Contacts of the helix formed by residues 235 - 245 (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 THR 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ARG* 5.2 5.2 - - - +
233B GLY 4.4 0.4 + - - -
234B LEU* 1.3 70.1 - - - +
236B PRO* 1.4 69.8 - - + -
237B ALA* 2.7 24.4 + - + +
238B GLU* 2.9 33.4 + - - +
239B THR* 3.0 8.5 + - - -
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Residues in contact with PRO 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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177B ARG* 3.5 31.0 - - - +
198B VAL* 4.4 28.7 - - + +
202B ILE 5.9 1.8 - - - +
204B VAL* 5.7 2.0 - - + +
205B ASP* 4.4 4.3 - - - +
234B LEU 3.6 5.8 - - - +
235B THR* 1.4 88.8 - - + -
237B ALA* 1.3 56.4 + - - +
239B THR* 3.7 11.0 - - - -
240B GLN* 3.1 36.0 + - + +
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Residues in contact with ALA 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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235B THR* 2.7 15.4 + - + +
236B PRO* 1.3 70.9 - - - +
238B GLU* 1.3 56.8 + - - +
239B THR 3.1 7.6 + - - -
240B GLN* 3.4 12.6 + - - +
241B ARG* 3.6 30.5 + - - +
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Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLY 4.8 1.4 - - - +
234B LEU* 3.7 21.4 - - + +
235B THR* 2.9 44.8 + - - +
237B ALA* 1.3 73.8 - - - +
239B THR* 1.3 56.7 + - - +
241B ARG* 4.1 18.1 - - - +
242B ALA* 3.6 19.0 + - - +
245B LYS* 5.7 0.7 + - - -
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Residues in contact with THR 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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198B VAL* 4.1 23.7 - - + +
199B THR* 4.3 19.7 - - + +
231B TYR* 4.5 15.3 + - + +
234B LEU* 2.7 45.6 + - + +
235B THR 3.0 6.3 + - - -
236B PRO* 3.7 10.7 - - - -
237B ALA 3.1 0.4 - - - -
238B GLU* 1.3 78.1 - - - +
240B GLN* 1.3 63.7 + - - +
241B ARG 3.6 0.2 - - - -
242B ALA* 3.3 5.7 - - - +
243B LEU* 3.3 20.1 + - + +
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Residues in contact with GLN 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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198B VAL 3.1 26.5 + - - -
199B THR* 3.7 11.1 + - - +
201B GLY* 3.3 24.4 - - - +
236B PRO* 3.1 20.7 + - - +
237B ALA* 3.4 5.4 + - - +
239B THR* 1.3 73.8 - - - +
241B ARG* 1.3 59.4 + - + +
242B ALA 2.9 4.5 - - - -
243B LEU* 2.9 29.9 + - - +
244B LYS* 2.9 13.6 + - - +
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Residues in contact with ARG 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 ALA* 3.6 32.0 + - - +
238B GLU* 4.1 14.8 - - - +
240B GLN* 1.3 78.4 - - + +
242B ALA* 1.3 55.9 + - - +
243B LEU 3.6 0.2 - - - -
244B LYS* 4.1 17.4 - - + +
245B LYS* 3.2 36.0 + - - +
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Residues in contact with ALA 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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231B TYR* 3.7 27.3 + - + -
234B LEU* 4.7 3.8 - - + -
238B GLU 3.6 17.1 + - - +
239B THR* 3.3 14.3 + - - +
240B GLN 2.9 0.4 - - - -
241B ARG* 1.3 79.0 - - - +
243B LEU* 1.3 60.3 + - - +
244B LYS 3.4 0.2 - - - -
245B LYS* 3.9 9.5 + - - +
246B LYS* 3.5 14.4 + - - -
247B MET* 3.8 28.5 + - + +
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Residues in contact with LEU 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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199B THR* 3.3 45.5 - - + +
229B PRO* 4.3 18.4 - - + -
231B TYR* 4.6 13.0 - - + +
239B THR* 3.3 8.8 + - + +
240B GLN* 2.9 17.1 + - - +
242B ALA* 1.3 78.3 - - - +
244B LYS* 1.3 63.4 + - - +
246B LYS* 3.6 18.7 + - + +
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Residues in contact with LYS 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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240B GLN 2.9 13.9 + - - +
241B ARG* 4.2 16.8 - - + +
243B LEU* 1.3 79.7 - - - +
245B LYS* 1.3 70.8 + - + +
246B LYS* 3.3 14.3 + - - +
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Residues in contact with LYS 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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238B GLU 5.7 0.8 + - - -
241B ARG* 3.2 31.3 + - - +
242B ALA* 3.9 7.0 + - - +
243B LEU 3.4 0.2 - - - -
244B LYS* 1.3 89.3 - - + +
246B LYS* 1.3 68.7 + - - +
247B MET* 3.3 38.0 + - + +
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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