Contacts of the helix formed by residues 6 - 18 (chain C) in PDB entry 1OVM
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 CYS 6 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C PRO 4.1 5.8 - - - +
5C TYR* 1.3 76.2 - - - +
7C VAL* 1.3 55.2 + - - +
8C ALA* 3.1 7.0 - - - -
9C ASP* 2.8 33.5 + - - +
10C TYR* 3.0 10.4 + - - +
37C HIS* 3.4 35.9 - - - -
172C ALA 3.2 19.1 - - - +
173C LYS* 3.6 13.2 - - - +
174C LYS 2.9 20.6 - - - +
175C ALA* 4.5 0.2 - - - -
176C ALA* 3.7 9.3 - - - +
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Residues in contact with VAL 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C CYS* 1.3 71.5 - - - +
8C ALA* 1.3 63.2 + - - +
10C TYR* 3.1 8.6 + - + +
11C LEU* 2.9 23.2 + - + +
140C LEU* 5.3 0.4 - - + -
142C GLU* 6.4 0.2 - - - -
145C ALA* 3.9 31.2 - - + -
146C CYS* 5.3 3.1 - - - -
149C ILE* 4.1 16.6 - - + -
167C LEU* 4.5 18.4 - - + -
171C VAL* 3.4 27.8 - - + +
172C ALA 3.8 0.2 - - - +
174C LYS* 2.9 25.7 + - + +
175C ALA 4.5 2.2 - - - +
176C ALA* 3.8 10.0 - - + +
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Residues in contact with ALA 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C CYS* 3.1 2.6 + - - -
7C VAL* 1.3 78.0 - - - +
9C ASP* 1.3 61.2 + - - +
11C LEU* 3.4 4.6 + - - +
12C LEU* 3.0 30.0 + - - +
34C PHE* 3.5 31.6 - - + -
37C HIS* 3.8 27.1 - - + -
167C LEU* 5.1 1.1 - - - -
172C ALA* 3.1 23.4 + - + +
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Residues in contact with ASP 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C THR 5.0 1.4 - - - +
4C PRO 3.7 2.8 - - - +
5C TYR* 3.4 32.5 - - + -
6C CYS* 2.8 33.8 + - - +
8C ALA* 1.3 74.1 - - - +
10C TYR* 1.3 64.7 + - - +
12C LEU* 3.2 8.6 + - - +
13C ASP* 2.9 27.0 + - - +
37C HIS* 2.7 34.2 + - - +
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Residues in contact with TYR 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C TYR* 3.4 16.0 + + + +
6C CYS 3.0 11.2 + - - +
7C VAL* 3.1 13.9 + - - +
9C ASP* 1.3 77.1 - - - +
11C LEU* 1.3 62.5 - - - +
13C ASP* 3.3 3.1 + - - +
14C ARG* 3.1 43.4 + - + +
146C CYS* 3.8 41.3 - - + +
149C ILE* 4.1 16.2 - - + -
150C ASP* 2.6 38.5 + - - -
176C ALA* 4.4 3.8 - - + -
177C THR 3.7 21.5 - - - -
179C PRO* 3.4 23.1 - - + +
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Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 2.9 12.6 + - + +
8C ALA 3.6 8.3 - - - +
10C TYR* 1.3 78.2 - - - +
12C LEU* 1.3 64.3 + - + +
14C ARG* 3.0 3.6 + - - +
15C LEU* 3.0 43.5 + - + +
34C PHE* 4.1 18.2 - - + -
97C LEU* 4.4 2.7 - - + -
99C ILE* 3.8 31.6 - - + -
140C LEU* 5.3 3.1 - - + -
149C ILE* 3.9 35.2 - - + -
153C LEU* 4.9 1.3 - - + -
165C LEU* 3.9 20.0 - - + -
167C LEU* 4.2 11.2 - - + -
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ALA 3.0 27.8 + - - +
9C ASP* 3.2 7.8 + - - +
11C LEU* 1.3 78.4 - - + +
13C ASP* 1.3 63.9 + - - +
15C LEU* 2.9 35.0 + - + +
16C THR* 3.0 18.0 + - - +
23C LEU* 5.0 2.5 - - + -
34C PHE* 3.8 25.8 - - + -
37C HIS* 3.9 26.0 - - + +
38C VAL* 4.0 25.1 - - + +
41C SER* 4.7 10.5 - - - +
44C ILE* 4.5 15.9 - - + -
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Residues in contact with ASP 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C TYR* 2.6 35.1 + - - +
9C ASP 2.9 14.4 + - - +
10C TYR 3.6 5.4 - - - +
11C LEU 3.2 0.2 - - - -
12C LEU* 1.3 76.4 - - - +
14C ARG* 1.3 57.2 + - - +
16C THR* 2.5 25.7 + - - +
17C ASP* 3.0 20.9 + - - +
43C ASP* 4.7 9.5 - - - +
178C PRO* 5.0 1.7 - - - +
179C PRO* 4.3 14.1 - - + +
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Residues in contact with ARG 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASP* 5.9 1.8 + - - +
10C TYR* 3.1 45.5 + - + +
11C LEU 3.0 8.6 + - - +
13C ASP* 1.3 75.0 - - - +
15C LEU* 1.3 65.2 + - - +
17C ASP* 3.1 15.2 + - - +
18C CYS* 3.0 27.9 + - - -
149C ILE* 4.2 5.2 - - + -
150C ASP* 2.8 32.6 + - - +
153C LEU* 3.4 22.4 - - + -
179C PRO* 3.6 23.4 - - - +
181C ASN 2.9 26.3 + - - -
183C LEU* 3.1 33.4 - - + +
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.0 31.1 + - + +
12C LEU* 2.9 34.4 + - + +
14C ARG* 1.3 76.6 - - - +
16C THR* 1.3 62.8 + - - +
18C CYS* 3.0 17.2 + - - +
19C GLY 3.3 0.5 + - - -
20C ALA* 3.2 22.6 + - + +
22C HIS 5.5 0.7 - - - +
23C LEU* 4.4 7.4 - - + -
44C ILE* 4.2 15.7 - - + -
68C PHE* 4.8 5.6 - - + -
70C ALA* 3.9 26.2 - - + -
97C LEU* 3.5 29.6 - - + -
99C ILE* 4.4 9.0 - - + -
153C LEU* 4.9 4.5 - - + -
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Residues in contact with THR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU 3.0 7.5 + - - +
13C ASP* 2.5 31.1 + - - +
15C LEU* 1.3 74.6 - - - +
17C ASP* 1.3 65.6 + - - +
19C GLY* 2.9 14.6 + - - -
20C ALA 3.4 10.5 - - - +
21C ASP* 5.3 4.1 - - - +
41C SER* 5.4 0.7 - - - +
43C ASP* 3.4 33.5 + - + +
44C ILE* 3.4 29.2 - - + -
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Residues in contact with ASP 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ASP* 3.0 17.3 + - - +
14C ARG* 3.1 39.8 + - - +
16C THR* 1.3 85.7 + - - +
18C CYS* 1.3 61.6 + - - +
19C GLY 3.4 0.3 + - - -
179C PRO* 5.3 1.4 - - - +
182C ALA* 3.2 25.8 - - + +
183C LEU* 4.0 18.2 - - + +
185C HIS* 4.5 12.0 + - - -
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Residues in contact with CYS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ARG 3.0 18.0 + - - +
15C LEU 3.0 9.6 + - - +
17C ASP* 1.3 79.6 - - - +
19C GLY* 1.3 56.0 + - - +
20C ALA 3.7 0.4 - - - -
66C LYS 5.2 1.2 - - - +
68C PHE* 3.3 40.5 - - + +
153C LEU* 4.0 27.6 - - - -
157C LEU* 3.9 29.3 - - + +
183C LEU* 4.3 10.8 - - - -
185C HIS* 5.1 5.8 - - - -
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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
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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