Contacts of the helix formed by residues 231 - 242 (chain B) in PDB entry 2IHM
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 SER 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B GLN* 2.9 14.0 + - - -
228B VAL* 3.1 16.6 + - - -
230B CYS* 1.3 78.9 - - - +
232B GLU* 1.3 66.4 + - - +
233B ARG* 4.2 9.0 - - - +
234B TYR* 3.4 13.2 + - - +
235B GLN* 3.1 23.0 + - - +
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Residues in contact with GLU 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 CYS 3.6 2.8 + - - -
231B SER* 1.3 72.0 - - - +
233B ARG* 1.3 64.1 + - - +
235B GLN* 4.7 6.7 - - - +
236B THR* 2.9 40.5 + - - +
255B TYR* 3.2 10.9 + - - +
260B ARG* 2.8 44.3 + - - +
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Residues in contact with ARG 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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169B PHE 3.0 24.4 + - - -
170B GLU* 2.7 40.0 + - - +
231B SER* 4.4 7.9 - - - +
232B GLU* 1.3 78.9 - - - +
234B TYR* 1.3 58.7 + - - +
236B THR* 4.0 0.9 - - - -
237B MET* 3.0 52.0 + - - +
252B ASN* 3.0 31.0 + - - +
255B TYR* 3.2 50.2 + - + +
256B GLN* 4.8 1.2 + - - -
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Residues in contact with TYR 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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162B THR* 4.3 14.0 + - + +
165B GLU* 2.7 29.6 + - + -
166B ALA* 4.2 12.8 - - + -
169B PHE* 3.8 29.2 - + - -
170B GLU* 5.9 0.4 - - - -
228B VAL* 3.0 47.8 - - + +
229B ARG* 3.8 24.5 - - + +
231B SER* 3.3 9.6 + - - +
233B ARG* 1.3 79.1 - - + +
235B GLN* 1.3 71.6 + - + +
237B MET* 3.3 3.7 + - - +
238B LYS* 2.9 48.8 + - + +
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Residues in contact with GLN 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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229B ARG 3.8 17.7 - - - +
230B CYS* 2.7 33.1 + - - +
231B SER 3.1 12.6 + - - +
232B GLU* 4.0 5.8 - - - +
234B TYR* 1.3 80.2 - - + +
236B THR* 1.3 58.8 + - - +
238B LYS* 3.7 5.3 + - - +
239B LEU* 3.1 26.5 + - - +
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Residues in contact with THR 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 GLU* 2.9 26.4 + - - +
233B ARG 4.0 0.2 - - - -
235B GLN* 1.3 76.3 - - - +
237B MET* 1.3 60.0 + - - +
239B LEU* 2.9 9.0 + - - +
240B PHE* 2.8 57.6 + - + +
255B TYR* 3.5 32.8 - - + -
260B ARG* 3.9 20.3 + - - +
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Residues in contact with MET 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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169B PHE* 3.3 50.7 - - + +
233B ARG* 3.0 55.8 + - - +
236B THR* 1.3 75.6 - - - +
238B LYS* 1.3 63.6 + - - +
240B PHE* 3.2 1.1 + - - -
241B THR* 2.8 33.8 + - - +
248B VAL* 3.7 17.0 - - + +
251B ALA* 3.5 30.7 - - + +
252B ASN* 3.6 18.4 - - + +
255B TYR* 4.6 4.9 - - + -
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Residues in contact with LYS 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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165B GLU* 3.0 34.1 + - - +
169B PHE* 3.4 16.5 - - + -
234B TYR* 2.9 42.7 + - + +
235B GLN* 3.8 6.5 - - - +
237B MET* 1.3 75.5 - - - +
239B LEU* 1.3 61.9 + - - +
241B THR* 3.6 1.0 + - - -
242B GLN* 3.2 27.6 + - + +
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Residues in contact with LEU 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 GLN 3.1 15.2 + - - +
236B THR* 2.9 11.1 + - - +
238B LYS* 1.3 79.4 - - - +
240B PHE* 1.3 68.8 + - + +
242B GLN* 3.5 5.5 - - - +
243B VAL* 3.7 7.8 - - - +
260B ARG 3.7 23.6 - - - +
261B THR* 4.5 1.1 - - - -
262B LEU* 4.0 29.2 - - + +
283B TYR* 3.3 40.3 + - + +
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Residues in contact with PHE 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 THR* 2.8 34.3 + - + +
237B MET* 5.4 0.2 - - - -
239B LEU* 1.3 80.2 - - + +
241B THR* 1.3 59.5 + - - +
242B GLN 3.1 1.6 - - - -
243B VAL* 3.0 21.4 + - - +
246B VAL* 3.1 23.0 - - + +
251B ALA* 3.5 37.0 - - + -
254B TRP* 3.6 30.5 - + + -
255B TYR 4.3 1.8 - - - -
259B LEU* 4.0 11.2 - - + -
260B ARG* 3.9 35.2 - - - -
261B THR 3.8 13.0 - - - -
262B LEU* 4.4 2.9 - - + -
265B LEU* 3.6 27.4 - - + -
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Residues in contact with THR 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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169B PHE* 3.2 30.4 - - + -
237B MET* 2.8 28.0 + - + +
238B LYS 3.6 2.3 + - - -
240B PHE* 1.3 66.8 - - - +
242B GLN* 1.3 62.9 + - - +
243B VAL 3.0 2.2 - - - -
246B VAL 3.5 9.0 - - - -
247B GLY* 3.7 19.3 - - - -
248B VAL* 3.7 11.0 - - + +
251B ALA* 3.6 20.9 - - + -
901B NA 2.7 24.3 - - - -
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Residues in contact with GLN 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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238B LYS* 3.2 21.9 + - + +
239B LEU* 3.5 6.7 - - - +
240B PHE 3.1 0.4 - - - -
241B THR* 1.3 78.9 + - - +
243B VAL* 1.3 61.8 + - - +
244B PHE* 3.4 2.3 + - - -
283B TYR* 3.2 28.0 + - + +
286B LEU* 3.4 28.2 + - - +
287B SER* 3.7 17.2 - - - +
329B HIS* 6.4 0.2 - - - +
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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