Contacts of the helix formed by residues 77 - 85 (chain A) in PDB entry 2COK
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 GLU 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LEU* 3.9 32.6 - - + +
23A SER* 4.0 13.3 - - - +
24A ARG* 3.2 39.9 + - - +
29A VAL* 4.2 9.1 - - + +
32A MET* 5.6 2.9 - - - +
51A ILE* 3.8 15.7 - - + +
76A SER* 1.3 71.0 - - - +
78A ASP* 1.3 55.9 + - - +
79A PHE 2.8 6.3 - - - -
80A LEU* 2.7 49.6 + - + +
81A GLN* 3.5 4.8 + - - +
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Residues in contact with ASP 78 (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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76A SER* 3.0 19.4 + - - +
77A GLU* 1.3 78.0 - - - +
79A PHE* 1.3 51.0 + - - +
81A GLN* 3.0 14.6 + - + +
82A ASP* 2.8 38.6 + - - +
97A HIS* 4.0 20.1 + - + +
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Residues in contact with PHE 79 (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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11A LEU* 3.9 13.2 - - + -
16A ILE* 5.4 1.3 - - + -
49A LEU* 3.4 15.7 - - + -
51A ILE* 4.0 6.5 - - + -
75A VAL* 3.8 18.6 - - + -
76A SER* 3.1 18.1 + - - +
77A GLU 2.8 0.4 + - - -
78A ASP* 1.3 79.1 - - - +
80A LEU* 1.3 75.7 + - + +
82A ASP* 3.0 5.2 + - - +
83A VAL* 2.5 58.2 + - + +
90A LEU* 3.7 11.4 - - + -
93A LEU* 4.2 19.3 - - + -
94A PHE* 3.1 43.3 - + - -
97A HIS* 4.3 13.6 - - + -
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Residues in contact with LEU 80 (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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11A LEU* 4.5 11.9 - - + -
29A VAL* 3.5 24.5 - - + -
32A MET* 3.0 34.1 - - + +
33A ILE* 3.6 31.2 - - + +
36A LEU* 4.5 2.0 - - + -
51A ILE* 3.1 32.3 - - + -
77A GLU* 2.7 33.8 + - + +
79A PHE* 1.3 86.5 - - + +
81A GLN* 1.3 62.4 + - - +
83A VAL* 3.4 5.5 - - + +
84A SER* 3.2 15.9 + - - -
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Residues in contact with GLN 81 (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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24A ARG* 5.2 8.5 + - - -
32A MET* 4.4 6.3 - - - +
77A GLU* 3.5 4.4 + - - +
78A ASP* 3.0 18.9 + - + +
80A LEU* 1.3 79.3 - - - +
82A ASP* 1.3 61.3 + - - +
84A SER* 5.1 3.8 - - - -
85A ALA* 3.2 30.0 + - - +
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Residues in contact with ASP 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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78A ASP* 2.8 14.2 + - - +
79A PHE* 3.4 7.2 - - - +
81A GLN* 1.3 82.8 - - - +
83A VAL* 1.3 56.2 + - - +
84A SER 2.8 4.3 - - - -
85A ALA 2.5 11.1 + - - -
86A SER* 2.5 56.5 + - - -
93A LEU* 3.7 12.0 - - + +
97A HIS* 3.3 29.6 + - - +
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Residues in contact with VAL 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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8A ASP* 4.5 6.2 - - - +
10A PRO* 3.6 27.3 - - + +
11A LEU* 3.5 14.4 - - + -
36A LEU* 3.4 26.4 - - + +
79A PHE* 2.5 26.6 + - + +
80A LEU* 3.4 18.2 - - + +
82A ASP* 1.3 72.4 - - - +
84A SER* 1.3 61.1 + - - +
86A SER 4.1 7.8 - - - +
90A LEU* 3.6 31.6 - - + -
93A LEU* 3.7 16.7 - - + +
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Residues in contact with SER 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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8A ASP* 4.5 10.0 - - - +
32A MET* 3.8 11.6 - - - +
35A LYS* 4.0 10.7 - - - +
36A LEU* 3.3 26.6 - - - +
80A LEU 3.2 15.0 + - - -
81A GLN* 4.4 5.2 - - - -
82A ASP 2.7 4.0 + - - -
83A VAL* 1.3 81.3 - - - +
85A ALA* 1.3 58.7 + - - +
86A SER 3.6 1.8 + - - -
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Residues in contact with ALA 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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81A GLN* 3.2 26.2 + - - +
82A ASP* 2.5 16.0 + - - +
84A SER* 1.3 75.6 - - - +
86A SER* 1.3 60.9 + - - +
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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