Contacts of the helix formed by residues 263 - 284 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ILE* 3.8 15.3 - - + -
258B SER* 4.3 2.2 + - - -
260B THR* 3.4 9.0 + - - -
261B PHE 3.8 0.4 - - - -
262B THR* 1.3 76.7 + - - +
264B GLN* 1.3 64.5 + - - +
265B GLU* 3.5 22.2 - - - +
266B THR* 3.2 7.0 + - - +
267B ILE* 3.0 22.2 + - - +
571B LYS* 5.3 9.2 + - - +
5002B G6Q 2.6 31.7 + - - +
442C HIS* 3.8 20.2 - - + -
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Residues in contact with GLN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B THR 3.2 6.5 + - - +
263B THR* 1.3 72.6 - - - +
265B GLU* 1.3 65.4 + - - +
267B ILE* 4.1 3.4 - - - +
268B THR* 2.7 37.6 + - - +
574B ALA* 5.5 5.3 - - - +
575B LYS* 6.1 1.6 - - - +
578B LEU* 3.8 19.6 - - - +
475C ILE* 3.4 34.4 + - + +
478C SER* 4.6 5.1 + - - -
479C ASN* 4.4 14.1 + - - +
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Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 3.9 11.9 - - + -
233B SER 3.9 14.4 - - - +
235B VAL* 3.6 29.2 - - + +
263B THR* 3.3 10.2 - - - +
264B GLN* 1.3 80.2 + - + +
266B THR* 1.3 58.8 + - - +
268B THR* 3.5 1.9 + - - -
269B ASN* 3.0 36.0 + - - -
571B LYS* 5.9 0.3 - - - -
438C THR* 2.9 32.5 + - - +
441C GLN* 4.0 6.1 + - - -
442C HIS* 2.7 33.6 + - - -
475C ILE* 6.3 0.2 - - + -
479C ASN* 4.6 5.5 - - - +
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 3.6 28.9 - - + +
204B GLY* 3.6 2.8 - - - -
205B ILE* 3.6 31.0 + - - +
233B SER 5.6 0.4 - - - -
256B VAL* 4.0 15.5 - - + -
257B ALA 3.7 12.5 + - - +
258B SER* 4.0 10.1 - - - -
263B THR* 3.2 15.9 + - - +
265B GLU* 1.3 72.5 - - - +
267B ILE* 1.3 64.2 + - + +
269B ASN* 3.4 6.0 + - - +
270B ALA* 2.8 31.1 + - - +
5002B G6Q 4.4 1.6 + - - -
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Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 5.2 0.2 - - + -
258B SER* 5.6 0.2 - - - +
261B PHE* 3.3 54.3 - - + +
262B THR* 4.0 10.5 - - - +
263B THR 3.0 16.7 + - - +
264B GLN* 4.3 3.4 - - - +
266B THR* 1.3 76.5 - - + +
268B THR* 1.3 60.6 + - - +
270B ALA* 3.3 5.7 + - + +
271B LEU* 2.9 49.1 + - + +
309B PHE* 5.1 10.3 - - + -
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 4.0 9.1 - - + +
264B GLN* 2.7 30.4 + - - +
265B GLU 3.7 3.8 - - - -
267B ILE* 1.3 77.2 - - - +
269B ASN* 1.3 61.2 + - - +
271B LEU* 3.5 9.1 + - - +
272B SER* 3.1 26.3 + - - +
471C ASP 5.6 0.2 - - - -
472C HIS* 3.6 29.4 - - + +
475C ILE* 3.8 32.3 - - + +
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Residues in contact with ASN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 3.6 20.8 - - + +
232B VAL* 3.6 23.5 + - + +
233B SER* 3.5 14.8 + - - +
234B ASN 3.0 27.1 + - - +
235B VAL* 4.6 1.1 - - - -
236B ASP 5.1 0.2 - - - +
240B ILE* 4.1 10.7 + - + +
265B GLU 3.0 22.4 + - - +
266B THR* 4.7 0.4 - - - +
268B THR* 1.3 74.5 - - - +
270B ALA* 1.3 58.3 + - - +
272B SER* 3.2 3.8 + - - -
273B ALA* 3.0 29.3 + - - +
472C HIS* 3.2 24.4 + - - -
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 4.0 12.9 - - + +
256B VAL* 3.8 25.8 - - + -
266B THR 2.8 19.3 + - - +
267B ILE* 3.6 7.6 - - + +
269B ASN* 1.3 75.8 - - - +
271B LEU* 1.3 57.3 + - - +
273B ALA* 3.4 3.1 + - - +
274B ARG* 3.0 28.9 + - - +
296B PHE* 4.1 1.6 - - - -
309B PHE* 3.5 26.3 - - + -
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 2.9 36.4 + - + +
268B THR* 3.8 8.3 - - - +
270B ALA* 1.3 74.8 - - - +
272B SER* 1.3 58.1 + - - +
274B ARG* 3.4 37.5 + - - +
275B ARG* 2.9 29.3 + - - +
309B PHE* 3.9 15.7 - - + -
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE* 4.5 12.1 - - - -
244B LEU* 5.1 2.9 - - - +
268B THR* 3.1 10.8 + - - +
269B ASN* 3.2 5.1 + - - -
271B LEU* 1.3 74.6 - - - +
273B ALA* 1.3 60.1 + - - +
275B ARG* 3.5 9.5 + - - +
276B ALA* 3.0 27.4 + - - +
469C ILE* 4.3 10.0 - - - +
470C GLY* 6.0 0.3 - - - -
472C HIS* 2.8 34.5 + - - -
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 3.7 22.0 - - + -
240B ILE* 4.4 11.6 - - + +
244B LEU* 5.3 0.2 - - - -
254B PHE* 4.0 24.5 - - + -
269B ASN 3.0 16.0 + - - +
270B ALA 3.6 5.6 - - - +
271B LEU 3.3 0.2 - - - -
272B SER* 1.3 73.8 - - - +
274B ARG* 1.3 64.0 + - - +
276B ALA* 3.3 7.7 + - - +
277B LEU* 3.1 22.2 + - - +
296B PHE* 3.7 10.1 - - + -
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA 3.0 17.2 + - - +
271B LEU* 3.4 29.4 + - - +
272B SER 3.3 0.2 - - - -
273B ALA* 1.3 74.5 - - - +
275B ARG* 1.3 64.1 + - - +
277B LEU* 3.3 2.9 + - - +
278B LEU* 3.2 38.8 + - + +
292B VAL* 4.2 28.3 - - + -
296B PHE* 3.5 18.6 - - + -
308B GLU 5.2 1.2 + - - -
309B PHE* 2.7 58.9 + - + +
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Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU 2.9 19.0 + - - +
272B SER* 3.7 9.2 - - - +
274B ARG* 1.3 75.9 - - - +
276B ALA* 1.3 57.8 + - - +
278B LEU* 3.4 7.6 + - - +
279B ASP* 2.8 57.5 + - - +
282B ARG* 6.3 0.4 - - - +
470C GLY* 5.2 13.1 - - - +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 3.8 36.3 - - + -
249B ILE* 3.8 7.8 - - + +
272B SER 3.0 17.3 + - - +
273B ALA 3.4 6.7 - - - +
274B ARG 3.2 0.2 - - - -
275B ARG* 1.3 75.0 - - - +
277B LEU* 1.3 64.0 + - - +
279B ASP* 3.8 6.8 - - - +
280B TYR* 3.0 24.9 + - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ILE* 3.8 27.5 - - + +
250B GLU* 5.9 0.2 - - - -
254B PHE* 4.9 2.0 - - + -
273B ALA 3.1 11.8 + - - +
274B ARG 3.3 7.6 + - - +
276B ALA* 1.3 74.9 - - - +
278B LEU* 1.3 64.7 + - + +
280B TYR* 3.3 4.2 + - - +
281B LEU* 3.2 46.2 + - + +
291B SER* 4.0 20.4 - - - +
292B VAL* 4.3 7.4 - - + +
295B HIS* 3.8 55.4 - - + +
296B PHE* 4.0 15.9 - - + -
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 3.2 32.8 + - + +
275B ARG* 3.9 5.2 - - - +
277B LEU* 1.3 78.2 - - + +
279B ASP* 1.3 57.6 + - - +
281B LEU* 3.5 5.0 + - + +
282B ARG* 3.0 45.7 + - - +
288B GLU* 3.6 43.7 - - + +
291B SER* 3.6 22.0 - - - +
292B VAL* 4.3 15.7 - - + -
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Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ARG* 2.8 49.8 + - - +
276B ALA* 3.8 7.5 + - - +
277B LEU 3.3 0.2 - - - -
278B LEU* 1.3 72.9 - - - +
280B TYR* 1.3 60.4 + - - +
282B ARG* 2.7 35.3 + - - +
283B SER* 3.0 30.5 + - - -
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ASP* 5.4 1.9 + - - -
249B ILE* 3.5 28.7 - - + -
250B GLU* 2.7 43.6 + - + -
276B ALA 3.0 16.8 + - - +
277B LEU* 3.3 5.1 + - + +
279B ASP* 1.3 76.3 - - - +
281B LEU* 1.3 74.0 + - + +
283B SER* 2.7 26.7 + - - -
284B ARG* 3.3 38.9 + - + +
286B ILE* 5.5 0.4 - - + -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B HIS* 3.9 17.5 - - + -
193B THR* 4.4 10.5 - - + -
250B GLU* 5.5 2.2 - - + -
277B LEU* 3.2 30.6 + - + +
278B LEU* 3.9 3.8 - - - +
280B TYR* 1.3 88.2 - - + +
282B ARG* 1.3 61.6 + - - +
284B ARG 3.2 3.5 + - - -
285B GLY 3.2 3.8 + - - -
286B ILE* 2.9 68.0 + - + +
288B GLU* 4.3 13.0 - - + -
291B SER* 3.7 33.4 - - - +
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ARG* 6.3 0.2 - - - +
278B LEU* 3.0 42.3 + - - +
279B ASP* 2.7 32.7 + - - +
281B LEU* 1.3 74.6 - - - +
283B SER* 1.3 60.8 + - - +
285B GLY* 3.1 14.5 + - - +
286B ILE 4.3 4.9 + - - +
288B GLU* 3.9 14.6 + - + +
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASP 3.0 14.5 + - - -
280B TYR* 2.7 26.4 + - - -
282B ARG* 1.3 75.9 - - - +
284B ARG* 1.3 64.4 + - - +
285B GLY 3.4 0.8 + - - -
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Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B THR* 5.1 0.6 - - - +
250B GLU* 3.2 32.5 + - - -
280B TYR* 3.3 38.9 + - + +
281B LEU 3.2 2.0 + - - +
282B ARG 3.2 0.4 - - - -
283B SER* 1.3 83.6 + - - +
285B GLY* 1.3 62.7 + - - +
286B ILE* 3.2 36.8 + - + +
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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) + - + + + + + -
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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