Contacts of the helix formed by residues 67 - 72 (chain H) in PDB entry 2OV2
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 LEU 67 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H VAL* 3.8 31.9 - - + +
37H PHE* 4.1 11.9 - - + -
64H TYR* 3.0 11.5 + - + +
66H ARG* 1.3 80.4 - - - +
68H ARG* 1.3 68.5 + - - +
69H PRO 3.4 0.2 - - - -
70H LEU* 3.2 29.7 + - + +
71H SER 4.4 0.5 + - - -
23P THR* 4.6 3.4 - - + -
32P PHE* 3.8 41.5 - - + -
35P LEU* 3.9 25.6 - - + -
39P TRP* 3.9 18.8 - - + -
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Residues in contact with ARG 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 4.4 2.0 - - - -
10H GLY 5.9 0.2 - - - +
58H THR* 3.8 31.0 - - + -
59H ALA* 2.8 26.2 + - + +
61H GLN 3.1 25.3 + - - -
64H TYR 3.4 6.8 + - - +
65H ASP* 2.8 40.2 + - - +
67H LEU* 1.3 79.3 - - - +
69H PRO* 1.3 65.8 - - + +
70H LEU 3.0 6.1 + - - -
71H SER* 3.0 22.6 + - - -
72H TYR* 3.4 22.8 - - + +
96H LYS* 4.1 0.6 - - - +
97H TRP* 3.7 26.3 - - - -
100H GLU* 3.1 27.0 + - - +
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Residues in contact with PRO 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ASP 3.2 18.2 - - - +
66H ARG* 4.0 7.0 - - - +
67H LEU 3.6 3.1 - - - -
68H ARG* 1.3 88.3 - - + +
70H LEU* 1.3 61.8 + - + +
71H SER 3.1 0.4 - - - -
72H TYR* 3.1 35.1 + - + +
73H PRO* 3.5 6.6 - - - +
100H GLU* 4.5 6.7 - - + +
104H HIS* 3.5 39.4 - - + +
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Residues in contact with LEU 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LYS* 5.1 1.0 + - - -
56H TRP* 5.0 1.0 - - - -
66H ARG 4.7 7.0 - - - +
67H LEU* 3.2 27.8 + - + +
68H ARG 3.0 2.0 + - - -
69H PRO* 1.3 78.1 - - + +
71H SER* 1.3 59.0 + - - +
72H TYR 3.3 0.2 - - - -
73H PRO* 3.6 11.7 - - - +
35P LEU* 5.7 0.7 - - + -
39P TRP* 3.4 58.8 + - + +
42P LEU* 4.1 38.7 - - + +
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Residues in contact with SER 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LYS* 2.9 32.2 + - - -
7H VAL* 3.7 21.0 - - - +
37H PHE* 3.2 32.1 - - - -
56H TRP* 3.5 10.0 - - - -
58H THR* 3.9 6.0 - - - +
68H ARG 3.0 12.9 + - - -
70H LEU* 1.3 78.3 - - - +
72H TYR* 1.3 58.1 + - - +
73H PRO* 3.6 1.1 - - - -
75H THR* 3.4 2.3 + - - -
39P TRP* 3.3 14.2 - - - -
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Residues in contact with TYR 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H VAL* 4.1 7.4 - - + -
9H VAL* 3.7 24.9 - - + +
68H ARG* 3.4 26.6 - - + -
69H PRO* 3.1 28.0 + - + +
71H SER* 1.3 81.4 - - - +
73H PRO* 1.3 67.7 - - + +
74H GLN 3.3 0.3 + - - -
75H THR* 2.6 26.0 + - - -
78H PHE* 3.8 18.2 - + - -
97H TRP* 4.9 0.9 - - - -
100H GLU* 2.6 39.0 + - + +
101H VAL* 4.5 13.1 - - + +
104H HIS* 3.6 40.6 - + + -
105H CYS* 3.6 14.5 - - - -
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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
------------------------------------------------------------
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