Contacts of the helix formed by residues 230 - 241 (chain B) in PDB entry 3VI4
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 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B PHE* 4.3 4.1 - - - -
168B VAL 3.3 11.0 + - - -
169B GLU* 3.7 11.6 + - - -
170B LYS 5.1 0.9 - - - -
198B SER* 4.9 5.5 + - - +
229B GLU* 1.3 73.7 - - - +
231B GLY* 1.3 63.0 + - - +
232B PHE 3.2 3.1 - - - -
233B ASP* 3.2 23.1 + - - +
234B ALA* 3.7 3.1 + - - +
263B HIS 5.0 0.2 - - - -
296B TYR* 3.7 26.5 - - - -
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Residues in contact with GLY 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE* 3.6 29.1 - - - -
229B GLU 3.3 6.9 + - - -
230B GLY* 1.3 73.6 - - - +
232B PHE* 1.3 53.6 + - - +
233B ASP 3.1 0.2 - - - -
234B ALA* 2.8 5.6 + - - +
235B ILE* 2.7 37.1 + - - +
256B PHE* 3.8 21.0 - - - -
262B PHE* 5.5 1.2 - - - +
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Residues in contact with PHE 232 (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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230B GLY 3.2 1.6 - - - -
231B GLY* 1.3 74.9 - - - +
233B ASP* 1.3 65.2 + - - +
235B ILE* 3.9 24.0 - - + -
236B MET* 3.2 16.1 + - - +
256B PHE* 5.0 5.2 - + - -
262B PHE* 3.2 51.8 - + + -
263B HIS 3.7 17.7 + - - +
264B PHE* 4.3 2.7 - - + -
296B TYR* 5.0 1.3 - - + -
297B PRO* 3.3 45.7 - - + +
299B ILE* 3.9 19.5 - - + -
302B LEU* 3.5 23.6 - - + +
328B LEU* 3.7 25.1 - - + -
332B ILE* 5.7 0.4 - - + -
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Residues in contact with ASP 233 (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 LYS* 2.6 44.0 + - - +
198B SER* 3.9 11.3 + - - +
230B GLY 3.2 13.3 + - - +
231B GLY 3.1 0.6 - - - -
232B PHE* 1.3 79.1 - - - +
234B ALA* 1.3 59.6 + - - +
236B MET* 3.7 3.5 - - - +
237B GLN* 3.2 28.3 + - - +
277B ASN* 4.0 4.2 - - - +
288B TYR* 3.8 31.8 + - + -
291B SER* 3.9 0.7 - - - -
295B ASP 3.8 4.0 - - - +
296B TYR* 3.3 21.0 - - - -
297B PRO* 3.6 4.6 - - - +
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Residues in contact with ALA 234 (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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128B LEU* 3.9 21.3 - - + -
167B PHE* 3.7 30.3 - - + -
198B SER 5.5 0.2 + - - -
199B TYR* 3.9 20.8 - - + +
230B GLY 3.7 0.8 + - - +
231B GLY 2.8 10.6 + - - +
233B ASP* 1.3 77.1 - - - +
235B ILE* 1.3 65.4 + - - +
237B GLN* 3.0 4.0 + - - +
238B VAL* 2.8 25.6 + - - +
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Residues in contact with ILE 235 (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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128B LEU* 3.8 11.2 - - + +
231B GLY 2.7 13.1 + - - +
232B PHE* 3.9 30.3 - - + +
234B ALA* 1.3 71.2 - - - +
236B MET* 1.3 64.7 + - - +
238B VAL* 3.0 5.7 + - - +
239B ALA* 2.9 21.1 + - - +
254B LEU* 4.1 13.7 - - + +
256B PHE* 3.5 44.2 - - + -
302B LEU* 3.8 23.6 - - + -
306B LEU* 3.9 24.7 - - + -
313B THR* 5.3 2.0 - - + -
315B PHE* 4.7 10.8 - - + -
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Residues in contact with MET 236 (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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232B PHE 3.2 17.7 + - - +
233B ASP 3.7 4.5 - - - +
235B ILE* 1.3 77.3 - - - +
237B GLN* 1.3 69.7 + - + +
239B ALA* 3.1 4.8 + - - -
240B VAL* 3.1 38.8 + - + +
277B ASN* 3.5 18.4 - - - +
279B GLY* 4.1 9.0 - - - -
280B GLN 5.6 0.2 - - - +
297B PRO* 3.8 9.9 - - + -
301B HIS* 2.8 41.1 - - + +
302B LEU* 3.6 23.5 - - + +
305B LYS* 3.7 29.2 - - + -
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Residues in contact with GLN 237 (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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199B TYR* 3.8 19.1 - - + -
233B ASP 3.2 16.2 + - - +
234B ALA 3.0 5.6 + - - +
236B MET* 1.3 84.7 - - + +
238B VAL* 1.3 62.1 + - - +
240B VAL* 3.8 5.4 - - - +
241B CYS* 3.1 42.2 + - - +
245B ILE* 3.9 1.7 - - - +
280B GLN 3.0 27.3 + - - -
281B CYS* 3.6 3.8 - - - +
282B HIS* 3.1 25.0 + - - +
283B LEU* 3.7 5.7 - - - +
288B TYR* 3.5 40.8 - - + -
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Residues in contact with VAL 238 (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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126B TYR* 4.0 23.6 - - + -
128B LEU* 3.8 18.8 - - + -
199B TYR* 3.6 26.0 - - + +
234B ALA 2.8 17.0 + - - +
235B ILE* 3.5 9.0 - - - +
237B GLN* 1.3 78.4 - - - +
239B ALA* 1.3 58.6 - - - +
241B CYS 4.3 0.9 + - - -
245B ILE* 4.0 13.3 - - + +
247B TRP* 2.9 48.8 + - + +
254B LEU* 4.4 14.4 - - + -
311B ILE* 5.9 0.7 - - + -
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Residues in contact with ALA 239 (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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235B ILE 2.9 11.9 + - - +
236B MET* 3.7 8.1 - - - +
238B VAL* 1.3 79.1 - - - +
240B VAL* 1.3 63.2 + - + +
241B CYS 3.6 0.2 - - - -
242B GLY* 5.2 1.4 + - - -
247B TRP* 4.7 7.0 + - - -
252B ARG* 5.6 0.2 + - - -
254B LEU* 5.9 0.6 - - + +
302B LEU* 6.4 0.2 - - + -
305B LYS* 4.2 16.6 - - + +
306B LEU* 4.0 24.2 - - + -
309B ASN* 3.0 26.2 - - - +
311B ILE* 4.1 17.0 - - + -
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Residues in contact with VAL 240 (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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236B MET* 3.1 38.7 + - + +
237B GLN* 3.8 25.4 - - - +
239B ALA* 1.3 79.6 - - - +
241B CYS* 1.3 60.7 - - - +
242B GLY 3.4 5.9 + - - -
279B GLY 3.7 20.4 - - - +
280B GLN* 3.9 15.0 - - - +
281B CYS* 3.9 10.8 + - - +
305B LYS* 4.1 18.4 - - + -
309B ASN* 4.4 7.9 - - - +
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Residues in contact with CYS 241 (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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237B GLN* 3.1 41.3 + - - +
238B VAL 4.3 2.2 + - - -
239B ALA 3.6 1.2 - - - -
240B VAL* 1.3 74.9 - - - +
242B GLY* 1.3 68.0 + - - +
243B SER 3.7 0.9 - - - -
244B LEU* 4.2 7.2 - - + -
245B ILE* 3.2 32.9 + - + +
247B TRP* 4.6 0.8 - - - -
281B CYS* 2.0 50.3 - - - -
283B LEU* 3.8 12.6 - - + -
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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