Contacts of the helix formed by residues 6 - 18 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO 4.0 5.6 - - - +
5A TYR* 1.3 76.8 - - - +
7A VAL* 1.3 58.9 + - - +
8A ALA* 3.1 7.0 - - - -
9A ASP* 2.8 43.3 + - - +
10A TYR* 3.0 10.4 + - - +
37A HIS* 3.4 26.5 - - - -
172A ALA 3.3 18.6 - - - +
173A LYS* 3.6 14.4 - - - +
174A LYS 3.0 17.0 - - - +
175A ALA* 4.5 0.4 - - - -
176A ALA* 3.7 8.1 - - - +
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A CYS* 1.3 71.5 - - - +
8A ALA* 1.3 65.6 + - - +
10A TYR* 3.0 9.4 + - + +
11A LEU* 2.9 22.8 + - + +
140A LEU* 5.4 0.7 - - + -
145A ALA* 3.9 32.3 - - + -
146A CYS* 5.3 2.7 - - - -
149A ILE* 4.2 15.9 - - + -
167A LEU* 4.5 18.8 - - + -
171A VAL* 3.4 25.6 - - + +
172A ALA 3.8 0.7 - - - +
174A LYS* 2.9 28.6 + - + +
175A ALA 4.5 2.2 - - - +
176A ALA* 3.7 9.8 - - + +
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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
----------------------------------------------------------
6A CYS* 3.1 9.2 - - - -
7A VAL* 1.3 77.2 - - - +
9A ASP* 1.3 61.5 + - - +
11A LEU* 3.4 4.7 + - - +
12A LEU* 3.0 30.2 + - - +
34A PHE* 3.5 31.5 - - + -
37A HIS* 3.9 19.5 - - + -
167A LEU* 5.1 1.6 - - - -
172A ALA* 3.1 24.8 + - + +
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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
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3A THR 5.0 1.2 - - - +
4A PRO 3.7 1.7 - - - +
5A TYR* 3.5 33.0 - - + -
6A CYS* 2.8 40.6 + - - +
8A ALA* 1.3 69.8 - - - +
10A TYR* 1.3 64.4 + - - +
12A LEU* 3.2 8.7 + - - +
13A ASP* 2.9 26.7 + - - +
37A HIS* 2.7 34.9 + - - +
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Residues in contact with TYR 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.3 15.4 + + + +
6A CYS 3.0 9.9 + - - +
7A VAL* 3.0 13.2 + - - +
9A ASP* 1.3 75.5 - - - +
11A LEU* 1.3 64.8 + - - +
13A ASP* 3.1 5.2 + - - +
14A ARG* 3.0 42.9 + - + +
146A CYS* 3.8 41.4 - - + +
149A ILE* 4.1 16.2 - - + -
150A ASP* 2.7 39.0 + - - -
176A ALA* 4.4 3.4 - - + -
177A THR 3.6 22.9 - - - -
179A PRO* 3.3 22.6 - - + +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 2.9 11.5 + - + +
8A ALA* 3.5 9.4 - - - +
10A TYR* 1.3 77.3 - - - +
12A LEU* 1.3 63.4 + - + +
14A ARG* 3.1 5.1 + - - +
15A LEU* 3.0 37.9 + - + +
34A PHE* 4.1 15.7 - - + -
97A LEU* 4.4 3.1 - - + -
99A ILE* 4.0 26.0 - - + -
140A LEU* 5.3 2.7 - - + -
149A ILE* 3.9 27.6 - - + +
153A LEU* 4.9 1.8 - - + -
165A LEU* 3.9 27.8 - - + -
167A LEU* 4.1 18.2 - - + -
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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
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8A ALA 3.0 27.8 + - - +
9A ASP* 3.2 8.7 + - - +
11A LEU* 1.3 79.4 - - - +
13A ASP* 1.3 63.5 + - - +
15A LEU* 3.0 35.5 + - + +
16A THR* 3.1 18.7 + - + +
23A LEU* 4.9 2.2 - - + -
34A PHE* 3.9 26.5 - - + -
37A HIS* 4.0 24.2 - - + +
38A VAL* 4.1 24.9 - - + +
41A SER* 4.8 10.1 - - - +
44A ILE* 4.1 16.1 - - + +
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 2.5 36.4 + - - +
9A ASP 2.9 10.8 + - - +
10A TYR* 3.5 8.1 - - - +
12A LEU* 1.3 76.1 - - - +
14A ARG* 1.3 57.6 + - - +
16A THR* 2.6 25.5 + - - +
17A ASP* 3.0 20.7 + - - +
43A ASP* 4.9 8.1 - - - +
178A PRO* 5.0 1.7 - - - +
179A PRO* 4.3 14.5 - - + +
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Residues in contact with ARG 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 TYR* 3.0 48.6 + - + +
11A LEU 3.1 7.4 + - - +
13A ASP* 1.3 74.4 - - - +
15A LEU* 1.3 66.1 + - - +
17A ASP* 3.0 23.4 + - - +
18A CYS* 3.0 26.3 + - - -
149A ILE* 4.2 4.3 - - + -
150A ASP* 2.8 31.9 + - - +
153A LEU* 3.4 22.0 - - + -
179A PRO* 3.7 23.8 - - - +
181A ASN 2.9 25.3 + - - -
183A LEU* 3.0 27.4 - - + +
191C ASP* 5.7 2.2 + - - +
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Residues in contact with LEU 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 LEU* 3.0 28.9 + - + +
12A LEU* 3.0 33.2 + - + +
14A ARG* 1.3 78.6 - - - +
16A THR* 1.3 63.1 + - - +
18A CYS* 3.0 17.0 + - - +
19A GLY 3.3 0.7 + - - -
20A ALA* 3.2 24.0 + - + +
22A HIS 5.4 0.2 - - - +
23A LEU* 4.5 7.6 - - + -
44A ILE* 4.1 17.3 - - + -
68A PHE* 4.8 3.8 - - + -
70A ALA* 3.9 26.0 - - + -
97A LEU* 3.5 31.9 - - + -
99A ILE* 4.4 9.0 - - + -
153A LEU* 4.9 3.1 - - + -
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Residues in contact with THR 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 3.4 9.4 - - - +
13A ASP* 2.6 27.0 + - - +
15A LEU* 1.3 74.8 - - - +
17A ASP* 1.3 67.3 + - - +
19A GLY* 2.8 15.9 + - - -
20A ALA 3.4 11.0 - - - +
21A ASP* 5.2 3.6 - - - +
41A SER* 5.4 0.2 - - - +
43A ASP* 3.5 26.8 + - + +
44A ILE* 3.4 30.5 - - + -
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 3.0 16.3 + - - +
14A ARG* 3.0 41.9 + - - +
16A THR* 1.3 85.5 + - - +
18A CYS* 1.3 59.8 + - - +
19A GLY* 3.5 0.3 + - - -
179A PRO* 5.3 1.0 - - - +
182A ALA* 3.3 26.7 - - + +
183A LEU* 4.1 18.3 - - + +
185A HIS* 4.6 12.6 + - - -
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Residues in contact with CYS 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 ARG 3.0 15.1 + - - +
15A LEU 3.0 11.0 + - - +
17A ASP* 1.3 79.8 - - - +
19A GLY* 1.3 56.5 + - - +
20A ALA 3.6 0.4 - - - -
66A LYS 5.1 1.4 - - - +
68A PHE* 3.3 47.5 - - + +
153A LEU* 4.2 21.5 - - - -
157A LEU* 3.7 31.5 - - + +
183A LEU* 4.3 7.9 - - - -
185A HIS* 5.2 4.8 - - - -
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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