Contacts of the helix formed by residues 31 - 41 (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 ASN 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D VAL 3.9 7.3 + - - -
28D GLY 2.7 40.8 + - - +
30D TYR* 1.3 74.6 - - - +
32D LEU* 1.3 58.5 + - - +
33D GLN 3.4 2.2 - - - -
34D PHE* 3.3 12.7 + - + +
35D LEU* 2.9 42.8 + - - +
72D LEU* 4.2 20.6 - - + +
73D THR 3.3 29.9 + - - -
74D THR* 3.8 7.3 - - - +
101D GLY* 4.1 13.5 - - - -
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Residues in contact with LEU 32 (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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468C GLU* 3.9 31.4 - - + +
471C ILE* 4.0 20.4 - - + -
472C HIS* 4.1 20.4 - - + +
478C TYR* 3.6 26.2 + - + +
479C ASN* 4.9 2.0 - - - +
550C ASN* 5.6 0.9 - - - +
27D PRO* 4.0 11.4 - - + -
28D GLY 3.0 35.0 - - - +
29D ASP* 3.7 19.8 + - - +
30D TYR 3.8 0.4 - - - -
31D ASN* 1.3 79.4 - - - +
33D GLN* 1.3 65.3 + - + +
35D LEU* 2.9 23.2 + - + +
36D ASP* 3.2 5.5 + - - -
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Residues in contact with GLN 33 (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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472C HIS* 4.0 20.9 + - + +
547C GLU* 3.1 21.3 - - - +
550C ASN* 3.5 20.0 - - + +
551C ASN* 3.3 15.8 + - - +
29D ASP 5.8 0.4 - - - +
30D TYR 5.6 0.4 - - - -
31D ASN 3.4 0.4 - - - -
32D LEU* 1.3 77.4 - - + +
34D PHE* 1.3 61.6 + - - +
36D ASP* 3.3 23.0 + - - +
37D HIS* 3.4 17.2 - - - -
169D ALA* 5.9 7.9 - - + +
172D ALA* 6.4 1.1 - - + -
173D LYS* 2.9 37.7 - - + +
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Residues in contact with PHE 34 (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* 3.5 42.2 - - + -
11D LEU* 4.1 16.2 - - + -
12D LEU* 3.8 25.4 - - + -
23D LEU* 4.2 11.9 - - + -
31D ASN* 3.3 14.0 + - + +
32D LEU 3.2 0.8 - - - -
33D GLN* 1.3 77.6 - - - +
35D LEU* 1.3 65.1 + - - +
37D HIS* 3.0 24.6 + - - +
38D VAL* 3.4 8.9 - - + +
72D LEU* 3.4 44.0 - - + -
99D ILE* 4.6 6.7 - - + -
167D LEU* 3.9 21.3 - - + -
172D ALA* 4.8 11.4 - - + +
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Residues in contact with LEU 35 (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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478C TYR* 3.5 34.5 - - + -
27D PRO* 3.8 24.5 - - + -
31D ASN* 2.9 32.8 + - - +
32D LEU* 3.0 14.8 - - - +
34D PHE* 1.3 77.7 - - - +
36D ASP* 1.3 60.4 + - - +
38D VAL* 3.0 30.5 - - + +
39D ILE* 3.0 16.3 + - + +
46D TRP* 3.7 24.2 - - + -
72D LEU* 3.5 23.6 - - + -
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Residues in contact with ASP 36 (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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472C HIS* 2.7 33.2 + - - -
476C GLN* 2.8 30.5 + - - +
478C TYR* 3.0 16.6 + - - -
32D LEU 3.2 3.0 + - - -
33D GLN* 3.4 14.6 + - - +
34D PHE 3.1 0.4 - - - -
35D LEU* 1.3 75.1 - - - +
37D HIS* 1.3 61.4 + - + +
39D ILE* 3.1 3.9 + - - +
40D ASP* 2.9 40.4 + - - +
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Residues in contact with HIS 37 (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* 5.6 12.1 - - + -
4D PRO 4.8 4.3 - - - -
6D CYS* 3.4 25.2 - - - -
8D ALA* 3.8 18.2 - - + -
9D ASP* 2.7 29.7 + - - +
12D LEU* 4.0 14.8 - - + +
33D GLN 3.4 25.1 + - - -
34D PHE* 3.0 8.9 + - - +
36D ASP* 1.3 79.6 - - + +
38D VAL* 1.3 57.0 + - - +
40D ASP* 3.3 7.6 + - - +
41D SER* 2.9 28.9 + - - -
172D ALA* 5.7 0.6 - - + -
173D LYS* 6.0 3.6 - - - +
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Residues in contact with VAL 38 (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* 4.1 15.1 - - + +
23D LEU* 4.2 21.3 - - + -
34D PHE* 3.4 12.1 - - + +
35D LEU* 3.0 42.0 - - + +
37D HIS* 1.3 75.2 - - - +
39D ILE* 1.3 60.2 + - - +
41D SER* 3.4 11.8 + - - -
44D ILE* 3.1 27.7 - - + +
46D TRP* 3.8 35.8 + - + +
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Residues in contact with ILE 39 (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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476C GLN* 4.1 16.8 - - - +
477C ARG* 4.0 40.6 - - + +
478C TYR* 3.4 35.2 - - + +
35D LEU 3.0 10.4 + - - +
36D ASP* 3.1 9.4 + - - +
38D VAL* 1.3 79.2 - - - +
40D ASP* 1.3 66.9 + - - +
41D SER 3.5 5.2 + - - +
46D TRP* 4.7 17.0 - - + +
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Residues in contact with ASP 40 (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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476C GLN* 5.3 3.4 + - - -
3D THR* 5.4 8.4 - - - +
36D ASP* 2.9 28.8 + - - +
37D HIS* 3.6 8.0 + - - +
39D ILE* 1.3 81.2 - - - +
41D SER* 1.3 64.9 + - - +
42D PRO* 3.5 6.6 - - - +
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Residues in contact with SER 41 (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* 4.8 11.2 - - - +
16D THR* 5.4 0.3 - - - +
37D HIS 2.9 16.4 + - - -
38D VAL* 3.6 14.1 - - - +
39D ILE 3.2 6.0 - - - +
40D ASP* 1.3 79.6 - - - +
42D PRO* 1.3 69.1 - - - +
43D ASP* 3.1 16.0 + - - +
44D ILE* 3.2 27.5 + - - +
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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