Contacts of the helix formed by residues 89 - 97 (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 SER 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A THR 4.3 0.2 + - - -
88A LYS* 1.3 74.5 - - - +
90A LEU* 1.3 58.4 + - - +
91A GLN* 4.4 6.5 - - - -
92A GLU* 2.8 24.0 + - - +
93A LEU* 2.6 33.3 + - - +
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Residues in contact with LEU 90 (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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10A PRO* 4.0 27.6 - - + +
11A LEU* 4.4 7.6 - - + -
14A MET* 5.3 4.9 - - - -
79A PHE* 3.7 6.1 - - + -
83A VAL* 3.6 27.6 - - + -
88A LYS 4.9 4.7 - - - +
89A SER* 1.3 70.8 - - - +
91A GLN* 1.3 62.0 + - - +
93A LEU* 2.8 5.7 + - + -
94A PHE* 2.6 73.8 + - + -
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Residues in contact with GLN 91 (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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73A ARG* 3.9 21.4 + - - +
89A SER* 3.2 5.5 - - - -
90A LEU* 1.3 82.3 + - - +
92A GLU* 1.3 66.7 + - + +
94A PHE* 3.4 19.3 - - - +
95A LEU* 3.1 30.8 + - + +
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Residues in contact with GLU 92 (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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88A LYS* 4.1 25.1 + - + -
89A SER* 2.8 31.9 + - - +
91A GLN* 1.3 72.8 - - + +
93A LEU* 1.3 54.8 + - - +
95A LEU* 2.9 12.2 + - - +
96A ALA* 2.5 39.5 + - + +
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Residues in contact with LEU 93 (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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79A PHE* 4.2 13.0 - - + -
82A ASP* 3.7 19.3 - - + +
83A VAL* 3.7 40.2 - - + +
86A SER* 3.6 28.5 - - - +
88A LYS* 3.4 32.1 - - + +
89A SER 2.6 15.2 + - - +
90A LEU* 2.8 14.0 + - + +
92A GLU* 1.3 71.4 - - - +
94A PHE* 1.3 52.4 + - - +
96A ALA* 2.9 10.6 + - + +
97A HIS* 2.8 43.8 + - + +
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Residues in contact with PHE 94 (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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14A MET* 4.8 8.5 - - + -
49A LEU* 2.9 41.5 - - + -
73A ARG* 3.2 47.3 - - - +
75A VAL* 3.7 9.8 - - + +
79A PHE* 3.1 24.7 - + - -
90A LEU* 2.6 54.5 + - + -
91A GLN* 3.4 15.7 - - - +
93A LEU* 1.3 71.4 - - - +
95A LEU* 1.3 52.0 - - - +
97A HIS 2.8 4.2 - - - -
98A ILE* 2.5 40.8 + - - -
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Residues in contact with LEU 95 (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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73A ARG* 3.9 19.1 - - - +
91A GLN* 3.1 20.1 + - + +
92A GLU* 2.9 13.0 + - - +
94A PHE* 1.3 80.6 - - - +
96A ALA* 1.3 60.6 + - - +
97A HIS 3.0 1.2 + - - -
98A ILE* 3.4 31.5 + - + +
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LYS* 6.0 4.3 - - + -
92A GLU* 2.5 22.0 + - + +
93A LEU* 2.9 15.7 + - + +
95A LEU* 1.3 73.2 - - - +
97A HIS* 1.3 82.8 + - + +
98A ILE 3.8 0.2 - - - -
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Residues in contact with HIS 97 (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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75A VAL* 2.8 25.9 - - + +
76A SER* 3.1 17.6 + - - +
78A ASP* 4.0 21.3 + - + +
79A PHE* 4.3 24.7 - - + -
82A ASP* 3.3 36.8 + - - -
93A LEU* 2.8 28.2 + - + +
94A PHE 2.8 4.7 - - - +
96A ALA* 1.3 98.8 + - + +
98A ILE* 1.3 59.8 + - - +
99A LEU* 4.9 3.4 - - - -
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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