Contacts of the strand formed by residues 161 - 165 (chain B) in PDB entry 4X2Q
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 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 4.5 4.7 - - + +
66B ALA* 3.8 18.2 - - + +
67B ARG* 3.8 46.4 - - + +
70B PHE* 5.2 0.7 - - + -
160B GLY* 1.3 71.4 - - - -
162B CYS* 1.3 60.4 + - - +
188B THR* 3.4 16.2 - - - +
190B VAL* 3.9 18.4 - - + -
237B GLY 4.0 11.9 - - - +
238B ILE* 3.9 17.9 - - + +
239B ASP* 3.0 30.2 + - - +
240B LYS* 3.1 9.7 + - - +
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Residues in contact with CYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 4.9 3.1 - - - -
160B GLY 4.0 1.1 - - - -
161B VAL* 1.3 75.0 - - - +
163B GLY* 1.3 64.0 + - - +
164B GLN* 3.8 8.0 + - + +
187B ASN* 3.7 34.1 - - - -
188B THR 2.9 12.9 + - - +
189B VAL* 3.6 10.9 - - + +
190B VAL 3.0 23.2 + - - +
240B LYS* 3.4 26.5 - - + +
485B TYR* 3.8 29.2 - - + -
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Residues in contact with GLY 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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162B CYS* 1.3 72.6 - - - +
164B GLN* 1.3 62.7 + - - +
190B VAL* 3.3 11.7 - - - -
232B ILE* 3.8 20.9 - - - -
238B ILE* 3.7 7.7 - - - +
240B LYS 2.6 15.6 + - - +
241B ILE* 3.2 9.2 - - - +
242B ALA* 2.8 25.3 + - - +
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Residues in contact with GLN 164 (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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162B CYS* 4.4 5.5 - - + +
163B GLY* 1.3 78.8 - - - +
165B ILE* 1.3 63.4 + - - +
178B LYS* 2.9 42.4 + - + +
179B ILE* 3.7 5.7 - - - +
182B ALA* 3.7 6.1 - - - +
189B VAL* 3.3 28.7 - - - +
190B VAL 2.9 8.7 + - - +
191B ILE* 3.4 21.9 - - + +
192B LYS* 2.7 32.8 + - - +
232B ILE* 4.5 1.5 - - - +
242B ALA* 3.5 7.4 - - + -
485B TYR* 2.9 35.5 + - - +
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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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164B GLN* 1.3 78.6 - - - +
166B ILE* 1.3 69.0 + - - +
192B LYS* 3.6 33.0 - - + +
229B GLY* 3.6 31.2 - - - +
232B ILE* 4.4 6.7 - - + -
241B ILE* 3.9 24.9 - - + -
242B ALA 3.2 8.8 + - - +
243B PHE* 3.7 22.0 - - + -
244B THR* 3.2 28.9 + - - +
253B ILE* 4.3 16.2 - - + -
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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