Contacts of the helix formed by residues 31 - 41 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C VAL 3.9 3.0 + - - -
28C GLY 2.7 43.2 + - - +
30C TYR* 1.3 74.0 - - - +
32C LEU* 1.3 57.6 + - - +
33C GLN 3.4 2.5 - - - -
34C PHE* 3.1 13.9 + - + +
35C LEU* 2.8 37.8 + - - +
72C LEU* 3.5 30.3 - - + +
73C THR 3.3 27.1 + - - -
74C THR* 3.7 7.9 - - - -
101C GLY* 4.2 12.1 - - - -
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PRO* 3.9 11.4 - - + -
28C GLY 2.9 37.5 - - - +
29C ASP* 3.7 17.1 + - - +
30C TYR 3.8 0.2 - - - -
31C ASN* 1.3 82.0 + - - +
33C GLN* 1.3 66.0 + - + +
35C LEU* 3.0 22.6 + - + +
36C ASP* 3.2 5.7 + - - -
468D GLU* 3.7 31.0 - - + +
471D ILE* 3.9 29.4 - - + -
472D HIS* 4.1 18.6 - - + +
478D TYR* 3.5 24.5 + - + +
550D ASN* 5.6 0.9 - - - +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TYR 5.6 0.2 - - - -
31C ASN 3.4 0.4 - - - -
32C LEU* 1.3 75.2 - - + +
34C PHE* 1.3 64.3 + - - +
36C ASP* 3.1 29.2 + - - +
37C HIS* 3.5 10.8 - - - -
169C ALA* 5.8 6.7 - - + +
172C ALA* 6.5 0.7 - - + -
173C LYS* 2.9 37.8 - - + +
472D HIS* 3.9 17.2 + - + -
547D GLU* 3.0 25.6 - - - +
550D ASN* 3.3 23.9 - - + +
551D ASN* 3.2 16.8 + - - +
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Residues in contact with PHE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ALA* 3.5 41.7 - - + -
11C LEU* 4.1 16.2 - - + -
12C LEU* 3.8 25.6 - - + -
23C LEU* 4.2 21.8 - - + -
30C TYR 5.6 0.4 - - - +
31C ASN* 3.1 16.8 + - + +
33C GLN* 1.3 79.5 - - - +
35C LEU* 1.3 65.8 + - + +
37C HIS* 3.1 23.0 + - - +
38C VAL* 3.3 13.3 - - + +
72C LEU* 4.3 24.9 - - + -
99C ILE* 4.5 8.3 - - + -
167C LEU* 3.8 22.2 - - + -
172C ALA* 4.8 10.7 - - + +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PRO* 3.8 24.9 - - + -
31C ASN* 2.8 35.7 + - - +
32C LEU* 3.0 13.7 + - - +
34C PHE* 1.3 76.8 - - + +
36C ASP* 1.3 63.5 + - - +
38C VAL* 3.1 21.7 - - + +
39C ILE* 3.0 25.2 + - + +
46C TRP* 3.7 30.5 - - + -
72C LEU* 4.0 12.8 - - + -
478D TYR* 3.5 32.3 - - + -
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Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 3.2 2.4 + - - -
33C GLN* 3.1 15.7 + - - +
35C LEU* 1.3 74.5 - - - +
37C HIS* 1.3 62.6 + - + +
39C ILE* 3.1 4.3 + - - +
40C ASP* 2.9 40.0 + - - +
472D HIS* 2.5 33.7 + - - -
476D GLN* 2.9 25.2 + - - +
478D TYR* 2.9 20.7 + - - -
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Residues in contact with HIS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C THR* 5.7 10.8 - - + -
4C PRO 4.8 4.7 - - - -
6C CYS* 3.4 26.9 - - - -
8C ALA* 3.8 17.3 - - + -
9C ASP* 2.7 29.3 + - - +
12C LEU* 3.9 13.8 - - + +
33C GLN 3.5 17.5 - - - -
34C PHE* 3.1 9.5 + - - +
36C ASP* 1.3 84.9 - - + +
38C VAL* 1.3 56.2 + - - +
40C ASP* 3.3 7.1 + - - +
41C SER* 2.9 29.3 + - - -
172C ALA 6.0 0.2 - - - -
173C LYS* 5.9 3.6 - - - +
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.0 16.4 - - + +
23C LEU* 4.3 12.6 - - + -
34C PHE* 3.3 26.9 - - + +
35C LEU* 3.1 32.8 - - + +
37C HIS* 1.3 76.3 - - - +
39C ILE* 1.3 61.8 + - - +
41C SER* 3.4 9.4 + - - -
44C ILE* 3.1 31.3 - - + +
46C TRP* 3.8 34.9 + - + +
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.0 12.7 + - + +
36C ASP 3.6 7.0 - - - +
38C VAL* 1.3 82.3 - - - +
40C ASP* 1.3 66.9 + - - +
41C SER 3.5 5.5 + - - +
46C TRP* 4.6 16.8 - - + +
476D GLN* 4.1 20.0 - - - +
477D ARG* 3.9 37.0 - - + +
478D TYR* 3.2 38.6 - - + +
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Residues in contact with ASP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C THR* 5.4 8.7 - - - +
36C ASP* 2.9 28.6 + - - +
37C HIS* 3.9 6.9 + - - +
38C VAL 3.3 0.2 - - - -
39C ILE* 1.3 80.4 - - - +
41C SER* 1.3 65.0 + - - +
42C PRO* 3.4 7.3 - - - +
476D GLN* 5.3 3.7 + - - -
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Residues in contact with SER 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.7 11.3 - - - +
16C THR* 5.4 0.3 - - - +
37C HIS 2.9 17.5 + - - -
38C VAL* 3.6 13.8 - - - +
39C ILE 3.2 5.4 - - - +
40C ASP* 1.3 79.1 - - - +
42C PRO* 1.3 70.4 - - - +
43C ASP* 3.1 15.9 + - - +
44C ILE* 3.3 26.8 + - - +
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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