Contacts of the helix formed by residues 256 - 277 (chain A) in PDB entry 6WCZ
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 GLU 256 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 1.3 97.7 - - - +
257A GLN* 1.3 57.3 + - - +
258A LEU 3.2 0.7 - - - -
259A GLU* 3.2 26.5 - - - +
260A THR* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN* 6.2 0.4 - - - +
142A GLN* 3.4 45.9 + - - +
255A LEU* 4.2 11.8 + - + +
256A GLU* 1.3 76.0 - - - +
258A LEU* 1.3 69.2 + - + +
260A THR* 2.4 25.9 + - - -
261A TRP* 2.9 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 5.2 2.2 - - + -
234A LYS* 5.0 11.0 - - + +
235A LEU* 4.0 33.4 - - + -
238A TRP* 3.6 35.7 - - + -
255A LEU 3.4 16.2 + - - +
256A GLU 3.2 0.2 - - - -
257A GLN* 1.3 85.1 - - + +
259A GLU* 1.3 60.1 + - - +
261A TRP* 3.5 32.9 - - + +
262A PHE* 2.9 36.6 + - + -
347A LEU* 5.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU 3.4 6.2 + - - +
256A GLU* 3.2 36.6 + - - +
258A LEU* 1.3 76.8 - - - +
260A THR* 1.3 51.8 - - - +
262A PHE* 3.8 1.9 - - - +
263A THR* 2.2 36.6 + - - -
345A ARG* 2.5 51.8 + - - +
347A LEU* 3.9 13.3 - - + +
349A ARG* 3.0 38.1 + - + +
394A GLN 4.8 1.0 - - - +
395A GLY* 4.2 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 5.2 1.6 + - - -
256A GLU* 2.9 16.6 + - + +
257A GLN* 2.4 33.2 + - - -
259A GLU* 1.3 76.3 - - - +
261A TRP* 1.3 67.3 + - - +
263A THR* 3.2 9.2 - - - -
264A ALA* 2.9 29.5 + - - +
349A ARG* 4.8 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN 4.5 0.7 - - - -
142A GLN* 3.5 40.4 - - + -
145A ILE* 3.5 36.8 - - + -
146A GLU* 3.3 29.2 + - + +
149A ILE* 5.1 14.1 - - + +
231A LEU* 3.8 25.8 - - + +
234A LYS* 5.8 6.1 - - + -
257A GLN* 2.9 44.4 + - + +
258A LEU* 3.3 25.5 + - + +
259A GLU 3.2 0.2 - - - -
260A THR* 1.3 86.9 + - - +
262A PHE* 1.3 66.5 + - + +
264A ALA* 4.6 3.1 - - + +
265A GLY* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 3.6 27.6 - - + -
235A LEU* 3.5 34.1 - - + -
258A LEU* 2.9 16.7 + - + +
261A TRP* 1.3 81.2 - - + +
263A THR* 1.3 60.1 + - - +
265A GLY* 3.7 2.2 - - - +
266A ALA* 3.0 30.8 + - - +
311A LEU* 4.7 16.8 - - + -
315A ALA* 3.6 24.0 - - + -
347A LEU* 3.2 52.9 - - + +
348A VAL* 3.5 27.1 - - + +
349A ARG 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU 2.2 29.8 + - - -
260A THR* 3.2 12.4 - - - -
262A PHE* 1.3 77.3 - - - +
264A ALA* 1.3 59.0 + - - +
267A LYS* 3.0 46.9 + - + +
349A ARG* 3.2 41.5 + - + +
350A LEU* 3.3 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 3.7 29.6 - - + -
153A ARG* 4.1 19.1 - - - +
260A THR 2.9 17.5 + - - +
261A TRP* 4.6 1.6 - - + +
263A THR* 1.3 71.4 - - - +
265A GLY* 1.3 60.2 + - - +
267A LYS* 4.2 9.2 - - - -
268A LEU* 2.9 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 4.5 5.8 - - - +
227A LEU* 6.0 6.1 - - - -
228A ILE* 6.0 3.1 - - - -
261A TRP 2.9 22.3 + - - -
262A PHE* 4.0 2.2 - - - -
264A ALA* 1.3 77.9 - - - +
266A ALA* 1.3 57.4 + - - +
268A LEU* 3.3 2.1 + - - -
269A LEU* 3.0 39.4 + - - +
311A LEU* 6.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 3.0 17.9 + - - +
265A GLY* 1.3 73.6 - - - +
267A LYS* 1.3 60.7 + - - +
269A LEU* 4.3 5.4 - - - +
270A PHE* 2.9 49.2 + - + +
308A LEU* 6.1 0.2 - - + -
311A LEU* 5.7 7.4 - - + +
312A LEU* 6.0 1.6 - - + -
348A VAL* 3.7 16.6 - - + -
350A LEU* 3.6 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 5.2 14.6 - - - +
263A THR* 3.0 35.9 + - + +
264A ALA* 3.8 7.2 - - - +
266A ALA* 1.3 77.0 - - - +
268A LEU* 1.3 60.7 + - + +
270A PHE* 5.0 0.7 - - - -
271A HIS* 2.8 34.1 + - - +
350A LEU* 3.7 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 4.0 22.2 - - + +
152A LEU* 3.7 50.3 - - + +
153A ARG* 4.6 15.3 - - + +
156A MET* 4.2 27.3 - - + +
224A LEU* 5.6 1.1 - - + -
264A ALA* 2.9 23.7 + - + +
265A GLY* 3.8 3.6 - - - +
267A LYS* 1.3 79.7 - - + +
269A LEU* 1.3 61.0 + - + +
271A HIS* 3.8 5.8 - - + +
272A LEU* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 5.3 2.2 - - + -
224A LEU* 3.6 34.8 - - + -
227A LEU* 6.3 0.4 - - + -
228A ILE* 4.6 17.9 - - + -
265A GLY* 3.0 28.5 + - - +
266A ALA* 4.2 5.2 - - - +
268A LEU* 1.3 79.0 - - + +
270A PHE* 1.3 60.2 + - - +
272A LEU* 3.4 6.3 + - + +
273A ARG* 2.9 28.8 + - - +
304A VAL* 4.8 18.8 - - + +
307A LEU* 4.0 22.2 - - + -
308A LEU* 4.5 26.2 - - + +
311A LEU* 6.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ALA* 2.9 38.8 + - + +
267A LYS* 4.4 1.1 - - - +
269A LEU* 1.3 76.7 - - - +
271A HIS* 1.3 57.8 + - - +
273A ARG* 3.9 6.7 - - - +
274A GLN 2.9 19.6 + - - -
308A LEU* 3.6 29.8 - - + -
312A LEU* 4.6 15.9 - - + -
350A LEU* 3.6 13.9 - - + -
437A TYR* 4.6 7.9 - + - -
439A TYR* 3.2 55.0 - + + -
440A GLN* 2.8 51.3 + - + +
442A LEU* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A MET* 3.4 37.7 - - + +
157A GLU* 4.4 9.8 + - - -
160A VAL* 3.7 28.5 - - + +
267A LYS 2.8 22.7 + - - +
268A LEU* 3.8 7.2 - - + +
270A PHE* 1.3 75.8 - - - +
272A LEU* 1.3 59.6 + - - +
274A GLN* 3.4 4.0 + - - +
275A LEU* 2.9 33.8 + - + +
440A GLN* 4.6 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A MET* 3.7 26.2 - - + -
159A LEU* 6.0 3.4 - - + -
220A LEU* 3.7 40.4 - - + -
221A LEU* 4.3 18.8 - - + -
224A LEU* 4.8 14.1 - - + -
268A LEU 3.0 17.5 + - - +
269A LEU* 3.9 7.0 - - + +
271A HIS* 1.3 75.0 - - - +
273A ARG* 1.3 60.5 + - - +
275A LEU* 3.9 2.2 - - + +
276A LEU* 2.9 43.1 + - + +
304A VAL* 4.5 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU 2.9 18.6 + - - +
270A PHE* 3.3 17.7 - - - +
272A LEU* 1.3 77.7 - - - +
274A GLN* 1.3 55.6 + - - +
276A LEU* 2.7 27.0 + - - +
277A LYS* 2.9 39.4 + - + +
301A ASN* 4.3 11.2 + - - +
304A VAL* 5.2 12.6 - - + +
305A THR* 3.1 32.7 + - - +
308A LEU* 3.9 11.8 - - + +
440A GLN* 3.5 16.0 + - - -
442A LEU* 3.5 42.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE 2.9 19.3 + - - +
271A HIS* 4.0 5.2 - - - +
273A ARG* 1.3 72.8 - - - +
275A LEU* 1.3 61.6 + - - +
277A LYS* 2.9 35.9 + - - +
278A GLU* 3.1 41.7 + - - +
440A GLN* 3.5 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A MET* 4.0 9.9 - - + -
159A LEU* 3.7 29.6 - - + -
160A VAL* 3.8 32.3 - - + -
163A ILE* 4.4 25.6 - - + -
271A HIS* 2.9 24.5 + - + +
272A LEU* 3.9 4.9 - - + +
274A GLN* 1.3 76.5 - - - +
276A LEU* 1.3 63.5 + - + +
277A LYS 3.3 0.5 + - - -
278A GLU* 3.5 12.4 + - - +
279A LEU* 3.7 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 6.4 2.2 - - + -
214A LEU* 6.3 1.8 - - + -
217A SER* 5.7 9.2 - - - -
272A LEU* 2.9 29.6 + - + +
273A ARG* 2.7 12.4 + - - +
275A LEU* 1.3 73.7 - - + +
277A LYS* 1.3 62.7 + - - +
278A GLU 3.2 1.3 + - - -
279A LEU* 3.6 27.2 + - + +
296A GLY 4.5 2.7 - - - +
297A VAL* 3.5 47.8 - - + +
300A ARG* 4.8 7.9 - - + -
301A ASN* 4.2 21.5 + - + +
304A VAL* 5.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 2.9 44.7 + - + +
274A GLN* 2.9 35.7 + - - +
275A LEU 3.2 0.8 - - - -
276A LEU* 1.3 77.8 - - - +
278A GLU* 1.3 79.7 + - - +
279A LEU 3.7 0.4 - - - -
280A LYS* 3.8 18.0 - - - +
297A VAL* 5.5 0.7 - - - -
301A ASN* 5.7 11.4 - - - +
440A GLN* 3.4 36.6 + - - +
----------------------------------------------------------
Back to top of page
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