Contacts of the strand formed by residues 92 - 97 (chain B) in PDB entry 2W8I
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 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLY 4.3 1.1 - - - +
91B ASP* 1.3 77.2 - - - +
93B LEU* 1.3 57.1 + - - +
114B SER* 3.7 20.2 - - - +
117B GLY* 3.2 34.3 - - - -
118B ASN 3.5 7.0 - - - +
119B TRP* 3.8 19.1 - - + +
165B ILE* 3.5 4.3 - - - -
166B ALA* 2.7 29.6 + - + -
167B ALA* 3.0 28.3 + - + +
169B ARG* 3.3 30.7 - - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 4.1 15.5 - - + -
91B ASP* 4.3 3.6 - - + -
92B VAL* 1.3 78.7 - - - +
94B MET* 1.3 59.3 + - - +
95B VAL* 4.5 11.7 - - + -
117B GLY* 3.4 6.6 - - - -
118B ASN* 2.9 40.4 + - + +
120B VAL* 4.1 15.0 - - + -
126B ILE* 4.0 29.4 - - + -
136B VAL* 4.3 21.1 - - + -
144B VAL* 4.6 10.5 - - + -
163B VAL* 4.6 6.5 - - + -
164B SER 3.5 8.3 - - - +
165B ILE* 3.5 25.6 - - + -
166B ALA* 4.2 2.7 - - - -
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Residues in contact with MET 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 1.3 70.4 - - - +
95B VAL* 1.3 65.3 + - - +
96B THR* 3.8 19.1 + - - +
104B THR* 6.4 1.6 - - + -
113B ALA* 3.6 30.3 - - + -
117B GLY* 5.4 1.6 - - - -
163B VAL* 3.2 6.4 - - - -
164B SER* 2.9 53.2 + - - +
165B ILE 5.2 0.4 - - - -
166B ALA* 3.9 18.5 - - + +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.9 13.1 + - + -
94B MET* 1.3 78.9 - - - +
96B THR* 1.3 59.6 + - - +
97B VAL* 4.0 2.2 + - + -
103B LEU 4.7 0.7 - - - +
104B THR* 4.1 16.3 - - - +
118B ASN* 3.6 21.7 - - - +
126B ILE* 4.8 2.9 - - + -
128B TYR* 3.4 44.3 + - + +
148B ILE* 4.0 23.8 - - + -
161B VAL* 3.9 17.9 - - + -
162B ASP 3.6 10.1 - - - +
163B VAL* 4.1 5.8 - - + -
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B MET* 3.8 20.2 + - - +
95B VAL* 1.3 70.6 - - - +
97B VAL* 1.3 66.5 + - - +
98B TRP* 3.7 38.2 - - + +
104B THR* 4.0 20.3 - - + +
160B GLN 3.6 0.7 - - - +
161B VAL* 3.3 4.9 - - - -
162B ASP* 2.9 42.2 + - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL 4.5 0.7 - - - +
96B THR* 1.3 80.9 - - - +
98B TRP* 1.3 73.7 + - - +
99B ASP 3.5 0.2 + - - -
100B HIS* 3.0 33.2 + - + +
103B LEU* 4.5 11.4 - - + -
104B THR* 3.0 24.2 + - - +
128B TYR* 3.4 27.1 - - + +
152B LEU* 4.7 6.3 - - + -
156B ILE* 4.9 8.5 - - + -
159B PRO* 5.5 0.9 - - + -
160B GLN 3.3 16.4 - - - +
161B VAL* 4.2 20.9 - - + -
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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