Contacts of the helix formed by residues 236 - 245 (chain B) in PDB entry 6V3O
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 THR 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B PRO* 1.3 78.3 - - - +
237B PRO* 1.3 70.9 - - - +
238B GLN* 3.6 13.1 + - - +
239B ASP* 3.1 32.9 + - - +
240B GLU* 2.8 26.0 + - - +
298B ARG* 4.6 10.3 - - - +
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Residues in contact with PRO 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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236B THR* 1.3 89.1 - - - +
238B GLN* 1.3 67.1 + - - +
240B GLU* 3.6 14.2 - - + +
241B MET* 3.1 23.0 + - - +
289B MET* 5.5 1.0 - - - +
290B GLY* 5.5 5.0 + - - +
298B ARG* 3.7 47.3 - - + +
299B VAL* 5.2 7.9 - - + -
303B VAL* 4.0 25.6 - - + -
307B VAL* 4.6 1.6 - - - +
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Residues in contact with GLN 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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236B THR* 3.2 12.9 + - - +
237B PRO* 1.3 81.8 - - - +
239B ASP* 1.3 67.9 + - - +
241B MET* 3.2 5.0 + - - +
242B ARG* 3.0 27.3 + - - +
302B GLU* 5.6 1.0 - - - +
303B VAL* 3.6 25.6 - - + +
306B ASP* 3.0 42.2 + - + +
307B VAL* 4.6 9.2 - - + -
310B LEU* 4.1 18.1 - - + +
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Residues in contact with ASP 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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363A LYS* 4.7 5.4 + - - +
235B PRO* 3.5 22.5 - - + +
236B THR* 3.1 25.3 + - - +
238B GLN* 1.3 76.6 - - - +
240B GLU* 1.3 60.8 + - - +
242B ARG* 3.0 30.3 + - - +
243B TYR* 2.9 49.4 + - + -
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Residues in contact with GLU 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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176B ALA* 3.6 30.5 - - + +
177B HIS 4.6 6.1 - - - +
181B SER* 4.1 17.7 + - - +
234B GLN* 4.6 6.2 - - + +
235B PRO* 4.1 15.6 - - + +
236B THR 2.8 17.9 + - - +
237B PRO* 3.6 13.7 - - - +
239B ASP* 1.3 77.1 - - - +
241B MET* 1.3 57.3 + - - +
243B TYR* 3.9 1.7 - - - +
244B GLY* 3.0 23.0 + - - -
289B MET* 3.9 16.6 - - - +
758B SER* 4.5 17.8 - - - -
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Residues in contact with MET 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 PRO 3.1 14.1 + - - +
238B GLN 3.5 6.5 - - - +
239B ASP 3.1 0.2 - - - -
240B GLU* 1.3 74.6 - - - +
242B ARG* 1.3 65.7 + - - +
244B GLY* 3.1 9.4 + - - -
245B MET* 3.2 34.5 + - + +
287B SER* 5.1 2.5 - - - +
289B MET* 4.0 28.4 - - + +
307B VAL* 3.4 50.0 - - + +
310B LEU* 4.1 13.9 - - - -
311B ALA* 3.9 11.2 - - + +
314B MET* 3.5 30.7 - - + -
451B VAL* 5.5 3.1 - - + -
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Residues in contact with ARG 242 (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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362A TRP* 4.9 12.5 - - - +
363A LYS* 3.2 32.2 - - - +
238B GLN* 3.0 17.4 + - - +
239B ASP* 3.0 32.3 + - - +
241B MET* 1.3 81.5 - - - +
243B TYR* 1.3 73.3 + - + +
245B MET* 3.3 19.2 + - - +
246B SER 3.8 3.5 + - - -
249B HIS* 5.6 0.7 - - - -
310B LEU* 4.1 30.7 - - + -
314B MET* 4.7 14.4 - - + +
1003B FLC 3.0 62.1 + - - +
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Residues in contact with TYR 243 (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 SER* 3.7 29.4 - - - -
182B ALA* 3.0 20.9 + - - +
183B ARG* 3.5 35.7 + - + -
232B ARG* 3.8 28.5 + - - -
235B PRO* 4.2 5.6 - - + -
239B ASP* 2.9 39.5 + - + +
240B GLU 4.1 2.7 - - - +
242B ARG* 1.3 90.0 + - + +
244B GLY* 1.3 57.8 + - - +
246B SER* 2.7 28.4 + - - -
247B TYR* 5.0 0.7 - - - -
1003B FLC 3.6 30.8 + - + -
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Residues in contact with GLY 244 (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 PHE* 5.6 1.6 - - - +
240B GLU 3.0 16.3 + - - -
241B MET 3.1 6.3 + - - -
243B TYR* 1.3 79.3 - - - +
245B MET* 1.3 64.5 + - - +
246B SER 3.1 1.3 + - - -
247B TYR* 4.0 12.6 + - - +
248B ILE* 3.8 10.7 - - - +
289B MET* 4.3 15.4 - - - +
677B ILE* 4.8 7.1 - - - +
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Residues in contact with MET 245 (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 PHE* 5.2 3.8 - - + -
241B MET* 3.2 24.1 + - + +
242B ARG 3.7 8.5 - - - +
243B TYR 3.2 0.8 - - - -
244B GLY* 1.3 76.7 - - - +
246B SER* 1.3 63.2 + - - +
247B TYR 3.2 0.9 - - - -
248B ILE* 3.1 25.3 + - + +
249B HIS* 3.1 27.5 + - + -
287B SER* 4.4 6.7 - - - +
289B MET* 3.9 25.6 - - + -
311B ALA* 6.0 0.7 - - - -
314B MET* 3.8 33.2 - - + -
450B LEU* 4.6 14.1 - - + -
451B VAL* 4.2 32.3 - - + -
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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