Contacts of the helix formed by residues 232 - 247 (chain A) in PDB entry 1OMW
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 GLY 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A PHE* 3.7 25.7 - - - -
227A ILE* 3.0 13.2 + - - +
230A LYS* 3.2 4.8 - - - +
231A GLN* 1.3 76.2 - - - +
233A GLU* 1.3 54.2 + - - +
234A THR 3.4 2.5 - - - -
235A LEU* 3.2 12.3 + - - +
236A ALA* 2.8 36.0 + - - +
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Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ILE* 3.6 21.4 - - + +
228A LYS* 3.2 35.6 - - + +
231A GLN* 3.2 23.1 - - - +
232A GLY* 1.3 73.8 - - - +
234A THR* 1.3 68.3 + - - +
236A ALA* 3.8 2.4 - - - +
237A LEU* 2.9 30.7 + - + +
502A ASP* 5.1 2.3 - - - +
505A LEU* 5.3 16.8 - - + -
506A TYR* 4.1 15.0 - - + +
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLN 4.7 4.7 + - - -
232A GLY 3.4 0.4 - - - -
233A GLU* 1.3 80.3 + - - +
235A LEU* 1.3 57.0 + - - +
237A LEU* 3.7 8.0 - - - +
238A ASN* 2.9 29.4 + - + +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PHE* 3.8 28.3 - - + -
232A GLY* 3.2 14.8 + - - +
233A GLU 3.2 0.4 - - - -
234A THR* 1.3 78.8 - - - +
236A ALA* 1.3 63.5 + - - +
238A ASN* 3.3 5.6 + - - +
239A GLU* 3.1 23.7 + - - +
335A ASP* 5.4 0.7 - - - +
337A GLY* 3.4 37.9 - - - +
338A LEU* 3.5 20.9 - - + -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PHE* 5.0 4.5 - - + -
222A LEU* 4.7 11.4 - - + -
227A ILE* 3.9 25.6 - - + -
232A GLY 2.8 20.9 + - - +
233A GLU* 3.8 4.7 - - - +
235A LEU* 1.3 69.3 - - - +
237A LEU* 1.3 70.7 + - - +
239A GLU* 3.2 19.7 + - - +
240A ARG* 3.4 11.8 + - - +
267A LEU* 5.0 8.1 - - + -
269A PHE* 4.5 4.2 - - - -
506A TYR* 5.3 4.7 - - + +
509A PHE* 5.0 3.4 - - - -
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLU* 2.9 19.7 + - + +
234A THR* 3.7 8.1 - - - +
236A ALA* 1.3 78.6 - - - +
238A ASN* 1.3 66.9 + - - +
240A ARG* 3.2 5.2 + - - +
241A ILE* 3.1 58.9 + - + +
505A LEU* 5.0 16.2 - - + +
506A TYR* 5.8 4.9 - - + -
509A PHE* 5.6 5.4 - - - -
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Residues in contact with ASN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A THR* 2.9 21.5 + - + +
235A LEU* 3.6 3.1 - - - +
236A ALA 3.1 0.6 - - - -
237A LEU* 1.3 77.4 - - - +
239A GLU* 1.3 51.8 + - - +
241A ILE* 3.1 8.4 + - - +
242A MET* 2.8 70.4 + - - +
316A ARG* 5.8 0.2 - - - +
336A LEU 3.8 0.2 + - - -
337A GLY 2.7 28.9 + - - +
338A LEU* 4.1 0.6 - - - +
339A ALA 2.9 24.6 + - - +
340A CYS* 6.1 0.2 - - - -
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PHE* 6.2 0.3 - - - -
220A LYS* 3.4 23.7 + - - +
222A LEU* 4.4 7.4 - - - +
235A LEU* 3.1 14.2 + - - +
236A ALA* 3.2 10.7 + - - +
238A ASN* 1.3 76.0 - - - +
240A ARG* 1.3 50.9 + - - +
242A MET* 3.0 3.3 + - - +
243A LEU* 2.6 52.4 + - + +
269A PHE* 3.8 18.6 - - + -
335A ASP* 2.6 28.9 - - - +
336A LEU* 4.0 19.1 + - + +
337A GLY* 3.6 19.4 + - - +
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Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ALA 3.4 2.3 + - - +
237A LEU 3.2 8.3 + - - +
239A GLU* 1.3 73.9 - - - +
241A ILE* 1.3 86.9 + - + +
242A MET 3.3 0.2 + - - -
243A LEU* 4.0 2.7 - - - +
244A SER* 3.3 22.0 + - - -
257A MET* 4.4 4.0 - - - -
260A ALA* 4.4 7.4 - - + -
269A PHE* 3.3 31.8 - - + -
508A ASN 3.1 26.7 + - - -
509A PHE* 3.2 53.5 + - + +
510A PRO 4.7 1.8 + - - -
511A LEU* 3.3 34.7 - - - +
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A LEU* 3.2 42.4 - - + +
238A ASN* 3.1 8.2 + - - +
240A ARG* 1.3 97.8 - - + +
242A MET* 1.3 73.7 + - + +
244A SER* 2.8 23.5 + - - +
245A LEU* 3.4 15.9 + - + +
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Residues in contact with MET 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASN* 2.8 51.3 + - - +
239A GLU 3.4 4.5 - - - +
241A ILE* 1.3 85.9 - - + +
243A LEU* 1.3 62.2 + - - +
244A SER 3.2 1.8 - - - -
245A LEU* 3.4 12.8 + - + +
246A VAL* 3.2 27.9 + - - +
313A VAL* 4.1 13.9 - - + -
336A LEU* 4.1 23.6 - - + +
339A ALA* 3.8 2.0 - - + -
340A CYS* 3.7 27.4 - - - -
341A ASP* 3.6 32.1 - - + +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LYS* 6.3 0.4 - - + -
239A GLU* 2.6 32.7 + - + +
240A ARG 3.5 2.2 + - - +
242A MET* 1.3 71.2 - - - +
244A SER* 1.3 58.2 + - - +
246A VAL* 3.9 5.2 - - + +
247A SER* 2.2 39.6 + - - +
255A VAL 3.9 13.5 - - - +
256A CYS* 4.7 0.2 - - - -
257A MET* 3.6 23.9 - - + +
269A PHE* 3.6 40.4 - - + -
271A LEU* 3.9 19.5 - - + -
336A LEU* 3.4 30.3 - - + +
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ARG* 3.3 16.9 + - - -
241A ILE* 2.8 20.4 + - - +
242A MET 3.2 0.4 - - - -
243A LEU* 1.3 77.6 - - - +
245A LEU* 1.3 66.2 + - - +
246A VAL 3.6 0.2 + - - -
247A SER 4.2 3.5 + - - -
248A THR* 4.4 13.9 + - - +
257A MET* 4.2 4.5 - - - -
511A LEU* 3.7 26.5 - - - -
513A ILE* 4.2 9.1 - - - +
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ILE* 3.6 17.9 - - + +
242A MET* 3.4 17.6 + - + +
244A SER* 1.3 85.8 + - - +
246A VAL* 1.3 57.4 + - - +
247A SER 3.6 0.2 - - - -
248A THR* 4.4 5.2 + - - +
311A ARG* 3.3 32.3 + - + +
313A VAL* 3.8 28.0 - - + -
341A ASP* 3.8 30.1 - - + +
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A MET 3.2 16.9 + - - +
243A LEU* 4.4 2.7 - - + +
245A LEU* 1.3 80.0 - - - +
247A SER* 1.3 61.5 + - - +
248A THR 3.5 1.6 - - - -
251A CYS* 5.2 0.2 - - - +
254A ILE* 3.8 38.6 - - + -
255A VAL 5.4 0.4 - - - +
256A CYS* 4.0 6.5 - - - -
307A HIS* 2.9 27.3 + - + -
308A MET* 3.8 26.7 - - + -
311A ARG* 4.5 4.9 - - + +
313A VAL* 4.4 17.5 - - + -
336A LEU* 4.1 19.1 - - + -
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU* 2.2 27.9 + - - -
244A SER* 4.2 0.6 + - - -
245A LEU 3.6 0.4 - - - -
246A VAL* 1.3 76.5 - - - +
248A THR* 1.3 61.6 + - - +
249A GLY 4.0 0.2 + - - -
256A CYS* 3.3 16.7 - - - +
257A MET* 3.0 38.8 + - - +
513A ILE* 4.0 13.8 - - - +
515A GLU* 5.7 0.2 - - - -
516A ARG* 3.1 28.5 + - - +
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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