A VAL* 4.5 8.7 - - + -
7A TYR* 3.5 25.4 - - + -
11A ARG 2.9 5.1 + - - +
13A ARG* 1.3 80.2 - - - +
15A ALA* 1.3 65.6 + - - +
16A ALA 3.3 2.7 - - - -
17A LEU* 3.3 19.0 + - + +
18A ARG* 2.9 51.0 + - - +
53A PRO* 3.4 33.2 - - - -
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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 ARG* 3.1 27.0 + - + -
12A GLY 3.8 10.1 - - - +
13A ARG 3.6 0.8 - - - -
14A CYS* 1.3 75.9 - - - +
16A ALA* 1.3 58.1 + - - +
18A ARG* 3.3 9.0 + - - +
19A MET* 3.0 36.5 + - + +
157A ASP* 3.3 26.5 - - - +
192A PHE* 5.0 0.3 - - - -
198A TYR* 4.9 12.8 - - + -
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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
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12A GLY 5.2 0.2 + - - -
13A ARG 5.1 3.5 + - - +
14A CYS 3.3 0.6 - - - +
15A ALA* 1.3 77.3 - - - +
17A LEU* 1.3 59.2 + - - +
19A MET* 3.3 14.9 + - + +
20A LEU* 3.0 27.9 + - - +
69A LEU* 4.3 11.7 - - + -
100A ARG* 4.9 0.7 - - - +
153A TYR* 3.7 7.6 - - - +
154A ASN* 3.7 42.6 - - + +
157A ASP* 4.3 6.7 + - + +
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Residues in contact with LEU 17 (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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5A VAL* 4.2 28.7 - - + -
13A ARG 3.8 20.1 + - - +
14A CYS* 3.3 24.6 - - + +
16A ALA* 1.3 78.3 - - - +
18A ARG* 1.3 63.0 + - + +
20A LEU* 3.5 5.2 + - - +
21A LEU* 3.1 40.9 + - + +
53A PRO* 5.0 0.2 - - + -
55A PHE* 4.7 2.5 - - + -
65A SER* 4.6 7.6 - - - +
68A ILE* 4.0 41.3 - - + -
69A LEU* 3.9 21.2 - - + +
72A LEU* 4.6 5.7 - - + +
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Residues in contact with ARG 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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5A VAL* 4.2 5.4 - - + +
7A TYR* 3.9 15.8 - - - +
8A PHE 4.3 4.2 + - - -
10A VAL 3.0 26.7 + - - -
11A ARG* 3.7 20.6 + - - +
14A CYS* 2.9 33.0 + - - +
15A ALA* 3.6 6.5 - - - +
17A LEU* 1.3 83.9 - - + +
19A MET* 1.3 58.5 + - - +
21A LEU* 3.3 2.7 + - - -
22A ALA* 2.9 31.4 + - - +
28A TRP* 3.6 17.8 - - + +
30A GLU* 2.9 40.6 + - - +
192A PHE* 3.8 23.1 - - + -
197A GLU* 6.1 0.2 - - - -
198A TYR* 6.3 1.1 - - + -
201A LEU* 3.8 17.7 - - - +
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Residues in contact with MET 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 3.0 15.6 + - - +
16A ALA* 3.5 13.5 - - - +
18A ARG* 1.3 75.8 - - - +
20A LEU* 1.3 57.3 + - - +
22A ALA* 3.8 0.7 - - - +
23A ASP* 2.9 33.4 + - - +
153A TYR* 3.1 38.9 - - + +
156A LEU* 4.4 13.0 - - + -
157A ASP* 3.4 27.1 - - + +
160A LEU* 4.7 7.0 - - - -
189A LEU* 4.0 19.3 - - + +
192A PHE* 4.1 23.6 - - + -
193A LEU* 4.1 19.5 - - + -
198A TYR* 4.9 5.8 - - + -
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Residues in contact with LEU 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 ALA 3.0 16.1 + - - +
17A LEU 3.5 5.4 - - - +
18A ARG 3.2 0.2 - - - -
19A MET* 1.3 77.3 - - - +
21A LEU* 1.3 60.0 + - - +
23A ASP* 3.9 0.7 - - - +
24A GLN* 3.0 35.7 + - + +
69A LEU* 4.0 16.2 - - + -
72A LEU* 4.2 24.0 - - + -
73A GLY 5.1 0.4 - - - +
76A LEU* 4.0 21.5 - - + -
78A LEU* 3.7 23.6 - - + -
150A PHE* 3.8 29.6 - - + -
153A TYR* 3.6 29.1 - - + -
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Residues in contact with LEU 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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3A TYR* 3.9 20.4 - - + -
17A LEU* 3.1 35.9 + - + +
18A ARG 3.7 1.6 - - - +
20A LEU* 1.3 77.7 - - + +
22A ALA* 1.3 61.7 + - - +
24A GLN 3.3 1.4 + - - -
25A GLY 3.2 3.6 + - - -
26A GLN* 2.8 50.9 + - + +
28A TRP* 3.5 49.4 - - + -
55A PHE* 4.6 12.6 - - + -
72A LEU* 4.3 21.8 - - + -
76A LEU* 4.9 1.3 - - + -
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Residues in contact with ALA 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 ARG 2.9 17.1 + - - +
19A MET 3.8 3.4 - - - +
21A LEU* 1.3 76.0 - - - +
23A ASP* 1.3 57.7 + - - +
25A GLY* 3.0 20.3 + - - -
26A GLN 4.7 0.7 - - - -
28A TRP* 3.5 4.2 - - + -
188A LYS* 3.6 14.2 - - - +
189A LEU* 5.6 0.7 - - - -
192A PHE* 3.6 34.5 - - + -
211A MES 3.6 27.0 + - - +
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Residues in contact with ASP 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 MET 2.9 19.2 + - - +
20A LEU 4.0 0.2 - - - +
22A ALA* 1.3 75.6 - - - +
24A GLN* 1.3 59.9 + - - +
25A GLY 3.2 0.9 - - - -
153A TYR* 2.7 32.9 + - + +
186A ARG* 2.9 40.8 + - - +
188A LYS* 3.4 25.7 + - - +
189A LEU* 3.3 32.2 + - + +
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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