Contacts of the helix formed by residues 31 - 41 (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 ASN 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B VAL 3.9 3.2 + - - -
27B PRO* 3.5 0.2 - - - +
28B GLY 2.7 45.0 + - - +
30B TYR* 1.3 75.1 - - - +
32B LEU* 1.3 58.0 + - - +
33B GLN 3.4 2.5 - - - -
34B PHE* 3.2 14.2 + - + +
35B LEU* 2.9 37.4 + - - +
72B LEU* 3.4 30.7 - - + +
73B THR 3.3 27.7 + - - -
74B THR* 3.8 7.1 - - - +
101B GLY* 4.1 12.8 - - - -
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Residues in contact with LEU 32 (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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468A GLU* 3.8 27.4 - - + +
471A ILE* 4.1 25.4 - - + -
472A HIS* 4.1 22.7 - - + +
478A TYR* 3.6 24.7 + - + +
479A ASN* 5.0 2.2 - - - +
550A ASN* 5.5 1.1 - - - +
27B PRO* 4.0 11.4 - - + -
28B GLY 3.0 35.0 - - - +
29B ASP* 3.7 17.5 + - - +
30B TYR 3.7 0.2 - - - -
31B ASN* 1.3 79.5 - - - +
33B GLN* 1.3 64.6 + - + +
35B LEU* 3.0 23.1 + - + +
36B ASP* 3.2 5.5 + - - -
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A HIS* 3.9 20.2 + - + +
547A GLU* 3.1 22.1 - - - +
550A ASN* 3.5 22.0 - - + +
551A ASN* 3.2 15.6 + - - +
29B ASP 5.9 0.2 - - - +
30B TYR 5.6 0.2 - - - -
31B ASN 3.4 0.6 - - - -
32B LEU* 1.3 76.4 - - + +
34B PHE* 1.3 62.1 + - - +
36B ASP* 3.2 28.9 + - - +
37B HIS* 3.4 11.2 - - - -
169B ALA* 5.9 7.6 - - + +
172B ALA* 6.4 1.1 - - + -
173B LYS* 3.0 39.1 - - + +
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Residues in contact with PHE 34 (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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8B ALA* 3.5 42.2 - - + -
11B LEU* 4.2 16.2 - - + -
12B LEU* 3.9 26.5 - - + -
23B LEU* 4.2 20.9 - - + -
30B TYR 5.6 0.4 - - - +
31B ASN* 3.2 15.8 + - + +
32B LEU 3.2 0.4 - - - -
33B GLN* 1.3 78.6 - - - +
35B LEU* 1.3 64.6 + - + +
37B HIS* 3.0 23.2 + - - +
38B VAL* 3.3 12.7 - - + +
72B LEU* 4.2 25.4 - - + -
99B ILE* 4.6 8.5 - - + -
167B LEU* 3.9 21.1 - - + -
172B ALA* 4.8 12.4 - - + +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A TYR* 3.6 31.4 - - + -
23B LEU* 4.8 0.2 - - + -
27B PRO* 3.9 24.0 - - + -
31B ASN* 2.9 35.5 + - - +
32B LEU* 3.0 15.9 - - - +
34B PHE* 1.3 76.4 - - + +
36B ASP* 1.3 64.0 + - - +
38B VAL* 3.0 22.6 - - + +
39B ILE* 3.0 24.7 + - + +
46B TRP* 3.8 32.1 - - + -
72B LEU* 4.1 12.1 - - + -
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Residues in contact with ASP 36 (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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472A HIS* 2.6 33.0 + - - -
476A GLN* 2.9 29.1 + - - +
478A TYR* 3.0 16.2 + - - -
32B LEU 3.2 3.5 + - - -
33B GLN* 3.2 16.2 + - - +
34B PHE 3.1 0.4 - - - -
35B LEU* 1.3 74.9 - - - +
37B HIS* 1.3 63.8 + - + +
39B ILE* 3.1 4.7 + - - +
40B ASP* 2.8 40.1 + - - +
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Residues in contact with HIS 37 (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* 5.7 10.8 - - + -
4B PRO 4.8 3.8 - - - -
6B CYS* 3.4 27.9 - - - -
8B ALA* 3.8 16.6 - - + -
9B ASP* 2.8 31.1 + - - +
12B LEU* 4.1 14.0 - - + +
33B GLN 3.4 18.8 - - - -
34B PHE* 3.0 9.3 + - - +
36B ASP* 1.3 84.0 - - + +
38B VAL* 1.3 58.2 + - - +
40B ASP* 3.3 6.9 + - - +
41B SER* 2.9 29.1 + - - -
172B ALA 6.1 0.2 - - - -
173B LYS* 6.0 3.2 - - - +
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Residues in contact with VAL 38 (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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12B LEU* 4.2 13.7 - - + +
23B LEU* 4.2 17.9 - - + -
34B PHE* 3.3 27.1 - - + +
35B LEU* 3.0 32.5 - - + +
37B HIS* 1.3 73.5 - - - +
39B ILE* 1.3 63.5 + - + +
41B SER* 3.3 12.1 + - - -
44B ILE* 3.1 32.1 - - + +
46B TRP* 3.7 34.1 - - + +
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Residues in contact with ILE 39 (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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476A GLN* 4.4 15.7 - - - +
477A ARG* 4.0 36.8 - - + +
478A TYR* 3.4 37.7 - - + +
35B LEU* 3.0 12.8 + - + +
36B ASP* 3.5 9.0 - - - +
38B VAL* 1.3 80.5 - - - +
40B ASP* 1.3 68.3 + - - +
41B SER 3.5 5.2 + - - +
46B TRP* 4.6 17.0 - - + +
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Residues in contact with ASP 40 (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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476A GLN* 5.4 3.9 + - - -
3B THR* 5.4 7.8 - - - +
36B ASP* 2.8 29.4 + - - +
37B HIS* 4.0 6.3 - - - +
39B ILE* 1.3 82.1 - - - +
41B SER* 1.3 64.8 + - - +
42B PRO* 3.4 7.1 - - - +
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.8 11.9 - - - +
16B THR* 5.4 0.2 - - - +
37B HIS 2.9 17.3 + - - -
38B VAL* 3.6 13.2 - - - +
39B ILE 3.2 5.6 - - - +
40B ASP* 1.3 79.8 - - - +
42B PRO* 1.3 70.7 - - - +
43B ASP* 3.1 15.6 + - - +
44B ILE* 3.3 29.0 + - - +
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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