Contacts of the helix formed by residues 173 - 182 (chain B) in PDB entry 3VZB
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 PHE 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B TRP 3.9 1.2 + - - -
172B GLY* 1.3 69.0 - - - +
174B ILE* 1.3 60.5 + - + +
176B ASP* 3.3 3.1 + - - +
177B VAL* 2.9 49.0 + - + +
196B THR* 3.5 26.2 - - + -
199B ARG* 3.6 20.8 - - + +
200B LEU* 3.6 30.1 - - + -
203B LEU* 3.8 24.5 - - + -
204B ARG 5.5 1.8 - - - -
206B TYR* 3.4 11.9 - - + -
258B VAL* 2.7 25.1 + - + +
259B LEU* 4.0 10.1 - - + +
299B LEU* 3.9 11.2 - - + -
401B SQS 3.8 32.8 - - + -
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Residues in contact with ILE 174 (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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170B ALA* 3.5 22.7 - - + -
171B TRP 4.6 0.9 + - - +
172B GLY 3.3 0.8 - - - -
173B PHE* 1.3 79.5 - - - +
175B ALA* 1.3 63.1 + - - +
177B VAL* 3.2 8.1 + - - +
178B ASP* 3.1 21.3 + - - +
259B LEU* 3.8 39.5 - - + +
260B VAL 5.1 0.2 - - - +
261B LEU* 4.0 28.3 - - + -
268B LEU* 4.5 7.6 - - + -
401B SQS 3.6 61.2 - - + +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ALA* 3.7 20.4 - - - +
171B TRP* 3.9 3.6 - - - -
172B GLY 3.1 8.0 + - - +
174B ILE* 1.3 79.0 - - - +
176B ASP* 1.3 59.0 + - - +
178B ASP* 3.2 4.5 + - - +
179B LEU* 2.8 28.3 + - - +
337B VAL* 3.4 28.9 - - + +
338B PHE 4.1 1.8 - - - -
339B ALA* 3.8 21.3 - - - +
344B LEU* 3.8 4.6 - - - +
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Residues in contact with ASP 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLY* 2.9 10.8 + - - +
173B PHE 3.5 8.5 - - - +
175B ALA* 1.3 80.6 - - - +
177B VAL* 1.3 50.7 + - - +
179B LEU* 3.3 13.3 + - + +
180B GLU* 2.8 43.6 + - + +
199B ARG* 3.9 24.9 + - + -
204B ARG* 4.5 0.7 - - - -
206B TYR* 2.4 42.9 + - - +
337B VAL* 4.9 11.3 - - - +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 2.9 43.7 + - + +
174B ILE* 3.2 8.0 + - - +
176B ASP* 1.3 73.2 - - - +
178B ASP* 1.3 57.0 + - - +
180B GLU* 3.7 5.6 - - - +
181B SER* 2.6 43.6 + - - +
192B PHE* 3.6 26.5 - - + +
195B GLY* 3.6 19.0 - - - +
196B THR* 3.7 13.7 - - - +
199B ARG* 4.0 6.7 - - + -
401B SQS 4.1 15.7 - - + -
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Residues in contact with ASP 178 (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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174B ILE 3.1 14.0 + - - +
175B ALA 3.5 7.0 - - - +
177B VAL* 1.3 73.7 - - - +
179B LEU* 1.3 66.1 + - - +
181B SER* 3.3 16.8 + - - -
182B GLU* 3.7 5.7 + - - +
192B PHE* 3.3 24.9 - - + -
339B ALA* 3.4 14.3 - - + +
342B GLY* 4.1 11.0 - - - +
344B LEU* 4.1 25.3 - - + +
401B SQS 2.7 44.0 + - - +
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Residues in contact with LEU 179 (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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175B ALA 2.8 16.8 + - - +
176B ASP* 3.3 17.7 - - - +
178B ASP* 1.3 73.6 - - - +
180B GLU* 1.3 64.7 + - + +
182B GLU* 2.9 56.0 - - - +
337B VAL* 4.5 25.4 - - + -
344B LEU* 3.9 16.9 - - + +
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Residues in contact with GLU 180 (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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176B ASP* 2.8 26.9 + - + +
177B VAL* 3.9 3.8 - - - +
179B LEU* 1.3 78.0 - - + +
181B SER* 1.3 60.9 + - - +
182B GLU* 3.2 1.1 + - - -
183B LYS* 3.4 20.7 + - - +
184B TYR* 4.1 10.4 - - + -
195B GLY* 3.6 24.6 - - - +
198B LEU* 4.1 19.6 - - + +
199B ARG* 2.7 46.2 + - - +
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 2.6 23.7 + - - +
178B ASP 3.4 7.6 - - - -
179B LEU 3.2 0.6 - - - -
180B GLU* 1.3 75.6 - - - +
182B GLU* 1.3 64.8 + - - +
183B LYS 3.1 1.3 + - - -
184B TYR* 3.2 10.2 + - - +
191B ARG* 2.9 39.2 + - - +
192B PHE* 3.0 48.4 - - - -
195B GLY* 5.0 1.4 - - - -
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Residues in contact with GLU 182 (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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178B ASP 3.7 4.7 + - - +
179B LEU* 2.9 40.5 + - - +
180B GLU 4.7 0.4 - - - +
181B SER* 1.3 78.0 - - - +
183B LYS* 1.3 68.4 + - + +
184B TYR 3.3 0.7 + - - -
185B ARG* 3.4 47.2 + - - +
191B ARG* 5.0 3.1 - - - +
344B LEU* 6.4 2.5 - - + -
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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