Contacts of the helix formed by residues 262 - 275 (chain A) in PDB entry 2O0K
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 ASN 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ILE* 3.5 0.8 + - - -
261A PRO* 1.3 90.6 + - - +
263A PHE* 1.3 66.3 + - - +
264A HIS* 3.1 6.3 + - - +
265A ASP* 3.3 23.2 + - + +
266A SER* 4.0 6.1 + - - -
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Residues in contact with PHE 263 (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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239A SER* 5.1 1.1 - - - -
254A ILE* 4.6 13.7 - - + -
257A CYS* 3.2 33.0 - - - -
260A ILE* 3.3 45.3 + - + +
261A PRO 3.3 1.0 - - - -
262A ASN* 1.3 78.0 - - - +
264A HIS* 1.3 58.0 + - - +
266A SER* 3.2 14.1 + - - +
267A TRP* 2.8 80.6 + + + +
270A ILE* 5.4 1.8 - - + -
293A HIS* 3.4 39.2 + + + +
297A ILE* 4.3 5.4 - - + -
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Residues in contact with HIS 264 (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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262A ASN* 3.1 4.1 - - - +
263A PHE* 1.3 79.8 - - - +
265A ASP* 1.3 63.5 + - - +
267A TRP* 3.3 20.4 - + - +
268A LEU* 2.9 49.1 + - + +
271A GLN* 6.1 0.7 - - - -
293A HIS* 5.6 2.1 + - + +
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Residues in contact with ASP 265 (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 PRO* 4.1 24.4 - - + +
262A ASN* 3.3 18.0 + - + +
263A PHE 3.2 0.6 - - - -
264A HIS* 1.3 82.4 - - - +
266A SER* 1.3 66.9 + - - +
268A LEU* 3.2 21.9 + - - +
269A ALA* 3.3 9.2 + - - +
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Residues in contact with SER 266 (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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189A LEU* 5.9 0.2 - - - -
239A SER* 3.2 29.0 + - - -
240A SER* 3.8 19.7 + - - -
241A PRO* 4.4 10.3 - - - +
244A VAL* 4.5 2.5 - - - +
260A ILE* 5.0 1.7 - - - +
262A ASN 4.2 6.4 + - - -
263A PHE* 3.2 16.9 + - - -
265A ASP* 1.3 78.4 - - - +
267A TRP* 1.3 61.2 + - - +
269A ALA* 3.5 4.6 + - - +
270A ILE* 3.1 36.9 + - - +
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Residues in contact with TRP 267 (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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254A ILE* 5.4 2.2 - - + -
263A PHE* 2.8 55.1 + + + +
264A HIS* 3.3 21.8 - + - +
266A SER* 1.3 74.2 - - - +
268A LEU* 1.3 66.0 + - + +
270A ILE* 3.1 21.3 + - + +
271A GLN* 3.1 43.7 + - + +
274A ILE* 4.0 21.3 - - + -
282A ILE* 5.8 0.2 - - + -
284A ILE* 4.7 11.4 - - + -
293A HIS* 6.3 2.2 - - + -
297A ILE* 4.1 25.4 - - + +
308A PHE* 4.1 27.8 - + - -
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Residues in contact with LEU 268 (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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264A HIS* 2.9 38.1 + - + +
265A ASP* 3.2 15.9 - - - +
267A TRP* 1.3 77.7 - - - +
269A ALA* 1.3 63.0 + - - +
271A GLN* 3.6 12.4 + - - +
272A PRO* 3.1 18.0 - - + +
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Residues in contact with ALA 269 (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 PRO* 4.1 20.9 - - + +
244A VAL* 3.4 28.3 - - + +
245A ARG* 4.2 18.0 - - + +
265A ASP 3.3 7.8 + - - +
266A SER 3.9 7.2 - - - +
267A TRP 3.3 0.2 - - - -
268A LEU* 1.3 80.1 - - - +
270A ILE* 1.3 58.3 + - - +
272A PRO* 3.0 20.2 - - - +
273A VAL* 4.8 2.1 + - - +
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Residues in contact with ILE 270 (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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189A LEU* 3.9 18.4 - - + -
239A SER* 5.8 0.2 - - - +
244A VAL* 3.7 22.4 - - + -
252A ILE* 4.3 11.4 - - + -
254A ILE* 3.8 26.2 - - + -
263A PHE* 5.4 2.0 - - + -
266A SER* 3.1 25.5 + - - +
267A TRP* 3.1 15.3 + - + +
269A ALA* 1.3 75.3 - - - +
271A GLN* 1.3 66.9 + - - +
272A PRO* 3.0 3.1 - - - -
273A VAL* 2.8 34.4 + - + +
274A ILE* 3.2 30.2 + - + -
282A ILE* 5.0 4.3 - - + -
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Residues in contact with GLN 271 (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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264A HIS* 6.1 1.0 - - - -
267A TRP* 3.1 56.8 + - + +
268A LEU* 4.1 10.5 - - - +
270A ILE* 1.3 75.0 - - - +
272A PRO* 1.3 64.3 - - + +
274A ILE* 3.6 19.1 - - + -
275A SER* 2.7 40.2 + - - +
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Residues in contact with PRO 272 (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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268A LEU* 3.1 15.5 - - + +
269A ALA* 3.0 23.1 - - - +
270A ILE 2.8 0.2 - - - -
271A GLN* 1.3 93.3 - - + +
273A VAL* 1.3 62.1 + - + +
275A SER* 3.3 18.7 + - - +
276A SER 4.1 5.9 - - - +
277A GLY* 5.0 2.6 - - - -
278A ARG 5.6 0.2 + - - -
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Residues in contact with VAL 273 (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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244A VAL* 5.1 11.2 - - + +
247A ASN 5.7 3.4 - - - +
248A SER* 5.9 1.6 - - - -
249A PHE* 4.9 11.9 - - + +
252A ILE* 3.5 31.6 - - + -
269A ALA 5.0 4.5 - - - +
270A ILE* 2.8 31.1 + - + +
272A PRO* 1.3 76.6 - - + +
274A ILE* 1.3 62.9 + - + +
278A ARG* 5.9 2.5 - - - +
279A ARG* 3.3 8.9 + - - +
280A SER* 2.9 44.9 + - - +
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Residues in contact with ILE 274 (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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154A ARG* 3.1 27.7 + - - +
155A MET* 3.3 31.4 - - + +
267A TRP* 4.0 24.5 - - + -
270A ILE* 3.3 34.1 - - + +
271A GLN* 3.0 17.6 + - + +
273A VAL* 1.3 81.6 - - + +
275A SER* 1.3 62.6 + - - +
279A ARG* 4.1 1.4 - - - +
280A SER 4.7 2.5 - - - +
282A ILE* 4.4 24.7 - - + -
308A PHE* 4.5 4.7 - - + -
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Residues in contact with SER 275 (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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271A GLN* 2.7 33.2 + - - +
272A PRO* 3.3 12.3 + - - +
273A VAL 4.0 1.7 - - - +
274A ILE* 1.3 79.3 - - - +
276A SER* 1.3 73.3 + - - +
277A GLY* 2.9 5.2 + - - -
279A ARG* 3.8 9.1 - - - +
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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