Contacts of the strand formed by residues 164 - 169 (chain B) in PDB entry 2C3V
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 GLY 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLY* 6.4 1.3 - - - -
85B ASP 4.3 12.1 + - - -
88B ASP 2.9 11.8 + - - -
90B THR 3.1 23.1 + - - +
162B SER 3.7 5.3 - - - +
163B SER* 1.3 78.4 - - - +
165B VAL* 1.3 67.8 - - - -
166B HIS* 4.0 2.4 + - - -
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLY* 6.3 2.9 - - - -
85B ASP 6.2 1.8 - - - +
90B THR* 3.4 19.5 - - + +
92B TYR* 3.3 36.6 - - + -
164B GLY* 1.3 76.8 - - - -
166B HIS* 1.3 73.7 + - - +
175B SER* 4.7 0.3 + - - -
176B GLY* 2.8 30.0 + - - +
177B THR* 3.9 17.3 - - + -
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Residues in contact with HIS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 5.8 0.2 - - + -
90B THR 3.0 6.3 + - - +
91B ILE* 3.5 4.7 - - - -
92B TYR* 3.0 25.1 + - - -
160B ASP 5.4 0.4 - - - -
161B PHE* 3.8 22.2 - + + -
162B SER* 3.6 41.7 + - - -
163B SER 3.9 11.8 + - - -
164B GLY* 4.5 1.6 - - - -
165B VAL* 1.3 90.4 + - - +
167B THR* 1.3 64.4 + - - +
173B ILE* 3.7 22.8 - - + +
174B LEU 3.4 5.5 + - - -
175B SER* 3.7 21.3 + - - -
176B GLY 3.4 2.2 - - - -
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B TYR* 3.4 8.9 - - + +
127B TYR* 3.1 42.0 - - + +
161B PHE* 5.2 0.2 - - - -
166B HIS* 1.3 74.5 + - - +
168B LEU* 1.3 61.6 + - - +
169B ALA* 4.8 2.7 - - + +
172B ARG 3.5 1.7 - - - +
173B ILE* 3.2 4.8 - - - -
174B LEU* 2.8 44.8 + - + +
176B GLY 2.7 22.1 + - - -
177B THR* 3.3 17.3 - - - -
178B PRO* 3.5 9.2 - - + +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B TYR 2.8 12.0 + - - +
93B TYR* 3.4 26.2 - - + -
94B LYS 2.7 31.9 + - - -
144B PHE* 3.2 34.5 - - + -
152B ASP* 4.9 0.7 - - - +
159B TYR* 3.6 42.4 - - + +
161B PHE* 4.1 15.4 - - + -
167B THR* 1.3 70.3 - - - +
169B ALA* 1.3 55.5 + - - +
171B GLY* 3.9 6.1 - - - +
172B ARG 3.5 25.4 - - - +
173B ILE* 3.8 10.3 - - + -
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B TYR* 6.0 0.2 - - - -
94B LYS* 3.6 16.4 - - + -
127B TYR* 3.5 27.4 - - + +
167B THR* 4.0 3.3 - - + -
168B LEU* 1.3 75.3 - - - +
170B ASP* 1.3 74.0 + - + +
171B GLY 3.1 2.5 - - - -
172B ARG* 2.7 29.9 + - - +
174B LEU* 4.8 9.4 - - + -
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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