Contacts of the helix formed by residues 263 - 280 (chain B) in PDB entry 6QVC
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 TYR 263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ILE* 3.5 35.4 - - + +
202B VAL* 3.6 25.0 - - + +
203B LEU 5.2 0.2 + - - -
204B LYS* 4.4 21.2 - - + +
207B LEU* 4.9 9.4 - - - +
262B TYR* 1.3 75.5 - - - +
264B SER* 1.3 76.0 + - - +
265B ASP 3.1 1.1 - - - -
266B ILE* 3.0 28.3 + - + +
267B LEU* 3.1 34.6 + - + +
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Residues in contact with SER 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 3.2 38.4 + - - +
263B TYR* 1.3 82.8 - - - +
265B ASP* 1.3 56.5 + - - +
267B LEU* 3.7 9.9 - - - +
268B THR* 2.4 41.9 + - - -
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR* 3.4 36.9 - - + +
263B TYR 3.1 0.2 - - - -
264B SER* 1.3 78.7 - - - +
266B ILE* 1.3 58.1 + - + +
268B THR* 3.3 3.1 + - - -
269B VAL* 2.9 35.5 + - + +
298B ALA* 5.3 0.3 - - - +
300B ARG* 6.2 0.2 - - - -
301B ASN* 2.8 42.5 + - - +
304B ARG* 3.8 15.4 + - - +
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 5.5 10.5 - - + -
240B SER* 4.8 3.4 - - - +
243B ALA* 3.8 17.7 - - + +
244B ALA* 4.0 34.8 - - + +
247B SER* 4.5 20.2 - - - +
262B TYR* 3.3 15.4 + - + +
263B TYR* 3.0 27.5 + - + +
265B ASP* 1.3 77.9 - - + +
267B LEU* 1.3 77.1 + - + +
269B VAL* 3.9 4.8 - - - +
270B GLY* 2.9 25.6 + - - -
304B ARG* 6.1 1.3 - - - +
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Residues in contact with LEU 267 (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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194B MET* 3.7 28.2 - - + +
197B ILE* 3.8 13.7 - - + -
198B LEU* 3.7 41.1 - - + +
240B SER* 3.9 18.0 + - - +
263B TYR* 3.1 52.3 + - + +
264B SER* 3.7 9.0 - - - +
265B ASP 3.3 0.2 - - - -
266B ILE* 1.3 89.6 - - + +
268B THR* 1.3 56.5 + - - +
270B GLY* 3.3 2.1 + - - -
271B CYS* 3.0 28.2 + - - +
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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
----------------------------------------------------------
198B LEU* 5.0 8.9 - - - +
264B SER* 2.4 30.0 + - - -
265B ASP* 3.3 6.4 + - - -
267B LEU* 1.3 73.2 - - - +
269B VAL* 1.3 60.4 + - + +
271B CYS* 3.2 4.6 + - - -
272B ALA* 3.0 14.4 + - - +
289B SER* 2.7 47.4 + - - +
290B ILE* 5.5 0.2 - - - -
293B THR* 5.1 6.8 + - - +
294B SER* 5.2 3.7 + - - +
297B PHE* 3.6 35.4 - - + -
301B ASN* 5.2 3.0 + - + +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 6.3 0.4 - - + -
121B LEU* 3.7 28.3 - - + -
124B LEU* 4.7 5.8 - - + -
265B ASP 2.9 21.1 + - - +
266B ILE* 4.1 5.4 - - - +
268B THR* 1.3 75.3 - - + +
270B GLY* 1.3 59.3 + - - +
272B ALA* 3.3 6.1 + - - +
273B VAL* 2.9 40.4 + - + +
301B ASN* 4.3 13.5 - - + +
304B ARG* 4.3 16.6 - - + +
305B GLY* 4.2 24.9 - - - +
308B ALA* 4.3 0.2 - - + -
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 5.6 2.0 - - - -
236B VAL 4.3 1.5 - - - +
239B ALA* 3.3 30.3 - - - +
240B SER* 4.2 8.7 - - - -
243B ALA* 4.4 5.7 - - - +
266B ILE 2.9 17.3 + - - -
267B LEU 3.7 3.4 - - - -
269B VAL* 1.3 77.0 - - - +
271B CYS* 1.3 55.5 + - - +
273B VAL* 3.5 4.2 + - - -
274B GLY* 2.9 23.9 + - - -
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Residues in contact with CYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ILE* 5.5 2.9 - - - -
194B MET* 4.2 11.1 - - + +
198B LEU* 6.4 0.4 - - + -
236B VAL* 3.8 27.9 - - + +
267B LEU 3.0 14.0 + - - +
268B THR* 3.2 10.7 + - - +
270B GLY* 1.3 76.6 - - - +
272B ALA* 1.3 61.5 + - - +
274B GLY* 3.3 1.0 + - - -
275B VAL* 3.1 25.6 + - - +
288B PHE* 4.1 17.0 - - - -
289B SER* 3.6 26.9 - - - +
293B THR* 4.9 12.6 - - - +
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Residues in contact with ALA 272 (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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268B THR 3.0 10.3 + - - +
269B VAL* 3.3 10.3 + - - +
271B CYS* 1.3 78.2 - - - +
273B VAL* 1.3 62.7 + - + +
274B GLY 3.3 0.2 + - - -
275B VAL* 3.6 1.9 - - - +
276B GLY* 3.0 23.0 + - - -
285B GLY* 3.8 12.7 - - - +
286B VAL* 4.3 18.4 - - + -
289B SER* 3.5 23.0 + - - +
305B GLY* 4.4 12.3 - - - +
309B ALA* 4.4 4.7 - - - +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.3 13.2 - - + -
125B GLY* 4.8 4.5 - - - -
128B MET* 3.7 31.6 - - + -
239B ALA* 5.2 0.7 - - + -
269B VAL* 2.9 26.0 + - + +
270B GLY* 4.0 5.2 - - - +
272B ALA* 1.3 74.7 - - + +
274B GLY* 1.3 57.4 + - - +
276B GLY 3.8 0.2 - - - -
277B CYS* 2.8 35.0 + - - +
308B ALA* 3.6 35.2 - - + -
309B ALA* 4.5 5.8 - - - +
312B SER* 3.6 19.4 - - - +
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 3.1 28.6 - - - -
236B VAL* 4.2 9.9 - - - -
239B ALA* 3.7 11.6 - - - +
270B GLY 2.9 17.6 + - - -
271B CYS 3.7 1.6 - - - -
272B ALA 3.2 0.4 - - - -
273B VAL* 1.3 76.9 - - - +
275B VAL* 1.3 57.2 + - - +
278B CYS* 2.9 24.7 + - - -
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLU* 5.1 9.0 - - + -
236B VAL* 4.0 6.6 - - + +
271B CYS 3.1 18.9 + - - +
272B ALA 3.6 4.9 - - - +
274B GLY* 1.3 74.9 - - - +
276B GLY* 1.3 64.6 + - - +
278B CYS* 3.2 9.2 + - - +
279B PHE* 3.1 27.3 + - + +
281B THR* 4.1 6.5 + - - +
285B GLY* 3.6 25.1 - - - +
288B PHE* 3.7 38.4 - - + -
289B SER 5.1 0.2 - - - +
545B ILE* 5.0 17.3 - - + -
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Residues in contact with GLY 276 (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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272B ALA 3.0 16.9 + - - -
273B VAL* 3.8 1.1 - - - -
275B VAL* 1.3 77.7 - - - +
277B CYS* 1.3 57.1 + - - +
280B GLY* 3.0 26.8 + - - -
281B THR 3.4 26.6 + - - -
282B PRO* 4.8 3.4 - - - -
285B GLY* 4.2 1.7 - - - -
309B ALA* 5.1 5.2 - - - -
312B SER* 5.0 2.2 - - - -
313B ALA* 4.0 11.9 - - - +
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Residues in contact with CYS 277 (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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128B MET* 3.3 46.7 - - + -
129B ALA* 3.6 13.9 - - - -
132B SER* 3.2 19.9 + - - -
235B PHE* 3.7 11.4 - - + -
273B VAL 2.8 20.3 + - - +
276B GLY* 1.3 75.0 - - - +
278B CYS* 1.3 67.4 + - - +
280B GLY* 5.4 0.2 - - - -
312B SER* 4.3 15.0 - - - -
313B ALA* 5.6 0.2 - - - +
316B PHE* 4.3 11.6 - - - -
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Residues in contact with CYS 278 (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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132B SER* 4.7 0.4 - - - -
231B LYS* 3.8 29.1 + - - +
232B GLU* 3.6 32.3 - - + -
235B PHE* 3.5 21.0 - - - -
274B GLY 2.9 24.2 + - - -
275B VAL* 3.3 10.3 - - - +
277B CYS* 1.3 79.0 - - - +
279B PHE* 1.3 85.3 + - + +
280B GLY 3.6 0.4 + - - -
316B PHE* 4.4 11.4 - - - -
332B LEU* 5.5 0.9 - - - +
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Residues in contact with PHE 279 (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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231B LYS* 4.6 15.3 - - + -
232B GLU* 5.0 9.9 - - + -
275B VAL* 3.1 11.8 + - + +
278B CYS* 1.3 99.2 - - + +
280B GLY* 1.3 64.6 + - - +
281B THR* 3.3 17.0 - - + +
316B PHE* 5.4 0.9 - - - -
331B ALA* 5.7 1.2 - - - +
332B LEU* 3.9 17.6 - - + +
421B ARG* 5.6 4.0 - - - -
484B PHE* 3.5 33.2 - + - -
485B MET* 3.5 32.5 - - + -
545B ILE* 4.2 18.6 - - + -
549B LEU* 3.3 44.4 - - + +
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Residues in contact with GLY 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLY 3.0 13.3 + - - -
277B CYS 4.5 1.4 + - - -
278B CYS 3.6 2.2 + - - -
279B PHE* 1.3 77.3 - - - +
281B THR* 1.3 60.0 + - - +
282B PRO* 3.4 8.7 - - - +
313B ALA* 3.5 26.8 - - - +
316B PHE* 4.9 11.2 - - - -
317B ARG* 5.5 6.6 - - - +
331B ALA* 6.0 2.1 - - - +
332B LEU* 5.7 0.2 - - - -
548B GLU* 3.9 5.5 - - - +
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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
------------------------------------------------------------
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