Contacts of the helix formed by residues 236 - 245 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234G GLN 3.6 3.0 + - - -
235G PRO* 1.3 75.2 - - - +
237G PRO* 1.3 68.4 - - - +
238G GLN* 2.6 31.5 + - + +
239G ASP* 3.1 38.8 + - - +
240G GLU* 2.9 25.9 + - - +
242G ARG* 5.2 1.6 - - - +
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Residues in contact with PRO 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235G PRO 4.4 1.6 - - - +
236G THR* 1.3 90.9 - - - +
238G GLN* 1.3 64.1 + - - +
240G GLU* 3.4 16.4 + - + +
241G MET* 2.9 23.2 + - - +
289G MET* 4.7 3.3 - - - +
290G GLY* 4.9 12.9 + - - +
296G ASN* 6.1 0.7 - - - +
298G ARG* 4.1 29.2 - - + +
299G VAL* 4.4 19.5 - - + -
303G VAL* 4.7 13.0 - - + -
307G VAL* 4.6 2.5 - - - +
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Residues in contact with GLN 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236G THR* 2.6 31.1 + - + +
237G PRO* 1.3 76.6 - - - +
239G ASP* 1.3 63.8 + - - +
241G MET* 3.0 5.5 + - - +
242G ARG* 2.9 48.7 + - - +
303G VAL* 3.7 31.6 - - - +
306G ASP* 2.9 35.3 + - + +
307G VAL* 4.0 23.1 - - + +
310G LEU* 4.2 7.2 - - + -
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Residues in contact with ASP 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G PRO* 4.4 6.4 - - + +
236G THR* 3.1 33.2 + - + +
238G GLN* 1.3 75.7 - - - +
240G GLU* 1.3 65.4 + - - +
242G ARG* 3.0 33.2 + - - +
243G TYR* 2.9 56.3 + - + -
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Residues in contact with GLU 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G ALA* 3.2 31.5 - - + +
177G HIS 5.6 1.2 - - - +
235G PRO* 4.4 22.8 - - + +
236G THR 2.9 11.5 + - - +
237G PRO* 3.4 20.3 - - - +
239G ASP* 1.3 75.1 - - - +
241G MET* 1.3 57.2 + - - +
243G TYR* 3.4 9.7 + - + +
244G GLY* 3.0 24.3 + - - -
289G MET* 4.2 19.6 - - + +
758G SER* 4.6 14.0 + - - -
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Residues in contact with MET 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237G PRO 2.9 13.6 + - - +
238G GLN 3.3 8.1 - - - +
240G GLU* 1.3 74.7 - - - +
242G ARG* 1.3 67.2 + - - +
244G GLY* 3.0 10.3 + - - +
245G MET* 3.0 37.3 + - + +
287G SER* 5.2 2.7 - - - +
289G MET* 3.9 25.3 - - + +
307G VAL* 3.2 53.4 - - + +
310G LEU* 4.3 8.1 - - - -
311G ALA* 3.7 13.0 - - + +
314G MET* 3.5 32.3 - - + -
451G VAL* 5.7 2.7 - - + -
453G LEU* 6.3 0.4 - - + -
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Residues in contact with ARG 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184G ARG* 3.9 14.1 + - - +
236G THR* 5.2 1.8 - - - +
238G GLN* 2.9 34.5 + - - +
239G ASP* 3.0 29.5 + - - +
241G MET* 1.3 83.8 - - - +
243G TYR* 1.3 71.1 + - + +
245G MET* 3.3 16.9 + - - +
246G SER* 3.4 9.5 + - - -
249G HIS* 5.6 0.9 - - - -
310G LEU* 3.9 29.5 - - + +
314G MET* 5.1 8.1 - - + +
364H GLN* 6.0 1.4 + - - +
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Residues in contact with TYR 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G SER* 2.9 32.3 - - - -
182G ALA* 3.3 27.2 - - + +
183G ARG* 3.9 11.3 + - + +
184G ARG* 2.9 28.9 - - - -
235G PRO* 4.8 8.5 - - + -
239G ASP* 2.9 45.3 + - + +
240G GLU* 3.8 8.7 - - + +
242G ARG* 1.3 81.4 - - + +
244G GLY* 1.3 58.1 + - - +
246G SER* 2.5 27.3 + - - -
247G TYR* 4.3 2.9 - - - -
1004G SO4 3.4 25.9 + - - -
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Residues in contact with GLY 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G PHE* 5.4 8.5 - - - -
240G GLU 3.0 10.5 + - - -
241G MET 3.0 4.4 + - - -
243G TYR* 1.3 74.9 - - - +
245G MET* 1.3 66.3 + - - +
246G SER 3.1 6.0 + - - -
247G TYR* 3.7 17.4 + - - +
248G ILE* 4.4 5.4 + - - +
289G MET* 3.8 25.8 - - - -
677G ILE* 6.1 3.3 - - - +
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Residues in contact with MET 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G PHE* 5.1 7.0 - - + -
241G MET* 3.0 29.7 + - + +
242G ARG 3.3 7.4 + - - +
244G GLY* 1.3 78.3 - - - +
246G SER* 1.3 65.1 + - - +
247G TYR 3.2 0.7 - - - -
248G ILE* 3.0 35.0 + - + +
249G HIS* 3.1 21.3 + - + +
287G SER* 4.5 13.0 - - - +
289G MET* 5.8 2.0 - - + -
311G ALA* 5.6 0.9 - - - -
314G MET* 3.7 33.7 - - + -
450G LEU* 4.5 16.2 - - + -
451G VAL* 3.8 32.5 - - + -
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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