Contacts of the helix formed by residues 263 - 284 (chain A) in PDB entry 2O2C
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 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 3.8 24.5 - - + -
258A SER* 4.3 2.4 + - - -
260A THR* 3.4 8.7 + - - +
261A PHE 3.8 0.4 - - - -
262A THR* 1.3 75.6 + - - +
264A GLN* 1.3 65.2 + - - +
265A GLU* 3.7 19.1 - - - +
266A THR* 3.2 7.1 + - - +
267A ILE* 3.0 24.3 + - - +
571A LYS* 5.4 12.5 + - - +
5001A G6Q 2.7 39.4 + - - +
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Residues in contact with GLN 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 5.3 3.1 - - + -
262A THR 3.1 7.3 + - - +
263A THR* 1.3 70.8 - - - +
265A GLU* 1.3 67.3 + - - +
267A ILE* 4.3 2.9 - - - +
268A THR* 2.7 43.3 + - - +
574A ALA* 5.5 9.7 - - - +
575A LYS* 5.1 14.4 - - - +
578A LEU* 3.7 26.3 - - - +
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 3.8 32.4 - - + +
233A SER 4.0 13.2 - - - +
235A VAL* 3.6 36.0 - - + +
263A THR* 3.3 14.3 - - - +
264A GLN* 1.3 81.8 + - - +
266A THR* 1.3 57.4 + - - +
268A THR* 3.8 1.9 - - - -
269A ASN* 3.0 36.7 + - - -
571A LYS* 5.8 2.6 - - - -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 3.6 32.4 - - - +
204A GLY* 3.6 3.3 - - - -
205A ILE* 3.6 30.3 + - - +
233A SER 5.7 0.4 - - - -
256A VAL* 3.9 16.4 - - + -
257A ALA 3.6 13.2 + - - +
258A SER* 4.0 9.6 - - - -
263A THR* 3.2 15.7 + - - +
265A GLU* 1.3 73.1 - - - +
267A ILE* 1.3 63.1 + - + +
269A ASN* 3.4 1.6 + - - +
270A ALA* 2.8 31.0 + - - +
5001A G6Q 4.3 1.6 + - - -
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Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 5.1 2.5 - - + -
261A PHE* 3.4 53.6 - - + +
262A THR* 4.0 10.8 - - - +
263A THR 3.0 17.0 + - - +
264A GLN* 4.3 4.0 - - - +
266A THR* 1.3 81.6 - - + +
268A THR* 1.3 59.6 + - - +
270A ALA* 3.3 4.9 + - + +
271A LEU* 2.9 55.3 + - + +
309A PHE* 5.6 6.1 - - + -
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 4.0 22.4 - - + +
264A GLN* 2.7 34.4 + - - +
265A GLU 3.8 3.4 - - - -
267A ILE* 1.3 77.0 - - - +
269A ASN* 1.3 62.8 + - - +
271A LEU* 3.5 10.4 + - - +
272A SER* 3.1 27.2 + - - +
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 3.6 20.4 - - + +
232A VAL* 3.5 25.6 + - + +
233A SER* 3.5 15.2 + - - +
234A ASN 3.0 27.7 + - - +
235A VAL* 4.4 9.4 - - - +
236A ASP 5.1 0.7 - - - +
237A GLY* 5.9 0.3 - - - -
240A ILE* 4.1 17.9 + - - +
265A GLU 3.0 21.3 + - - +
266A THR* 4.9 0.4 - - - +
268A THR* 1.3 77.4 - - - +
270A ALA* 1.3 57.9 + - - +
272A SER* 3.2 6.6 + - - -
273A ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 4.0 12.3 - - + +
256A VAL* 3.9 28.3 - - + -
266A THR 2.8 18.6 + - - +
267A ILE* 3.3 8.0 + - + +
269A ASN* 1.3 75.4 - - - +
271A LEU* 1.3 58.3 + - - +
273A ALA* 3.3 3.1 + - - +
274A ARG* 3.0 28.4 + - - +
296A PHE* 4.0 1.2 - - - -
309A PHE* 3.5 24.2 - - + -
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE* 2.9 40.5 + - + +
268A THR* 3.8 8.3 - - - +
270A ALA* 1.3 76.1 - - - +
272A SER* 1.3 57.2 + - - +
274A ARG* 3.5 32.7 + - - +
275A ARG* 3.0 28.1 + - - +
309A PHE* 3.7 19.1 - - + -
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 4.6 20.6 - - - +
244A LEU* 5.1 2.8 - - - +
268A THR* 3.1 19.0 + - - +
269A ASN* 3.2 10.3 + - - -
271A LEU* 1.3 75.2 - - - +
273A ALA* 1.3 60.3 + - - +
275A ARG* 3.5 8.8 + - - +
276A ALA* 3.0 28.4 + - - +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 3.7 22.9 - - + -
240A ILE* 4.6 11.6 - - + +
244A LEU* 5.4 0.2 - - - -
254A PHE* 4.0 20.4 - - + -
269A ASN 2.9 17.0 + - - +
270A ALA 3.3 6.3 + - - +
272A SER* 1.3 75.0 - - - +
274A ARG* 1.3 62.8 + - - +
276A ALA* 3.4 8.3 + - - +
277A LEU* 3.2 21.5 + - - +
296A PHE* 3.7 12.2 - - + -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA 3.0 16.2 + - - +
271A LEU* 3.6 29.6 + - - +
272A SER 3.3 0.2 - - - -
273A ALA* 1.3 74.5 - - - +
275A ARG* 1.3 64.8 + - - +
277A LEU* 3.2 4.0 + - - +
278A LEU* 3.1 39.6 + - + +
292A VAL* 4.1 29.4 - - + -
296A PHE* 3.5 18.1 - - + -
308A GLU 5.1 0.8 + - - -
309A PHE* 2.7 60.8 + - + +
7005A GOL 5.8 0.2 - - - -
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Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU 3.0 17.7 + - - +
272A SER* 3.7 9.4 - - - +
273A ALA 3.4 0.2 - - - -
274A ARG* 1.3 75.9 - - - +
276A ALA* 1.3 52.5 + - - +
278A LEU* 3.4 8.5 + - - +
279A ASP* 2.8 65.0 + - - +
282A ARG* 6.0 1.1 - - - +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 3.8 36.1 - - + -
249A ILE* 3.9 8.9 - - + +
272A SER 3.0 17.7 + - - +
273A ALA 3.5 6.7 - - - +
274A ARG 3.2 0.2 - - - -
275A ARG* 1.3 74.3 - - - +
277A LEU* 1.3 63.8 + - - +
279A ASP* 3.4 7.6 + - - +
280A TYR* 3.0 24.4 + - - +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 3.9 28.0 - - + +
250A GLU* 5.8 0.4 - - - -
254A PHE* 5.0 2.0 - - + -
273A ALA 3.2 12.2 + - - +
274A ARG 3.2 8.3 + - - +
276A ALA* 1.3 76.2 - - - +
278A LEU* 1.3 63.0 + - + +
280A TYR* 3.3 2.8 + - - +
281A LEU* 3.2 45.1 + - + +
291A SER* 4.0 23.6 - - - +
292A VAL* 4.3 6.7 - - + +
295A HIS* 3.8 51.6 - - + +
296A PHE* 3.9 15.9 - - + -
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 3.1 34.1 + - + +
275A ARG* 3.9 5.8 - - + +
277A LEU* 1.3 75.7 - - + +
279A ASP* 1.3 59.6 + - - +
281A LEU* 3.6 5.5 + - + +
282A ARG* 3.1 43.7 + - - +
288A GLU* 3.2 35.3 - - + +
291A SER* 3.7 21.8 - - - +
292A VAL* 4.5 5.4 - - + -
7005A GOL 3.6 23.3 - - - +
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Residues in contact with ASP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ARG* 2.8 56.7 + - - +
276A ALA* 3.7 7.5 - - - +
278A LEU* 1.3 70.0 - - - +
280A TYR* 1.3 65.1 - - - +
282A ARG* 2.8 37.6 + - - +
283A SER* 3.1 24.8 + - - -
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Residues in contact with TYR 280 (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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248A ASP* 5.7 1.1 - - - -
249A ILE* 3.5 28.9 - - + -
250A GLU* 2.5 44.0 + - + -
276A ALA 3.0 16.8 + - - +
277A LEU 3.3 4.7 + - - +
279A ASP* 1.3 78.0 - - - +
281A LEU* 1.3 75.9 + - + +
283A SER* 2.7 24.6 + - - -
284A ARG* 2.8 44.1 + - + +
286A ILE* 5.2 1.1 - - + -
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A HIS* 3.9 24.5 - - + -
193A THR* 4.5 9.2 - - + -
250A GLU* 5.5 2.0 - - + -
277A LEU* 3.2 31.9 + - + +
278A LEU* 4.0 4.9 - - - +
279A ASP 3.4 0.2 - - - -
280A TYR* 1.3 90.9 - - + +
282A ARG* 1.3 58.4 + - - +
284A ARG* 3.3 3.4 + - - -
285A GLY 3.0 7.6 + - - -
286A ILE* 2.9 61.2 + - + +
288A GLU* 4.2 13.9 - - + -
291A SER* 3.8 32.1 - - - +
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ARG* 6.0 1.6 - - - +
278A LEU* 3.1 37.1 + - - +
279A ASP* 2.8 36.2 + - - +
281A LEU* 1.3 76.9 - - - +
283A SER* 1.3 61.2 + - - +
285A GLY* 3.2 13.1 + - - -
286A ILE 4.4 3.8 + - - -
288A GLU* 4.4 15.0 + - - +
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Residues in contact with SER 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASP 3.1 13.8 + - - -
280A TYR* 2.7 27.2 + - - -
282A ARG* 1.3 76.4 - - - +
284A ARG* 1.3 62.4 + - - +
285A GLY 3.4 0.6 + - - -
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 5.9 0.6 - - - +
250A GLU* 3.1 18.2 + - - -
280A TYR* 2.8 63.9 + - + +
281A LEU 3.8 1.1 - - - +
282A ARG 3.2 0.4 - - - -
283A SER* 1.3 81.2 + - - +
285A GLY* 1.3 61.4 + - - +
286A ILE* 3.3 33.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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