Contacts of the helix formed by residues 174 - 186 (chain B) in PDB entry 2WTV
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 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B PHE* 4.0 18.2 - - + -
169B LEU* 3.0 30.5 + - + +
172B ALA* 4.2 9.2 - - + +
173B GLY* 1.3 81.1 - - - +
175B GLU* 1.3 59.8 + - - +
176B HIS 3.4 2.5 - - - -
177B GLN* 3.2 24.4 + - - +
178B LEU* 2.8 29.5 + - - +
277B TRP* 3.6 35.7 - - + -
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Residues in contact with GLU 175 (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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166B LYS* 4.0 23.3 - - + +
169B LEU* 3.6 24.2 + - + -
170B GLU* 3.6 39.9 - - - +
174B VAL* 1.3 78.8 - - - +
176B HIS* 1.3 63.9 + - - +
178B LEU* 3.4 6.3 + - + +
179B ARG* 3.2 51.8 + - - +
206B VAL* 6.4 0.4 - - + -
1395B EDO 3.2 20.9 + - - +
1396B EDO 5.1 0.9 + - - -
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Residues in contact with HIS 176 (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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173B GLY 5.2 0.6 + - - +
175B GLU* 1.3 77.4 - - - +
177B GLN* 1.3 65.9 + - - +
179B ARG* 3.0 31.3 + - - +
180B ARG* 3.0 44.3 + - + +
1395B EDO 3.5 30.7 + - - +
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Residues in contact with GLN 177 (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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173B GLY 4.8 3.5 + - - +
174B VAL* 3.2 30.2 + - - +
176B HIS* 1.3 78.0 - - - +
178B LEU* 1.3 58.8 + - - +
180B ARG* 3.4 28.1 + - - +
181B GLU* 2.9 58.6 + - + +
277B TRP* 3.5 33.3 - - + +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 3.8 17.3 - - + -
169B LEU* 3.7 31.2 - - + -
174B VAL 2.8 19.9 + - - +
175B GLU* 3.6 5.8 - - + +
177B GLN* 1.3 69.0 - - - +
179B ARG* 1.3 57.3 + - - +
181B GLU* 4.5 0.9 - - - +
182B VAL* 2.8 49.3 + - + +
206B VAL* 4.2 12.3 - - + -
208B LEU* 4.1 10.8 - - + -
275B PHE* 4.0 15.0 - - + -
277B TRP* 3.9 27.1 - - + -
1396B EDO 4.1 14.6 - - - +
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Residues in contact with ARG 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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166B LYS* 5.9 4.9 - - - +
175B GLU* 3.2 43.4 + - - +
176B HIS* 3.0 36.8 + - - +
178B LEU* 1.3 80.5 - - - +
180B ARG* 1.3 64.4 + - + +
182B VAL* 3.4 4.4 + - - +
183B GLU* 3.2 21.3 + - - +
206B VAL* 6.1 1.6 - - - +
1396B EDO 3.8 36.7 + - - +
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Residues in contact with ARG 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 HIS* 3.0 40.8 + - + +
177B GLN* 3.6 31.9 - - - +
179B ARG* 1.3 77.1 - - + +
181B GLU* 1.3 60.2 + - + +
183B GLU* 3.2 9.2 + - - +
184B ILE* 3.0 36.9 + - + +
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Residues in contact with GLU 181 (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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177B GLN* 2.9 37.8 + - + +
178B LEU* 3.8 3.1 - - - +
180B ARG* 1.3 77.0 - - + +
182B VAL* 1.3 56.0 + - - +
184B ILE* 3.8 11.6 - - + +
185B GLN* 2.7 37.8 + - - +
275B PHE* 3.6 25.8 + - + -
277B TRP* 2.8 35.3 + - - -
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Residues in contact with VAL 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 LEU* 2.8 42.7 + - + +
179B ARG* 3.8 6.1 - - - +
181B GLU* 1.3 72.9 - - - +
183B GLU* 1.3 63.2 + - - +
185B GLN* 4.3 4.9 - - - -
186B SER* 3.0 24.9 + - - -
196B LEU* 3.8 4.9 - - + +
199B TYR* 3.2 47.6 - - + +
208B LEU* 4.1 18.6 - - + -
275B PHE* 4.0 12.3 - - + -
1396B EDO 4.5 8.1 - - - +
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Residues in contact with GLU 183 (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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179B ARG 3.2 11.8 + - - +
180B ARG* 3.2 13.2 + - - +
181B GLU 3.2 0.4 - - - -
182B VAL* 1.3 76.8 - - - +
184B ILE* 1.3 67.3 + - + +
186B SER* 2.9 20.3 + - - -
187B HIS* 3.2 37.7 + - + +
199B TYR* 4.2 13.0 + - - -
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Residues in contact with ILE 184 (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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180B ARG* 3.0 22.0 + - + +
181B GLU* 3.8 12.1 - - + +
183B GLU* 1.3 79.7 - - + +
185B GLN* 1.3 65.7 + - - +
187B HIS* 3.0 21.7 + - - +
188B LEU* 3.7 15.0 - - + +
252B VAL* 4.1 29.8 - - + -
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Residues in contact with GLN 185 (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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181B GLU 2.7 24.2 + - - +
182B VAL 3.9 2.9 - - - +
184B ILE* 1.3 74.4 - - - +
186B SER* 1.3 58.1 + - - +
187B HIS 3.1 4.4 + - - -
188B LEU* 3.2 23.8 + - - +
193B ILE* 3.7 9.9 - - - +
194B LEU 3.5 9.5 + - - -
196B LEU* 3.9 24.5 + - + +
255B ARG* 2.4 31.2 + - - +
274B ASP* 3.0 40.5 + - - +
275B PHE* 4.1 12.1 - - + -
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Residues in contact with SER 186 (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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182B VAL 3.0 15.6 + - - -
183B GLU* 2.9 24.4 + - - -
184B ILE 3.1 0.2 + - - -
185B GLN* 1.3 75.3 - - - +
187B HIS* 1.3 71.4 + - - +
188B LEU 3.5 1.1 - - - -
189B ARG* 4.7 14.6 + - - +
196B LEU* 4.1 24.1 - - - +
198B GLY* 6.4 0.4 - - - -
199B TYR* 4.3 14.4 + - - -
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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