Contacts of the helix formed by residues 67 - 72 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 3.6 33.4 - - + +
37E PHE* 4.1 11.0 - - + -
64E TYR* 3.1 14.1 + - + +
66E ARG* 1.3 82.0 - - - +
68E ARG* 1.3 65.4 + - - +
69E PRO 3.4 0.2 - - - -
70E LEU* 3.2 22.9 + - + +
71E SER 4.3 0.3 + - - -
23M THR* 4.8 2.0 - - + -
32M PHE* 3.6 38.1 - - + -
35M LEU* 4.0 26.0 - - + -
39M TRP* 4.0 19.3 - - + -
43M ILE* 4.0 13.7 - - + -
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Residues in contact with ARG 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 4.4 2.2 - - - -
58E THR* 3.9 29.2 - - + -
59E ALA* 2.9 30.4 + - + +
61E GLN 3.3 18.6 + - - -
64E TYR 3.2 6.1 + - - +
65E ASP* 2.9 35.7 + - - +
67E LEU* 1.3 79.3 - - - +
69E PRO* 1.3 63.2 - - + +
71E SER* 3.0 30.2 + - - -
72E TYR* 3.3 24.7 - - + +
96E LYS* 4.1 0.8 - - - +
97E TRP* 3.5 29.0 - - - -
100E GLU* 3.0 30.4 + - - +
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Residues in contact with PRO 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ASP 3.2 20.2 - - - +
66E ARG 3.7 7.6 - - - +
67E LEU 3.4 3.8 - - - -
68E ARG* 1.3 87.2 - - + +
70E LEU* 1.3 60.9 + - + -
71E SER 3.0 6.1 - - - -
72E TYR* 3.1 31.2 + - + +
73E PRO* 3.4 9.5 - - - +
100E GLU* 4.3 7.4 - - - +
104E HIS* 3.7 37.5 - - + +
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS* 5.0 0.9 + - - -
56E TRP* 4.9 1.4 - - - -
66E ARG 4.4 6.7 - - - +
67E LEU* 3.2 17.9 + - + +
68E ARG 3.1 0.6 + - - -
69E PRO* 1.3 78.3 - - + +
71E SER* 1.3 59.1 + - - +
72E TYR 3.3 0.2 - - - -
73E PRO* 3.7 11.4 - - - +
39M TRP* 3.3 52.8 + - + +
42M LEU* 4.5 23.1 - - + +
43M ILE* 3.9 39.7 - - + -
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Residues in contact with SER 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS* 2.6 33.7 + - - -
7E VAL* 3.8 8.0 - - - +
37E PHE* 3.2 32.6 - - - -
56E TRP* 3.6 9.9 - - - -
58E THR* 4.1 13.4 - - - +
68E ARG* 3.0 15.7 + - - -
70E LEU* 1.3 78.8 - - - +
72E TYR* 1.3 61.9 + - - +
73E PRO* 3.7 0.7 - - - -
75E THR* 3.5 1.9 + - - -
39M TRP* 3.3 12.1 - - - -
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Residues in contact with TYR 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E VAL* 4.1 6.3 - - + -
9E VAL* 3.9 18.1 - - + +
68E ARG* 3.3 29.6 - - + -
69E PRO* 3.5 24.2 - - + +
71E SER* 1.3 80.9 - - - +
73E PRO* 1.3 69.3 - - + +
74E GLN 3.2 0.9 + - - -
75E THR* 2.7 25.3 + - - -
78E PHE* 3.6 28.9 - + - -
97E TRP* 4.8 1.0 - - - -
100E GLU* 2.6 37.6 + - + +
101E VAL* 4.5 9.3 - - + +
104E HIS* 3.6 35.9 - + + -
105E CYS* 3.6 20.7 - - - -
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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