Contacts of the strand formed by residues 81 - 87 (chain A) in PDB entry 2KNO
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ARG* 5.2 1.6 + - - -
33A ILE* 4.0 22.7 - - + -
36A LEU* 3.5 45.1 - - + -
59A ALA* 4.6 0.2 - - + -
60A LEU 3.4 3.4 - - - +
61A LYS* 4.3 9.4 - - + -
77A VAL* 3.0 20.8 + - + +
78A GLU 3.1 16.9 - - - +
79A GLN* 3.1 4.2 - - - +
80A LEU* 1.3 80.5 - - - +
82A ARG* 1.3 69.3 + - - +
83A HIS* 3.5 31.0 + - + +
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 5.2 8.9 - - - +
58A LEU 3.6 0.9 - - - +
59A ALA* 3.4 3.1 - - - -
60A LEU* 2.8 37.2 + - + +
62A VAL* 3.7 30.3 - - + -
65A PRO* 3.7 20.4 + - - +
79A GLN* 2.9 54.2 + - - +
80A LEU 4.4 0.2 - - - +
81A VAL* 1.3 79.7 + - - +
83A HIS* 1.3 65.0 + - - +
84A PHE* 3.6 33.4 - - + -
122A PRO* 5.1 3.1 - - + -
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Residues in contact with HIS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 3.4 67.3 + - + +
32A ALA* 4.3 1.0 - - - +
33A ILE* 3.6 11.4 - - + +
47A ARG* 4.4 16.8 - - - +
57A GLY* 6.1 0.9 - - - -
58A LEU 3.3 4.7 - - - +
59A ALA* 3.8 23.8 - - + +
78A GLU 5.3 0.4 - - - -
81A VAL* 3.5 30.1 + - + -
82A ARG* 1.3 81.0 + - - +
84A PHE* 1.3 71.0 + - - +
85A LEU* 5.5 1.2 - - - +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY* 3.5 3.1 - - - -
58A LEU* 2.7 50.0 + - + +
60A LEU* 4.6 3.8 - - + -
82A ARG* 3.6 38.6 - - + -
83A HIS* 1.3 84.0 - - - +
85A LEU* 1.3 68.8 + - - +
95A ILE* 3.3 21.8 - - + -
96A LYS 3.8 15.3 - - - +
97A GLY* 4.9 7.4 - - - -
120A SER* 4.2 12.6 - - - -
121A LEU* 4.3 8.5 - - + -
122A PRO* 4.1 27.6 - - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A SER* 3.6 22.9 - - - +
51A SER* 4.5 3.4 - - - -
52A PHE* 3.6 30.3 - - + -
55A ALA* 3.9 8.3 - - + -
56A TYR 3.1 14.4 - - - +
57A GLY* 4.4 1.6 - - - -
58A LEU 4.3 0.2 - - - +
83A HIS 5.5 0.9 - - - +
84A PHE* 1.3 82.2 - - - +
86A ILE* 1.3 60.7 + - - +
87A GLU* 3.6 14.9 + - + +
95A ILE* 4.3 1.1 - - - -
96A LYS* 2.7 63.3 + - + +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.8 18.4 - - + -
55A ALA* 3.1 1.9 - - - -
56A TYR* 2.7 49.6 + - + +
58A LEU* 4.1 21.1 - - + -
85A LEU* 1.3 73.7 - - - +
87A GLU* 1.3 59.7 + - - +
93A VAL* 3.3 36.6 - - + -
94A LYS 3.2 11.7 - - - +
95A ILE* 3.9 15.7 - - + -
107A LEU* 3.5 27.8 - - + -
110A LEU* 4.1 13.7 - - + -
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 3.6 24.9 - - - +
54A GLY 3.6 6.5 - - - +
55A ALA* 3.8 12.6 - - + -
85A LEU* 3.8 12.4 - - + +
86A ILE* 1.3 75.4 - - - +
88A THR* 1.3 60.8 + - - +
92A GLY 3.1 6.8 - - - +
93A VAL* 3.6 3.9 - - - -
94A LYS* 2.9 51.3 + - - +
96A LYS* 2.7 46.4 + - + +
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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