Contacts of the strand formed by residues 83 - 90 (chain A) in PDB entry 2C0O
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 GLN 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.1 7.6 - - + +
62A VAL 3.4 8.3 - - - +
63A VAL* 4.3 8.1 - - + +
81A GLY 3.9 10.3 - - - +
82A ASP* 1.3 75.8 + - - +
84A MET* 1.3 66.9 + - - +
98A SER* 3.8 1.9 + - - -
99A LEU* 2.9 49.5 + - + +
100A ALA* 4.3 2.6 + - - +
115A VAL* 3.7 31.9 - - - +
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Residues in contact with MET 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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61A ILE* 3.5 5.9 - - - +
62A VAL* 2.9 43.6 + - + +
64A ALA* 5.9 0.7 - - - -
76A LEU* 3.4 32.5 - - + -
78A PHE* 3.9 24.7 - - + -
82A ASP* 4.4 8.3 - - + +
83A GLN* 1.3 81.9 - - - +
85A VAL* 1.3 63.2 + - - +
96A ALA* 4.1 11.2 - - + -
97A ARG 3.2 9.0 - - - +
98A SER* 3.4 24.0 - - - +
99A LEU* 4.3 3.1 - - - +
107A ILE* 3.8 29.8 - - + -
112A VAL* 5.0 6.1 - - + -
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Residues in contact with VAL 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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59A ARG* 3.6 52.9 - - + +
60A ILE 3.9 6.3 - - - +
61A ILE* 4.7 6.1 - - + +
84A MET* 1.3 73.0 - - - +
86A VAL* 1.3 72.1 + - - +
87A LEU* 3.5 10.7 + - + +
96A ALA* 3.1 7.8 - - - +
97A ARG* 2.9 50.0 + - + +
99A LEU* 3.7 21.5 - - + -
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Residues in contact with VAL 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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60A ILE* 3.0 35.7 + - + +
62A VAL* 3.7 28.0 - - + -
85A VAL* 1.3 77.3 - - - +
87A LEU* 1.3 66.0 + - - +
88A GLU* 3.8 20.2 - - - +
89A GLU* 4.0 21.1 - - + +
94A TRP* 3.5 29.4 - - + -
95A LYS 3.9 4.9 - - - +
96A ALA* 4.5 3.4 - - + -
107A ILE* 5.3 0.7 - - + -
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Residues in contact with LEU 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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85A VAL* 4.0 18.4 - - + +
86A VAL* 1.3 80.0 - - - +
88A GLU* 1.3 68.4 + - - +
95A LYS* 2.8 31.5 + - + +
96A ALA* 4.1 19.1 - - - +
97A ARG* 3.8 24.0 - - - +
104A GLU* 3.9 31.2 - - + +
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Residues in contact with GLU 88 (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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86A VAL* 3.7 3.8 - - - +
87A LEU* 1.3 83.5 - - - +
89A GLU* 1.3 66.7 + - - +
90A SER* 3.8 14.9 + - - +
94A TRP* 3.4 13.2 - - - +
95A LYS* 3.3 50.6 + - + +
106A TYR* 4.5 6.6 + - - -
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Residues in contact with GLU 89 (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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60A ILE* 4.5 15.8 - - - +
86A VAL* 4.0 11.2 - - + +
88A GLU* 1.3 78.3 - - - +
90A SER* 1.3 58.5 + - - +
91A GLY 3.5 5.4 + - - -
94A TRP* 3.2 49.3 - - + +
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Residues in contact with SER 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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88A GLU* 3.8 24.6 + - - +
89A GLU* 1.3 71.6 - - - +
91A GLY* 1.3 62.9 + - - +
92A GLU 3.3 3.3 + - - -
93A TRP 3.3 19.9 + - - +
94A TRP* 3.7 1.5 - - - -
95A LYS 4.7 1.2 + - - -
106A TYR* 5.1 1.6 - - - -
231A LYS* 3.3 28.2 + - - -
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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