Contacts of the helix formed by residues 6 - 18 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PRO 4.0 5.2 - - - +
5B TYR* 1.3 76.1 - - - +
7B VAL* 1.3 55.1 + - - +
8B ALA* 3.1 6.7 - - - -
9B ASP* 2.7 45.4 + - - +
10B TYR* 3.0 10.0 + - - +
37B HIS* 3.4 26.7 - - - -
172B ALA 3.4 18.2 - - - +
173B LYS* 3.7 13.0 - - - +
174B LYS 2.9 20.2 - - - +
175B ALA* 4.5 0.2 - - - -
176B ALA* 3.7 9.3 - - - +
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Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B CYS* 1.3 70.8 - - - +
8B ALA* 1.3 64.4 + - - +
10B TYR* 3.0 8.6 + - - +
11B LEU* 2.9 23.7 + - + +
140B LEU* 5.4 0.9 - - + -
145B ALA* 4.0 31.2 - - + -
146B CYS* 5.5 2.2 - - - -
149B ILE* 4.1 16.4 - - + -
167B LEU* 4.5 17.9 - - + -
171B VAL* 3.4 28.9 - - + +
172B ALA 3.8 0.4 - - - +
174B LYS* 2.9 26.1 + - + +
175B ALA 4.6 2.2 - - - +
176B ALA* 3.7 10.2 - - + +
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Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B CYS* 3.1 4.6 - - - -
7B VAL* 1.3 76.0 - - - +
9B ASP* 1.3 61.8 + - - +
11B LEU* 3.4 4.3 + - - +
12B LEU* 2.9 30.8 + - - +
34B PHE* 3.5 31.5 - - + -
37B HIS* 3.8 24.9 - - + -
167B LEU* 5.1 1.8 - - - -
172B ALA* 3.1 23.4 + - + +
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Residues in contact with ASP 9 (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 THR 5.0 1.4 - - - +
4B PRO 3.7 1.6 - - - +
5B TYR* 3.5 33.5 - - + -
6B CYS* 2.7 41.4 + - - +
8B ALA* 1.3 69.8 - - - +
10B TYR* 1.3 64.8 + - - +
12B LEU* 3.3 7.6 + - - +
13B ASP* 2.9 27.1 + - - +
37B HIS* 2.8 32.7 + - - +
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Residues in contact with TYR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 3.3 17.4 + + + +
6B CYS 3.0 9.7 + - - +
7B VAL* 3.4 13.7 - - - +
9B ASP* 1.3 76.6 - - - +
11B LEU* 1.3 63.8 + - - +
13B ASP* 3.3 3.9 + - - +
14B ARG* 3.1 43.2 + - + +
146B CYS* 3.7 41.9 - - + +
149B ILE* 4.0 16.4 - - + -
150B ASP* 2.6 38.3 + - - -
176B ALA* 4.4 3.4 - - + -
177B THR 3.8 20.4 - - - -
179B PRO* 3.4 22.2 - - + -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 2.9 14.0 + - + +
8B ALA* 3.6 8.5 - - - +
10B TYR* 1.3 78.8 - - - +
12B LEU* 1.3 64.4 + - + +
14B ARG* 3.0 14.6 + - - +
15B LEU* 3.0 29.8 + - + +
34B PHE* 4.2 15.7 - - + -
97B LEU* 4.4 2.5 - - + -
99B ILE* 3.8 33.0 - - + -
140B LEU* 5.4 3.4 - - + -
149B ILE* 3.8 34.3 - - + -
153B LEU* 4.8 1.8 - - + -
165B LEU* 3.9 18.8 - - + -
167B LEU* 4.2 12.1 - - + -
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA 2.9 31.4 + - - +
9B ASP* 3.3 7.8 + - - +
11B LEU* 1.3 78.3 - - + +
13B ASP* 1.3 65.0 + - - +
15B LEU* 2.9 36.6 + - + +
16B THR* 3.0 17.3 + - - +
23B LEU* 4.9 2.2 - - + -
34B PHE* 3.9 27.8 - - + -
37B HIS* 4.1 20.6 - - + +
38B VAL* 4.2 23.1 - - + +
41B SER* 4.8 9.9 - - - +
44B ILE* 4.4 19.1 - - + -
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Residues in contact with ASP 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 2.4 35.7 + - - +
9B ASP* 2.9 11.2 + - - +
10B TYR* 3.6 8.7 - - - +
12B LEU* 1.3 76.4 - - - +
14B ARG* 1.3 59.0 + - - +
16B THR* 2.6 27.4 + - - +
17B ASP* 3.0 19.6 + - - +
43B ASP* 4.9 8.3 - - - +
178B PRO* 4.9 1.9 - - - +
179B PRO* 4.3 14.2 - - + +
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 3.1 43.4 + - + +
11B LEU 3.0 9.6 + - - +
13B ASP* 1.3 74.3 - - - +
15B LEU* 1.3 65.3 + - - +
17B ASP* 3.2 13.4 + - - +
18B CYS* 3.0 28.1 + - - -
149B ILE* 4.2 4.3 - - + -
150B ASP* 2.7 32.9 + - - +
153B LEU* 3.4 21.5 - - + -
179B PRO* 3.6 24.2 - - - +
181B ASN 2.9 25.7 + - - -
183B LEU* 3.1 34.2 - - + +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.0 26.0 + - + +
12B LEU* 2.9 33.8 + - + +
14B ARG* 1.3 77.8 - - - +
16B THR* 1.3 64.0 + - - +
18B CYS* 3.0 16.9 + - - +
19B GLY 3.3 0.5 + - - -
20B ALA* 3.2 22.9 + - + +
22B HIS 5.5 0.7 - - - +
23B LEU* 4.3 11.2 - - + -
44B ILE* 4.2 15.5 - - + -
68B PHE* 4.7 6.3 - - + -
70B ALA* 3.7 26.9 - - + -
97B LEU* 3.4 29.6 - - + -
99B ILE* 4.4 5.2 - - + -
153B LEU* 4.8 4.9 - - + -
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Residues in contact with THR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.0 9.5 + - + +
13B ASP* 2.6 27.2 + - - +
15B LEU* 1.3 75.0 - - - +
17B ASP* 1.3 66.1 + - - +
19B GLY* 2.9 15.2 + - - -
20B ALA 3.4 10.1 - - - +
21B ASP* 5.2 4.0 - - - +
41B SER* 5.4 0.2 - - - +
43B ASP* 3.5 32.9 + - + +
44B ILE* 3.4 27.4 - - + -
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ASP* 3.0 15.6 + - - +
14B ARG* 3.2 30.7 + - - +
15B LEU 3.2 0.4 - - - -
16B THR* 1.3 85.4 + - - +
18B CYS* 1.3 62.0 + - - +
19B GLY 3.4 1.0 + - - -
179B PRO* 5.4 1.0 - - - +
182B ALA* 3.2 37.5 - - + +
183B LEU* 4.0 18.0 - - + +
185B HIS* 4.6 11.5 + - - -
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Residues in contact with CYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG 3.0 15.1 + - - -
15B LEU 3.0 10.7 + - - +
17B ASP* 1.3 78.3 - - - +
19B GLY* 1.3 56.6 + - - +
20B ALA 3.7 0.4 - - - -
66B LYS 5.2 1.0 - - - +
68B PHE* 3.2 42.0 - - + +
153B LEU* 4.1 22.4 - - - -
157B LEU* 3.8 29.9 - - + +
183B LEU* 4.2 16.6 - - - -
185B HIS* 5.1 6.0 - - - -
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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