Contacts of the helix formed by residues 236 - 241 (chain B) in PDB entry 2OT7
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 ALA 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B CYS* 3.3 10.2 - - - -
235B GLU* 1.3 78.7 - - - +
237B PHE* 1.3 56.8 + - - +
238B LEU* 3.1 3.6 - - - -
239B ARG* 2.9 36.3 + - + +
240B HIS* 4.2 1.4 + - - -
304B VAL* 3.6 30.5 - - + +
305B LEU 3.6 19.7 - - - +
306B CYS* 3.8 2.6 - - - +
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Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLU 5.4 0.9 - - - -
223B ALA* 3.8 32.8 - - + -
224B LYS* 4.2 12.6 - - + -
227B PHE* 3.9 21.1 - + + -
230B SER* 3.7 25.4 - - - +
231B ALA* 3.8 31.4 - - + -
234B CYS* 3.5 15.8 + - + +
235B GLU 3.3 9.6 + - - -
236B ALA* 1.3 74.8 - - - +
238B LEU* 1.3 71.6 + - + +
239B ARG 3.1 0.2 - - - -
240B HIS* 3.2 39.3 + - + +
241B LYS 4.5 0.2 + - - -
242B MET* 5.5 0.9 + - - +
243B THR* 3.5 23.5 + - - -
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Residues in contact with LEU 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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187B TRP* 3.5 28.9 - - + +
188B HIS* 4.4 2.6 - - - +
219B LEU* 5.2 6.1 - - + +
220B GLU* 4.4 13.7 - - + +
223B ALA* 3.9 21.8 - - + -
236B ALA 3.0 1.7 + - - -
237B PHE* 1.3 88.4 - - + +
239B ARG* 1.3 56.1 + - + +
240B HIS 3.0 5.6 - - - -
241B LYS* 2.9 20.1 + - - +
242B MET 4.6 1.0 + - - +
243B THR* 3.6 39.0 + - + +
245B ILE* 5.7 0.7 - - + -
275B TYR* 3.5 42.2 - - + +
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Residues in contact with ARG 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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188B HIS* 5.4 3.8 - - - -
189B THR* 3.3 19.9 + - - +
190B GLU 3.0 29.3 + - - -
191B ASP* 4.2 10.4 - - - +
192B MET 4.7 1.3 - - - -
193B ASP* 2.9 27.3 + - - +
236B ALA* 2.9 25.1 + - + +
238B LEU* 1.3 73.2 - - + +
240B HIS* 1.3 58.3 + - - +
241B LYS* 3.0 24.7 + - - +
273B TYR* 6.1 0.4 - - - -
303B ALA* 4.1 6.3 - - - +
304B VAL 2.7 35.8 + - - +
305B LEU* 3.9 11.3 - - - +
306B CYS* 4.0 20.9 - - + +
312B MET* 6.2 0.2 - - - +
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Residues in contact with HIS 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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230B SER* 6.4 0.2 - - - -
233B SER* 6.4 0.4 - - - -
234B CYS* 3.6 6.4 - - + -
236B ALA 4.5 0.7 - - - -
237B PHE* 3.2 31.8 + - + +
238B LEU 3.0 0.4 - - - -
239B ARG* 1.3 77.1 - - - +
241B LYS* 1.3 68.7 + - - +
242B MET* 3.3 21.4 + - + +
306B CYS* 3.9 5.4 - - + -
308B CYS* 3.3 12.5 - - - -
309B ARG* 3.7 42.4 + - - +
312B MET* 6.1 0.4 - - - -
502B ZN 2.1 37.1 - - - -
12D GLY* 3.7 2.3 - - - -
13D GLY 3.6 12.5 + - - -
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Residues in contact with LYS 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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84B GLN* 4.4 3.1 + - - -
86B ASN* 4.2 5.7 + - - -
186B ALA* 3.3 26.0 - - + +
187B TRP 4.7 0.7 - - - -
188B HIS* 3.9 47.6 + - + +
189B THR 4.7 4.7 + - - -
190B GLU* 5.6 1.8 + - - +
191B ASP* 4.6 14.2 + - - +
238B LEU 2.9 13.6 + - - -
239B ARG* 3.5 15.7 - - - +
240B HIS* 1.3 78.5 - - - +
242B MET* 1.3 57.3 + - - +
9D MLZ 4.5 19.8 - - - +
10D SER 2.9 29.3 + - - +
11D THR* 3.8 15.2 - - - +
12D GLY* 3.7 18.1 - - - +
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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