Contacts of the helix formed by residues 263 - 280 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ILE* 3.5 33.4 - - + +
202A VAL* 3.6 24.2 - - + +
204A LYS* 4.4 23.2 + - + +
207A LEU* 4.9 10.2 - - - +
262A TYR* 1.3 74.9 - - - +
264A SER* 1.3 75.6 + - - +
265A ASP 3.1 0.9 - - - -
266A ILE* 3.0 26.8 + - + +
267A LEU* 3.1 36.1 + - + +
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.2 38.4 + - - +
263A TYR* 1.3 82.7 - - - +
265A ASP* 1.3 54.9 + - - +
267A LEU* 3.7 9.8 - - - +
268A THR* 2.4 41.2 + - - -
301A ASN* 5.6 0.2 - - - -
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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
----------------------------------------------------------
262A TYR* 3.4 37.4 - - + +
263A TYR 3.1 0.2 - - - -
264A SER* 1.3 78.4 - - - +
266A ILE* 1.3 59.1 + - + +
268A THR* 3.3 2.4 + - - -
269A VAL* 2.9 35.3 + - - +
298A ALA* 5.3 0.2 - - - +
300A ARG* 6.2 0.2 - - - -
301A ASN* 2.8 44.2 + - - +
304A ARG* 3.8 15.4 + - - +
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Residues in contact with ILE 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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120A PHE* 5.5 10.1 - - + -
240A SER* 4.6 3.1 + - - +
243A ALA* 3.8 18.4 - - + +
244A ALA* 4.0 34.5 - - + +
247A SER* 4.5 20.6 - - - +
262A TYR* 3.3 15.7 + - + +
263A TYR* 3.0 28.3 + - + +
265A ASP* 1.3 76.7 - - + +
267A LEU* 1.3 76.2 + - + +
269A VAL* 4.1 4.8 - - - +
270A GLY* 2.9 25.6 + - - -
304A ARG* 6.1 1.6 - - - +
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Residues in contact with LEU 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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194A MET* 3.7 28.9 - - + +
197A ILE* 3.8 14.4 - - + -
198A LEU* 3.7 40.8 - - + +
240A SER* 3.9 16.7 + - - +
263A TYR* 3.1 51.5 + - + +
264A SER* 3.7 9.4 - - - +
266A ILE* 1.3 91.2 - - + +
268A THR* 1.3 55.7 + - - +
270A GLY* 3.3 1.9 + - - -
271A CYS* 3.0 27.2 + - - +
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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
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198A LEU* 5.0 9.3 - - - +
264A SER* 2.4 29.9 + - - -
265A ASP* 3.7 5.8 - - - -
267A LEU* 1.3 73.0 - - - +
269A VAL* 1.3 63.3 + - + +
271A CYS* 3.2 4.2 + - - +
272A ALA* 3.0 9.9 + - - +
289A SER* 2.7 46.8 + - - +
290A ILE* 5.5 0.2 - - - -
293A THR* 5.1 6.2 + - - +
294A SER* 5.2 4.6 + - - +
297A PHE* 3.6 35.2 - - + -
301A ASN* 5.2 3.4 + - + +
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.7 28.7 - - + -
124A LEU* 4.7 5.8 - - + -
265A ASP 2.9 22.3 + - - +
266A ILE* 4.1 4.7 - - - +
268A THR* 1.3 75.3 - - + +
270A GLY* 1.3 59.0 + - - +
272A ALA* 3.3 6.6 + - - +
273A VAL* 2.9 39.7 + - + +
301A ASN* 4.3 13.5 - - + +
304A ARG* 4.3 16.4 - - + +
305A GLY* 4.2 24.9 - - - +
308A ALA* 4.3 0.2 - - + -
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Residues in contact with GLY 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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124A LEU* 5.6 1.6 - - - -
236A VAL 4.3 1.0 - - - +
239A ALA* 3.3 31.7 - - - +
240A SER* 4.2 8.3 - - - -
243A ALA* 4.4 5.7 - - - +
266A ILE 2.9 16.2 + - - -
267A LEU 3.7 3.4 - - - -
269A VAL* 1.3 77.2 - - - +
271A CYS* 1.3 56.6 + - - +
273A VAL* 3.9 4.2 - - - -
274A GLY* 2.9 23.4 + - - -
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Residues in contact with CYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 5.5 3.1 - - - -
194A MET* 4.2 10.7 - - + +
198A LEU* 6.3 0.4 - - + -
236A VAL* 3.8 28.7 - - + +
267A LEU 3.0 13.3 + - - +
268A THR* 3.2 11.0 + - - +
270A GLY* 1.3 76.4 - - - +
272A ALA* 1.3 61.6 + - - +
274A GLY* 3.3 1.7 + - - -
275A VAL* 3.1 25.6 + - - +
288A PHE* 4.1 16.8 - - - -
289A SER* 3.6 26.5 - - - +
293A THR* 4.9 12.3 - - + +
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Residues in contact with ALA 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 THR 3.0 10.2 + - - +
269A VAL* 3.6 9.6 - - - +
271A CYS* 1.3 77.5 - - - +
273A VAL* 1.3 62.1 + - + +
275A VAL* 3.4 2.4 + - - +
276A GLY* 3.0 22.7 + - - -
285A GLY* 3.8 13.9 - - - +
286A VAL* 4.3 18.4 - - + -
289A SER* 3.5 23.5 + - - -
305A GLY* 4.4 11.9 - - - +
309A ALA* 4.4 4.7 - - + +
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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
----------------------------------------------------------
124A LEU* 4.3 12.8 - - + -
125A GLY* 4.8 4.7 - - - -
128A MET* 3.7 31.4 - - + -
239A ALA* 5.2 0.2 - - + -
269A VAL* 2.9 26.4 + - + +
270A GLY* 4.0 5.4 - - - +
272A ALA* 1.3 75.5 - - + +
274A GLY* 1.3 56.5 + - - +
277A CYS* 2.8 34.9 + - - +
308A ALA* 3.6 34.8 - - + -
309A ALA* 4.5 5.2 - - - +
312A SER* 3.6 20.3 - - - +
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Residues in contact with GLY 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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235A PHE* 3.1 29.1 - - - -
236A VAL* 4.2 9.4 - - - -
239A ALA* 3.7 11.6 - - - +
270A GLY 2.9 18.7 + - - -
271A CYS 3.7 1.3 - - - -
272A ALA 3.2 0.4 - - - -
273A VAL* 1.3 76.8 - - - +
275A VAL* 1.3 57.1 + - - +
278A CYS* 2.9 25.0 + - - -
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A GLU* 5.1 9.0 - - + -
236A VAL* 4.0 7.1 - - + +
271A CYS 3.1 18.7 + - - +
272A ALA 3.6 5.4 - - - +
274A GLY* 1.3 74.7 - - - +
276A GLY* 1.3 65.8 + - - +
278A CYS* 3.2 9.5 + - + +
279A PHE* 3.1 25.7 + - + +
281A THR* 4.1 6.5 + - - +
285A GLY* 3.6 25.1 - - - +
288A PHE* 3.7 37.5 - - + -
289A SER 5.1 0.2 - - - +
545A ILE* 5.0 17.9 - - + -
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Residues in contact with GLY 276 (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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272A ALA 3.0 16.2 + - - -
273A VAL 3.8 0.4 - - - -
275A VAL* 1.3 78.9 - - - +
277A CYS* 1.3 57.3 + - - +
280A GLY* 3.0 27.1 + - - -
281A THR 3.4 26.2 + - - -
282A PRO* 4.8 2.9 - - - -
285A GLY* 4.2 2.0 - - - -
309A ALA* 5.1 5.2 - - - -
312A SER* 5.0 2.5 - - - -
313A ALA* 4.0 11.8 - - - +
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Residues in contact with CYS 277 (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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128A MET* 3.3 45.1 - - + -
129A ALA* 3.6 14.8 - - - -
132A SER* 3.2 20.1 + - - -
235A PHE* 3.7 11.0 - - + -
273A VAL 2.8 21.2 + - - +
276A GLY* 1.3 74.2 - - - +
278A CYS* 1.3 66.1 + - - +
279A PHE 3.4 0.2 - - - -
280A GLY 4.5 0.9 - - - +
312A SER* 4.3 15.3 - - - -
316A PHE* 4.3 11.9 - - - -
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Residues in contact with CYS 278 (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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132A SER* 4.7 0.2 - - - -
231A LYS* 3.8 28.4 + - - +
232A GLU* 3.6 32.3 - - + -
235A PHE* 3.5 21.5 - - - -
274A GLY 2.9 23.9 + - - -
275A VAL* 3.3 10.1 - - - +
277A CYS* 1.3 80.0 - - - +
279A PHE* 1.3 86.0 + - + +
280A GLY 3.9 0.2 + - - -
316A PHE* 4.4 11.3 - - - -
332A LEU* 5.5 1.0 - - - +
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Residues in contact with PHE 279 (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 LYS* 4.6 15.0 - - + -
232A GLU* 5.0 9.0 - - + -
275A VAL* 3.1 10.7 + - + +
278A CYS* 1.3 100.3 - - + +
280A GLY* 1.3 64.3 + - - +
281A THR* 3.3 16.9 - - + +
316A PHE* 5.4 0.7 - - - -
331A ALA* 5.7 1.2 - - - +
332A LEU* 3.9 17.3 - - + +
421A ARG* 5.6 4.3 - - - -
484A PHE* 3.5 32.5 - + - -
485A MET* 3.5 32.8 - - + -
545A ILE* 4.2 18.4 - - + -
549A LEU* 3.3 45.0 - - + +
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Residues in contact with GLY 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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276A GLY 3.0 12.9 + - - -
277A CYS 4.5 1.6 + - - -
278A CYS 3.6 1.8 + - - -
279A PHE* 1.3 77.4 - - - +
281A THR* 1.3 60.2 + - - +
282A PRO* 3.4 9.0 - - - +
313A ALA* 3.5 25.9 - - - +
316A PHE* 4.9 11.9 - - - -
317A ARG* 5.5 5.6 - - - +
331A ALA* 6.0 2.6 - - - +
332A LEU* 5.7 0.7 - - - -
548A GLU* 3.9 5.4 - - - +
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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