Contacts of the strand formed by residues 175 - 180 (chain A) in PDB entry 1V72
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 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A MET* 3.5 21.5 + - - -
143A ALA 3.1 11.9 + - - -
144A CYS* 3.1 5.2 - - - -
145A VAL 2.7 30.5 + - - -
169A CYS* 3.9 2.7 - - - -
173A SER 4.3 0.4 + - - -
174A LEU* 1.3 73.7 - - - +
176A LEU* 1.3 53.7 + - - -
204A ASP* 3.3 9.6 - - - -
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Residues in contact with LEU 176 (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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79A MET* 3.3 3.7 - - - +
145A VAL* 3.5 12.3 - - + +
147A ILE* 4.3 11.7 - - + -
162A ILE* 4.5 10.5 - - + +
165A ILE* 4.0 20.6 - - + -
166A GLY* 4.0 23.1 - - - +
169A CYS* 3.9 15.0 - - + -
174A LEU 3.9 0.2 + - - -
175A GLY* 1.3 72.1 - - - -
177A HIS* 1.3 71.4 + - - +
201A ALA 4.6 0.7 - - - +
202A GLY* 3.6 31.9 - - - +
203A VAL* 3.8 17.8 - - + +
204A ASP* 2.7 37.5 + - - +
205A ALA 3.4 4.7 + - - -
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Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 3.5 23.7 + - + -
75A CYS* 3.5 27.7 - - + +
76A LEU* 3.9 22.8 - - + +
79A MET* 4.0 13.6 - - - +
94A ILE* 5.6 0.7 - - + -
145A VAL 2.8 14.6 + - - +
146A SER* 3.0 24.3 + - - -
147A ILE* 3.0 28.6 + - - +
176A LEU* 1.3 75.8 - - - +
178A MET* 1.3 71.5 + - - +
179A ASP* 3.5 21.1 - - + -
205A ALA 3.3 14.8 - - - +
207A SER* 3.0 21.0 + - - -
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Residues in contact with MET 178 (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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147A ILE* 3.3 18.4 - - + +
149A GLN* 3.6 35.7 - - + -
162A ILE* 4.0 16.2 - - + -
177A HIS* 1.3 78.2 + - - +
179A ASP* 1.3 62.0 + - - +
180A GLY 3.1 2.3 + - - +
183A PHE* 4.0 14.4 - - - -
197A MET* 3.4 25.8 - - - +
198A THR* 4.2 3.4 - - - -
203A VAL* 3.9 25.3 - - + +
205A ALA 2.8 9.3 + - - +
206A LEU* 3.7 22.4 - - + -
207A SER 2.9 27.7 + - - -
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Residues in contact with ASP 179 (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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72A ASN* 3.0 27.1 + - - +
93A HIS* 4.1 5.2 + - - +
94A ILE* 4.9 3.0 - - + +
146A SER* 4.7 3.4 - - - +
147A ILE 2.9 9.7 + - - +
148A THR* 3.4 22.6 + - - +
149A GLN 3.0 21.8 + - - +
177A HIS* 3.5 14.1 - - + +
178A MET* 1.3 68.9 - - - +
180A GLY* 1.3 57.9 + - - +
181A SER* 3.2 16.6 + - - -
207A SER* 4.2 2.0 - - - -
513A PLP 2.8 39.7 + - - +
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Residues in contact with GLY 180 (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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149A GLN 3.5 14.4 - - - -
178A MET* 3.1 5.8 + - - -
179A ASP* 1.3 70.0 + - - +
181A SER* 1.3 60.1 + - - +
182A ARG 3.0 3.1 - - - -
183A PHE* 3.0 20.1 + - - +
206A LEU* 4.0 7.2 - - - -
207A SER 2.9 22.4 + - - -
209A GLY 2.7 24.4 + - - -
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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