Contacts of the helix formed by residues 186 - 200 (chain B) in PDB entry 2VF8
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 GLN 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B ARG* 3.7 23.0 - - - +
185B PRO* 1.3 80.7 - - - +
187B ALA* 1.3 73.9 + - + +
188B TRP 3.6 0.7 + - - -
189B GLY* 3.7 3.8 + - - -
190B GLY* 3.4 4.9 + - - -
277B ARG* 3.4 42.4 + - - +
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Residues in contact with ALA 187 (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* 3.4 14.6 + - - +
186B GLN* 1.3 78.1 - - + +
188B TRP* 1.3 69.0 + - + +
190B GLY* 2.9 16.5 + - - -
191B GLN* 3.4 6.4 + - - +
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Residues in contact with TRP 188 (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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187B ALA* 1.3 76.1 - - + +
189B GLY* 1.3 72.4 + - - +
190B GLY 2.6 12.6 + - - -
191B GLN* 2.8 45.3 + - + +
192B ASN* 2.8 43.6 + - + +
232B PRO* 6.1 1.2 - - - +
251B TYR* 3.5 47.5 + + - -
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Residues in contact with GLY 189 (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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185B PRO* 3.5 24.8 - - - +
186B GLN 3.7 3.9 + - - -
187B ALA 3.4 0.6 - - - -
188B TRP* 1.3 93.5 - - - +
190B GLY* 1.3 63.5 + - - +
192B ASN* 3.8 6.3 - - - +
193B GLN* 3.7 19.6 + - - +
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Residues in contact with GLY 190 (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* 6.1 2.5 - - - -
184B TRP* 4.8 10.3 - - - -
185B PRO* 3.3 19.2 + - - -
186B GLN 3.4 5.0 + - - -
187B ALA 2.9 9.4 + - - -
188B TRP 2.6 5.3 + - - -
189B GLY* 1.3 75.5 - - - +
191B GLN* 1.3 54.3 + - - -
192B ASN 2.7 14.0 + - - -
193B GLN* 3.0 11.1 + - - +
194B ARG* 3.4 8.6 + - - +
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Residues in contact with GLN 191 (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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187B ALA 3.4 6.4 + - - +
188B TRP* 2.8 39.1 + - + +
190B GLY* 1.3 69.6 - - - +
192B ASN* 1.3 58.2 + - - +
194B ARG* 3.3 43.3 + - - +
195B ASP* 2.9 45.4 + - - +
232B PRO* 5.5 6.8 - - - +
251B TYR* 5.6 0.9 + - - +
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Residues in contact with ASN 192 (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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188B TRP* 2.8 51.9 + - + +
189B GLY* 3.8 8.4 - - - +
190B GLY 2.7 6.1 + - - -
191B GLN* 1.3 72.0 - - - +
193B GLN* 1.3 72.4 + - - +
194B ARG 3.2 0.2 - - - -
195B ASP* 3.7 2.5 + - - +
196B ILE* 3.3 33.2 + - - +
251B TYR* 3.3 36.0 + - - -
253B GLY* 4.9 1.8 - - - -
254B THR 4.8 2.4 - - - +
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Residues in contact with GLN 193 (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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184B TRP* 3.5 36.1 - - + +
185B PRO* 5.5 2.2 - - + -
189B GLY 3.7 12.3 - - - +
190B GLY 3.0 7.3 + - - +
192B ASN* 1.3 81.6 + - - +
194B ARG* 1.3 58.7 + - - +
196B ILE* 3.4 15.8 + - - +
197B LEU* 3.0 32.1 + - - +
254B THR 3.2 24.7 + - - -
255B PHE* 3.4 11.7 - - + +
256B SER* 2.7 42.8 + - - +
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Residues in contact with ARG 194 (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 ILE* 5.3 5.7 + - + +
177B ARG* 3.5 58.1 + - - +
179B ARG* 5.9 4.0 - - - +
184B TRP* 4.4 9.7 - - + -
190B GLY 3.4 4.8 + - - +
191B GLN* 3.3 43.8 + - - +
193B GLN* 1.3 73.7 - - - +
195B ASP* 1.3 79.1 + - - +
196B ILE 3.1 1.6 - - - -
197B LEU* 2.9 24.7 + - - +
198B VAL* 3.0 20.0 + - + +
204B VAL* 3.8 23.8 - - + -
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Residues in contact with ASP 195 (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 ARG* 5.4 0.9 + - - -
191B GLN* 2.9 33.5 + - - +
192B ASN 3.7 2.9 + - - +
194B ARG* 1.3 92.8 + - - +
196B ILE* 1.3 58.9 + - - +
198B VAL* 3.2 23.6 - - + +
199B THR* 2.8 21.5 + - - -
230B VAL* 3.6 21.2 - - + +
231B TYR 4.9 4.2 + - - +
232B PRO* 3.6 30.3 - - - +
233B GLY 4.5 2.5 + - - -
251B TYR* 4.2 5.1 + - - +
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Residues in contact with ILE 196 (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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192B ASN* 3.3 27.7 + - - +
193B GLN* 3.4 16.6 - - - +
194B ARG 3.1 0.2 - - - -
195B ASP* 1.3 75.4 - - - +
197B LEU* 1.3 68.8 + - + +
199B THR* 3.4 8.5 - - - -
200B LEU* 3.3 22.0 + - + +
228B VAL* 3.1 28.5 - - + +
230B VAL* 4.0 15.0 - - + -
253B GLY* 3.4 15.9 - - - +
254B THR 3.2 27.8 - - - +
255B PHE* 3.8 26.0 - - + -
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Residues in contact with LEU 197 (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 ILE* 4.8 10.3 - - + -
184B TRP* 3.8 23.8 - - + -
193B GLN 3.0 15.7 + - - +
194B ARG* 2.9 10.6 + - - +
196B ILE* 1.3 76.8 - - + +
198B VAL* 1.3 59.2 + - - +
200B LEU* 2.9 26.6 + - + -
201B GLY 3.2 7.1 + - - -
202B ILE* 3.4 24.0 + - + +
204B VAL* 4.0 14.4 - - + -
218B TRP* 4.5 9.0 - - + -
219B ILE* 3.7 35.4 - - + -
255B PHE* 3.8 27.1 - - + -
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ARG* 4.9 3.6 - - - +
194B ARG* 3.0 20.0 + - + +
195B ASP* 3.2 28.9 - - + +
197B LEU* 1.3 73.8 - - - +
199B THR* 1.3 55.7 + - - +
201B GLY* 3.3 3.5 + - - -
202B ILE 4.1 10.0 + - - +
204B VAL* 3.5 27.1 - - + +
231B TYR 5.9 1.6 - - - +
234B LEU 5.1 2.7 - - - +
236B PRO* 4.4 31.5 - - + +
239B THR* 4.1 24.6 - - + +
240B GLN* 3.1 24.4 + - - -
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Residues in contact with THR 199 (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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195B ASP 2.8 16.1 + - - -
196B ILE* 3.4 11.2 - - - -
197B LEU 2.9 0.2 + - - -
198B VAL* 1.3 77.6 - - - +
200B LEU* 1.3 58.6 + - + +
201B GLY 3.0 8.6 + - - -
228B VAL* 4.3 12.6 - - + -
229B PRO* 2.9 36.7 + - + +
230B VAL* 3.9 6.4 - - - -
231B TYR* 4.7 3.9 + - + -
239B THR* 4.3 16.4 - - + +
240B GLN* 3.7 7.7 + - - +
243B LEU* 3.3 36.0 - - + +
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Residues in contact with LEU 200 (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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196B ILE* 3.3 10.2 + - + +
197B LEU* 2.9 13.1 + - + +
199B THR* 1.3 77.6 - - - +
201B GLY* 1.3 61.9 + - - +
202B ILE* 3.9 14.1 - - + +
218B TRP* 4.8 13.7 - - + -
226B PRO* 4.5 21.8 - - + -
228B VAL* 3.8 29.2 - - + -
255B PHE* 6.3 0.2 - - + -
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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