Contacts of the strand formed by residues 77 - 83 (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 VAL 77 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4H ILE* 4.1 7.2 - - + -
5H LYS 3.2 1.0 + - - -
6H CYS* 3.3 26.5 - - + +
7H VAL 3.0 23.6 + - - -
75H THR* 3.3 7.5 - - - +
76H ASP* 1.3 78.5 - - - +
78H PHE* 1.3 65.7 + - - +
79H LEU* 4.7 0.7 - - + -
108H THR* 4.1 0.2 - - - -
109H PRO* 3.4 15.7 - - + +
111H LEU* 3.5 32.5 - - + -
172H ALA* 3.8 24.0 - - + +
175H ALA* 4.4 0.4 - - + -
176H VAL* 3.7 23.8 - - + -
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Residues in contact with PHE 78 (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* 3.4 27.6 - - + -
9H VAL* 4.7 4.5 - - + -
72H TYR* 3.8 29.8 - + - -
75H THR* 3.6 18.8 - - + -
77H VAL* 1.3 74.3 - - - +
79H LEU* 1.3 64.0 + - - +
80H ILE* 3.9 4.5 - - + +
101H VAL* 3.4 38.6 - - + -
105H CYS* 3.6 27.8 - - - -
108H THR* 3.7 26.5 - - + -
109H PRO 2.8 13.3 + - - +
110H ILE* 3.3 11.1 - - + -
111H LEU 2.7 32.4 + - - +
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Residues in contact with LEU 79 (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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6H CYS* 3.8 17.3 - - - -
7H VAL 3.0 6.5 + - - +
8H VAL* 3.5 22.8 - - + -
9H VAL* 2.9 28.1 + - - +
19H LEU* 4.3 8.1 - - + -
77H VAL* 4.2 1.3 + - + -
78H PHE* 1.3 79.4 - - - +
80H ILE* 1.3 61.2 + - - +
81H CYS* 3.8 10.7 + - - -
111H LEU* 3.4 22.9 - - + -
113H VAL* 4.3 10.1 - - + -
168H VAL* 3.9 24.5 - - + -
169H PHE* 4.2 17.0 - - + -
172H ALA* 4.3 20.9 - - + -
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Residues in contact with ILE 80 (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* 3.5 19.5 - - + -
78H PHE* 3.9 4.0 - - + -
79H LEU* 1.3 73.1 - - - +
81H CYS* 1.3 60.2 + - - +
93H VAL* 4.0 24.0 - - + -
97H TRP* 3.7 28.3 - - + +
98H TYR* 4.1 23.6 - - - +
101H VAL* 4.2 7.6 - - + -
110H ILE* 3.9 35.7 - - + -
111H LEU 3.0 8.7 + - - +
112H LEU* 3.5 15.1 - - + +
113H VAL 2.9 23.6 + - - -
149H ILE* 4.4 6.5 - - + -
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Residues in contact with CYS 81 (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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8H VAL* 3.6 30.1 - - - -
9H VAL 2.8 14.3 + - - +
10H GLY* 3.5 17.2 - - - -
11H ASP 4.1 2.8 + - - -
14H VAL* 3.8 21.0 - - + +
16H LYS* 4.1 5.4 - - + -
19H LEU* 4.7 9.2 - - - -
79H LEU* 4.0 12.1 - - - -
80H ILE* 1.3 81.9 - - - +
82H PHE* 1.3 61.6 + - - +
89H SER 5.0 0.9 - - - +
93H VAL* 4.5 2.4 - - - +
97H TRP* 5.0 0.7 - - - -
113H VAL* 3.3 17.9 - - - +
115H THR* 4.0 11.7 - - + -
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Residues in contact with PHE 82 (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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14H VAL* 4.3 3.1 - - - -
81H CYS* 1.3 76.0 - - - +
83H SER* 1.3 62.9 + - - +
84H LEU* 3.5 22.9 - - + -
89H SER* 3.5 29.4 - - - +
90H PHE* 3.5 42.2 - + + -
93H VAL* 3.8 4.9 - - + -
112H LEU* 3.9 24.5 - - + -
113H VAL 3.0 11.6 + - - +
114H GLY* 3.7 11.0 - - - -
115H THR* 2.7 34.6 + - - -
137H ILE* 3.9 12.1 - - + -
154H TYR* 3.6 35.9 - + - -
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Residues in contact with SER 83 (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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13H ALA 5.1 0.7 - - - -
14H VAL* 3.9 17.3 - - - +
82H PHE* 1.3 80.9 - - - +
84H LEU* 1.3 63.8 + - - +
85H VAL* 3.0 28.7 + - - +
86H SER* 3.1 29.2 + - - +
89H SER* 3.0 13.6 + - - -
115H THR* 3.2 14.5 + - - -
116H LYS* 3.7 16.1 - - - +
137H ILE* 4.5 0.7 - - - +
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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