Contacts of the strand formed by residues 86 - 90 (chain A) in PDB entry 2O2C
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLY 2.7 24.0 + - - -
83A GLN* 3.2 18.7 + - - +
84A ARG 3.4 3.8 + - - +
85A TYR* 1.3 76.7 - - - +
87A VAL* 1.3 67.5 + - - +
100A PHE* 3.6 27.6 - - - -
101A LEU 3.1 13.7 - - - -
102A ASP* 4.0 5.6 - - - -
103A TYR* 3.8 3.8 + - - -
367A GLN* 4.6 5.2 + - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 1.3 80.3 - - - +
88A LYS* 1.3 70.5 + - - +
89A VAL* 4.3 4.0 - - + -
99A LEU 3.8 1.7 - - - +
100A PHE* 3.5 5.7 - - - -
101A LEU* 2.9 33.8 + - + +
103A TYR* 4.6 4.9 - - + +
359A HIS* 4.9 0.4 - - + -
366A GLU 4.4 1.8 - - - +
367A GLN* 3.5 49.6 - - + +
369A VAL* 3.8 20.6 - - + +
372A LEU* 4.0 27.1 - - + -
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Residues in contact with LYS 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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87A VAL* 1.3 78.0 - - - +
89A VAL* 1.3 64.8 + - - +
90A SER* 4.1 10.7 + - - +
96A GLU 5.1 2.2 + - - -
97A ASN 5.5 0.2 + - - -
98A PHE* 3.2 59.1 - - + +
99A LEU 3.7 2.5 - - - -
100A PHE* 3.9 17.5 - - + -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 4.3 2.2 - - + -
88A LYS* 1.3 75.8 - - - +
90A SER* 1.3 72.7 + - - +
91A LEU* 3.7 1.0 + - - +
98A PHE* 3.3 3.2 - - - -
99A LEU* 2.9 45.3 + - + +
355A VAL* 5.0 2.5 - - + -
356A ILE* 3.9 22.0 - - + -
359A HIS* 3.5 50.3 - - + +
369A VAL* 3.6 24.5 - - + -
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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
----------------------------------------------------------
88A LYS* 4.1 10.5 + - - +
89A VAL* 1.3 80.0 - - - +
91A LEU* 1.3 64.0 + - - +
92A GLY* 3.3 14.2 + - - -
96A GLU* 5.7 2.6 - - - -
97A ASN 3.9 9.2 + - - -
98A PHE* 4.3 4.3 - - - -
355A VAL* 3.5 15.2 - - - +
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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