Contacts of the helix formed by residues 6 - 19 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D PRO 4.0 5.6 - - - +
5D TYR* 1.3 76.2 - - - +
7D VAL* 1.3 58.3 + - - +
8D ALA* 3.1 7.9 - - - -
9D ASP* 2.7 44.7 + - - +
10D TYR* 3.0 10.6 + - - +
37D HIS* 3.4 27.1 - - - -
172D ALA 3.4 15.7 - - - +
173D LYS* 3.5 16.2 - - - +
174D LYS 3.0 15.9 - - - +
175D ALA* 4.6 0.2 - - - -
176D ALA* 3.7 8.5 - - - +
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Residues in contact with VAL 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D CYS* 1.3 70.6 - - - +
8D ALA* 1.3 63.9 + - - +
10D TYR* 3.0 9.4 + - + +
11D LEU* 2.9 23.5 + - + +
140D LEU* 5.3 0.7 - - + -
142D GLU* 6.4 0.2 - - - -
145D ALA* 3.9 31.0 - - + -
146D CYS* 5.4 2.5 - - - -
149D ILE* 4.2 16.2 - - + -
167D LEU* 4.4 19.3 - - + -
171D VAL* 3.4 28.9 - - + +
172D ALA 3.8 0.4 - - - +
174D LYS* 2.9 27.0 + - + +
175D ALA 4.6 1.8 - - - +
176D ALA* 3.7 9.7 - - + +
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Residues in contact with ALA 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D CYS* 3.1 9.8 - - - -
7D VAL* 1.3 79.7 - - - +
9D ASP* 1.3 61.5 + - - +
11D LEU* 3.5 3.9 + - - +
12D LEU* 2.9 30.2 + - - +
34D PHE* 3.5 30.4 - - + -
37D HIS* 3.8 19.7 - - + -
167D LEU* 5.1 1.6 - - - -
172D ALA* 3.1 22.0 + - + +
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Residues in contact with ASP 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR 4.9 1.6 - - - +
4D PRO 3.7 2.6 - - - +
5D TYR* 3.4 32.4 - - + -
6D CYS* 2.7 40.0 + - - +
8D ALA* 1.3 69.6 - - - +
10D TYR* 1.3 64.5 + - - +
12D LEU* 3.3 8.4 + - - +
13D ASP* 2.9 26.3 + - - +
37D HIS* 2.7 35.3 + - - +
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Residues in contact with TYR 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D TYR* 3.3 16.0 + + + +
6D CYS 3.0 9.7 + - - +
7D VAL* 3.3 13.9 - - - +
9D ASP* 1.3 77.1 - - - +
11D LEU* 1.3 63.4 + - - +
13D ASP* 3.2 4.7 + - - +
14D ARG* 3.0 46.7 + - + +
146D CYS* 3.8 40.0 + - + +
149D ILE* 4.1 16.6 - - + -
150D ASP* 2.7 37.6 + - - -
176D ALA* 4.4 4.0 - - + -
177D THR 3.7 21.3 - - - -
179D PRO* 3.3 22.8 - - + +
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 2.9 11.9 + - + +
8D ALA* 3.6 9.0 - - - +
10D TYR* 1.3 78.5 - - - +
12D LEU* 1.3 64.6 + - + +
14D ARG* 3.0 6.3 + - - +
15D LEU* 3.0 44.2 + - + +
34D PHE* 4.1 18.8 - - + -
97D LEU* 4.4 3.1 - - + -
99D ILE* 3.8 30.3 - - + -
140D LEU* 5.3 2.9 - - + -
149D ILE* 3.9 34.1 - - + +
153D LEU* 5.1 1.3 - - + -
165D LEU* 3.9 19.3 - - + -
167D LEU* 4.2 11.2 - - + -
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ALA 2.9 28.5 + - - +
9D ASP* 3.3 8.7 + - - +
11D LEU* 1.3 77.9 - - + +
13D ASP* 1.3 64.5 + - - +
15D LEU* 2.9 34.6 + - + +
16D THR* 3.0 18.4 + - - +
23D LEU* 5.0 2.2 - - + -
34D PHE* 3.8 29.4 - - + -
37D HIS* 4.0 21.1 - - + +
38D VAL* 4.1 24.9 - - + +
41D SER* 4.8 9.0 - - - +
44D ILE* 4.2 17.7 - - + +
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Residues in contact with ASP 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 2.6 34.3 + - - +
9D ASP* 2.9 10.8 + - - +
10D TYR 3.2 8.5 + - - +
12D LEU* 1.3 77.2 - - - +
14D ARG* 1.3 57.9 - - - +
16D THR* 2.6 26.9 + - - +
17D ASP* 3.0 21.6 + - - +
43D ASP* 4.8 8.7 - - - +
178D PRO* 4.9 1.9 - - - +
179D PRO* 4.3 14.1 - - + +
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Residues in contact with ARG 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ASP* 5.8 1.0 + - - +
10D TYR* 3.0 47.9 + - + +
11D LEU 3.0 9.4 + - - +
13D ASP* 1.3 74.7 - - - +
15D LEU* 1.3 64.6 + - - +
17D ASP* 3.1 13.7 + - - +
18D CYS* 3.1 28.4 + - - -
149D ILE* 4.2 3.6 - - + -
150D ASP* 2.7 31.5 + - - +
153D LEU* 3.3 22.9 - - + -
179D PRO* 3.7 22.5 - - + +
181D ASN 3.0 24.9 + - - -
182D ALA 3.5 0.2 - - - -
183D LEU* 3.0 37.2 - - - +
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.0 30.8 + - + +
12D LEU* 2.9 33.5 + - + +
14D ARG* 1.3 77.3 - - - +
16D THR* 1.3 62.4 + - - +
18D CYS* 3.0 17.7 + - - +
19D GLY 3.3 0.7 + - - -
20D ALA* 3.2 24.4 + - + +
22D HIS 5.3 0.7 - - - +
23D LEU* 4.3 11.0 - - + -
44D ILE* 4.1 16.8 - - + -
68D PHE* 4.8 4.3 - - + -
70D ALA* 3.8 26.7 - - + -
97D LEU* 3.5 28.9 - - + -
99D ILE* 4.4 4.5 - - + -
153D LEU* 5.1 4.0 - - + -
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Residues in contact with THR 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU 3.0 9.6 + - - +
13D ASP* 2.6 27.0 + - - +
15D LEU* 1.3 75.6 - - - +
17D ASP* 1.3 67.6 + - - +
19D GLY* 3.0 13.9 + - - -
20D ALA 3.4 10.3 - - - +
21D ASP* 5.2 4.5 - - - +
41D SER* 5.4 0.4 - - - +
43D ASP* 3.5 32.5 + - + +
44D ILE* 3.4 27.4 - - + -
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Residues in contact with ASP 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ASP* 3.0 17.4 + - - +
14D ARG* 3.1 39.6 + - - +
15D LEU 3.2 0.4 - - - -
16D THR* 1.3 86.0 + - - +
18D CYS* 1.3 61.1 + - - +
19D GLY* 3.4 1.0 + - - -
179D PRO* 5.4 1.6 - - - +
182D ALA* 3.2 26.5 - - + +
183D LEU* 4.1 17.1 - - + +
185D HIS* 4.6 11.9 + - - -
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Residues in contact with CYS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG 3.1 16.2 + - - +
15D LEU 3.0 10.9 + - - +
17D ASP* 1.3 78.3 - - - +
19D GLY* 1.3 55.3 + - - +
20D ALA 3.7 0.2 - - - -
66D LYS 5.2 1.0 - - - +
68D PHE* 3.3 41.7 - - + +
153D LEU* 4.1 28.3 - - - -
157D LEU* 3.7 30.8 - - + +
183D LEU* 4.3 8.1 - - - -
185D HIS* 5.1 5.3 - - - -
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Residues in contact with GLY 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D THR 3.0 11.3 + - - -
17D ASP 3.2 2.0 + - - -
18D CYS* 1.3 80.5 - - - +
20D ALA* 1.3 61.3 + - - +
21D ASP* 4.3 3.6 - - - +
66D LYS* 3.6 36.4 + - - +
68D PHE* 4.7 6.3 - - - -
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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