Contacts of the strand formed by residues 76 - 81 (chain E) in PDB entry 2KVQ
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 ASP 76 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E ARG 3.5 1.0 - - - +
10E LEU* 3.2 6.4 - - - -
11E LYS* 2.9 52.4 + - + +
75E VAL* 1.3 72.4 - - - +
77E VAL* 1.3 80.1 + - - +
78E GLN* 4.2 16.4 + - - +
167G ARG* 2.9 32.1 - - - +
168G ALA 4.7 2.6 - - - +
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Residues in contact with VAL 77 (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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8E ILE* 4.9 0.4 - - + -
9E ARG 3.5 3.8 - - - +
10E LEU* 2.9 31.2 - - + -
25E ILE* 4.8 1.1 - - + -
71E LEU* 3.4 36.6 - - + -
75E VAL* 3.8 13.9 + - + +
76E ASP* 1.3 84.6 + - - +
78E GLN* 1.3 59.6 + - - +
79E ILE* 4.0 17.5 + - + +
164G ILE* 5.3 2.0 - - + -
165G PHE* 5.0 9.6 - - + -
167G ARG* 4.2 6.8 - - + +
168G ALA 4.4 4.9 - - - +
169G THR* 3.9 20.0 + - - +
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Residues in contact with GLN 78 (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 ARG 3.7 1.0 - - - +
8E ILE* 3.3 2.6 - - - +
9E ARG* 2.9 61.9 + - + +
11E LYS* 4.5 21.3 - - - +
76E ASP* 4.4 15.6 + - - +
77E VAL* 1.3 73.9 - - - +
79E ILE* 1.3 64.8 + - - +
170G PRO* 3.9 32.1 - - + +
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Residues in contact with ILE 79 (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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6E ILE* 5.0 4.7 - - + -
7E ARG 3.3 4.7 - - - +
8E ILE* 3.5 32.3 - - + -
25E ILE* 6.3 0.2 - - + -
66E LEU* 4.5 18.2 - - + -
67E MET* 5.6 2.0 - - - -
77E VAL* 4.5 15.0 - - + +
78E GLN* 1.3 81.4 - - - +
80E SER* 1.3 61.5 + - - +
141G PHE* 3.1 33.2 - - + -
164G ILE* 5.2 9.9 - - + -
169G THR* 3.0 34.0 - - + +
170G PRO 3.5 7.3 + - - +
171G VAL* 3.2 20.3 - - - +
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Residues in contact with SER 80 (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 ARG 3.5 0.7 + - - +
6E ILE* 3.2 9.1 - - - +
7E ARG* 2.9 53.0 + - - +
79E ILE* 1.3 75.4 - - - +
81E LEU* 1.3 64.3 + - - +
82E GLY 5.4 0.2 + - - -
141G PHE* 5.4 2.7 - - - -
170G PRO 5.2 1.3 - - - -
171G VAL* 3.9 13.5 - - - -
172G GLU* 4.5 16.6 - - - -
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Residues in contact with LEU 81 (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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4E GLN* 3.1 47.1 + - + +
5E ARG 3.5 4.7 - - - +
6E ILE* 4.1 22.4 - - + -
58E PRO* 5.1 6.3 - - + -
63E VAL* 4.5 18.8 - - + -
80E SER* 1.3 78.8 - - - +
82E GLY* 1.3 61.6 + - - +
139G GLY* 5.6 2.5 - - - -
140G PRO* 4.6 12.8 - - + -
141G PHE* 5.1 9.6 - - + -
171G VAL* 4.4 6.6 - - + +
172G GLU* 4.3 13.7 + - - +
173G LEU* 5.9 2.5 - - + +
177G GLN* 5.6 3.1 + - - +
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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