Contacts of the strand formed by residues 160 - 165 (chain B) in PDB entry 6C1A
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 LYS 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG* 3.4 35.2 - - + +
150B MET 3.3 15.0 - - - +
151B ASP* 4.7 3.1 - - + +
152B CYS* 4.5 2.0 - - - -
158B GLY 3.9 11.2 - - - +
159B TRP* 1.3 78.0 - - - +
161B LYS* 1.3 60.0 + - - +
179B TYR* 3.4 13.4 - - - -
180B PHE* 3.0 37.9 + - + +
181B SER 6.0 0.2 - - - +
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Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LYS 3.0 15.9 - - - +
149B ARG* 3.5 2.6 - - - -
150B MET* 2.8 28.2 + - + +
151B ASP 5.6 0.4 - - - +
152B CYS* 4.4 9.9 - - + -
160B LYS* 1.3 75.2 - - - +
162B GLU* 1.3 65.7 + - - +
163B GLU* 5.9 4.5 - - + -
177B VAL* 3.6 12.8 - - + -
178B TYR 3.5 7.0 - - - +
179B TYR* 3.3 36.3 - - + +
180B PHE* 5.2 0.4 - - - -
209B ARG 3.2 27.1 - - - -
210B THR* 3.5 19.7 - - - +
211B GLY* 4.4 2.0 - - - -
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Residues in contact with GLU 162 (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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148B LYS* 3.7 21.4 + - + +
149B ARG* 2.9 40.8 + - - +
161B LYS* 1.3 79.6 - - - +
163B GLU* 1.3 63.3 + - - +
164B VAL* 3.2 27.4 - - + +
176B ASP 3.8 0.9 - - - +
177B VAL* 3.4 5.1 - - - +
178B TYR* 2.8 45.6 + - + +
180B PHE* 4.0 17.2 - - + -
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Residues in contact with GLU 163 (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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148B LYS* 4.6 10.8 + - - +
161B LYS* 5.9 4.0 - - + -
162B GLU* 1.3 76.4 - - - +
164B VAL* 1.3 67.1 + - - +
165B ILE* 4.3 10.2 - - + +
175B SER* 2.4 33.8 + - - +
176B ASP 3.4 5.2 - - - +
177B VAL* 4.3 13.9 - - + +
209B ARG* 3.7 10.6 + - - +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLU* 3.2 30.5 - - + +
163B GLU* 1.3 79.8 - - - +
165B ILE* 1.3 70.9 + - - +
166B ARG 3.7 0.3 + - - -
175B SER* 3.3 3.6 - - - -
176B ASP* 2.9 36.9 + - - +
178B TYR* 4.0 13.5 - - + -
306B UNX 4.1 8.3 - - - -
308B UNX 3.4 22.9 - - - -
309B UNX 4.1 8.7 - - - -
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Residues in contact with ILE 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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163B GLU* 4.7 11.7 - - + +
164B VAL* 1.3 78.5 - - - +
166B ARG* 1.3 76.2 + - - +
167B LYS* 3.7 3.2 + - - +
173B GLY* 3.9 24.7 - - - +
174B LYS 3.8 1.3 - - - +
175B SER* 3.6 20.0 - - - -
306B UNX 2.6 31.4 - - - -
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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