Contacts of the strand formed by residues 77 - 83 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4G ILE* 4.1 7.2 - - + -
5G LYS 3.1 2.4 + - - +
6G CYS* 3.2 26.9 - - + -
7G VAL 3.0 23.0 + - - -
75G THR* 3.3 7.7 - - - +
76G ASP* 1.3 80.8 - - - +
78G PHE* 1.3 65.7 + - - +
79G LEU* 4.9 1.1 - - + -
108G THR* 4.2 0.4 - - - -
109G PRO* 3.5 11.2 - - + +
111G LEU* 3.7 29.4 - - + -
172G ALA* 4.1 22.0 - - + +
175G ALA* 4.3 5.6 - - + -
176G VAL* 3.6 20.0 - - + -
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Residues in contact with PHE 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G VAL* 3.3 28.5 - - + -
9G VAL* 4.5 4.0 - - + -
72G TYR* 3.6 31.0 - + - -
75G THR* 3.6 22.4 - - + -
77G VAL* 1.3 75.4 - - - +
79G LEU* 1.3 64.0 + - - +
80G ILE* 4.0 3.4 - - + -
101G VAL* 3.6 37.7 - - + -
105G CYS* 3.6 32.1 - - + -
108G THR* 3.8 19.1 - - + -
109G PRO 2.9 12.5 + - - +
110G ILE* 3.4 13.6 - - + -
111G LEU 2.8 31.4 + - - -
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Residues in contact with LEU 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G CYS* 3.8 22.2 - - - -
7G VAL 3.0 6.9 + - - +
8G VAL* 3.5 29.2 - - + +
9G VAL* 2.9 29.3 + - - +
19G LEU* 4.5 5.6 - - + -
77G VAL* 4.9 1.1 - - + -
78G PHE* 1.3 80.6 - - - +
80G ILE* 1.3 61.8 + - - +
81G CYS* 3.8 2.2 + - - -
111G LEU* 3.4 24.9 - - + -
113G VAL* 4.0 14.6 - - + -
168G VAL* 4.0 20.6 - - + -
169G PHE* 4.1 17.3 - - + -
172G ALA* 4.3 15.7 - - + -
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Residues in contact with ILE 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.4 14.4 - - + +
78G PHE* 4.0 3.1 - - + -
79G LEU* 1.3 73.7 - - - +
81G CYS* 1.3 63.0 + - - +
93G VAL* 4.0 24.5 - - + -
97G TRP* 3.5 30.7 - - + +
98G TYR* 4.1 23.1 - - - +
101G VAL* 4.5 6.1 - - + -
110G ILE* 3.6 39.3 - - + -
111G LEU 3.0 7.6 + - - +
112G LEU* 3.5 11.1 - - + +
113G VAL 2.9 23.7 + - - -
149G ILE* 4.2 8.5 - - + -
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Residues in contact with CYS 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 3.6 30.7 - - - -
9G VAL 2.8 13.8 + - - +
10G GLY* 3.6 18.2 - - - -
11G ASP 4.2 1.9 + - - -
14G VAL* 4.0 19.2 - - + +
16G LYS* 4.2 5.4 - - + -
19G LEU* 4.3 12.1 - - - -
79G LEU* 4.1 6.5 - - - -
80G ILE* 1.3 81.5 - - - +
82G PHE* 1.3 62.6 + - - +
89G SER 5.1 1.2 - - - +
93G VAL* 4.7 1.9 - - - +
97G TRP* 5.0 1.6 - - - -
113G VAL* 3.3 22.9 - - - +
115G THR* 4.1 9.6 - - + -
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Residues in contact with PHE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G VAL* 4.2 7.2 - - - -
81G CYS* 1.3 75.5 - - - +
83G SER* 1.3 67.5 + - - +
84G LEU* 3.9 10.8 - - + -
89G SER* 3.4 25.6 - - - +
90G PHE* 3.4 45.8 - + + -
93G VAL* 4.0 4.7 - - + -
112G LEU* 3.7 28.0 - - + -
113G VAL 3.0 9.9 + - - +
114G GLY* 3.4 18.8 - - - -
115G THR* 2.7 35.0 + - - -
137G ILE* 3.8 16.6 - - + -
154G TYR* 3.9 24.7 - + - -
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Residues in contact with SER 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ALA 5.1 0.4 - - - -
14G VAL* 3.9 15.6 - - - +
82G PHE* 1.3 78.2 - - - +
84G LEU* 1.3 63.4 + - - +
85G VAL* 3.0 27.5 + - - +
86G SER* 3.0 38.2 + - - +
89G SER* 3.1 6.2 + - - -
115G THR* 3.3 13.6 + - - -
116G LYS* 3.4 20.0 + - - +
137G ILE* 4.6 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