Contacts of the helix formed by residues 258 - 277 (chain A) in PDB entry 2WO6
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 SER 258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 1.3 73.7 - - - +
259A LEU* 1.3 60.0 + - - +
260A ASN* 3.6 8.0 + - - +
261A LEU* 3.1 23.1 + - - +
262A THR* 2.9 29.8 + - - -
355A HIS* 3.7 0.9 - - - -
438A ARG* 3.2 15.7 - - - +
441A GLU* 4.7 0.9 - - - -
444A HIS* 3.5 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER* 1.3 71.0 - - - +
260A ASN* 1.3 56.8 + - - +
262A THR* 3.1 6.3 + - - -
263A ARG* 2.7 39.0 + - - +
355A HIS* 3.7 20.3 - - + +
443A GLY 3.7 9.2 - - - +
444A HIS* 3.0 23.3 + - + -
448A ASP* 3.4 44.4 - - + +
449A TYR* 4.1 18.2 - - + -
452A PHE* 3.8 33.0 - - + -
478A PHE* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER* 3.3 8.4 - - - +
259A LEU* 1.3 79.1 - - - +
261A LEU* 1.3 61.5 + - - +
263A ARG* 3.0 27.5 + - - +
264A LYS* 3.2 32.9 + - - +
442A SER 5.3 0.6 + - - -
443A GLY* 3.9 29.9 + - - +
444A HIS* 6.0 1.2 - - - -
448A ASP* 5.4 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.7 5.6 - - + -
257A VAL* 3.9 25.4 - - + -
258A SER* 3.1 21.7 + - - +
260A ASN* 1.3 74.3 - - - +
262A THR* 1.3 65.7 + - - +
264A LYS* 3.3 9.0 + - + +
265A PHE* 3.0 50.6 + - + -
301A SER* 3.6 31.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 3.3 17.3 + - - +
258A SER 2.9 16.4 + - - -
259A LEU* 3.4 13.7 - - + -
261A LEU* 1.3 76.9 - - - +
263A ARG* 1.3 56.0 + - - +
265A PHE* 3.3 10.5 + - - +
266A ALA* 2.8 27.4 + - - +
351A LEU* 3.8 32.4 - - + +
354A MET* 4.2 3.1 - - + +
355A HIS* 3.9 10.3 + - + +
452A PHE* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 2.7 24.7 + - - +
260A ASN* 3.0 36.0 + - - +
262A THR* 1.3 72.6 - - - +
264A LYS* 1.3 64.5 + - + +
266A ALA* 3.1 3.2 + - - +
267A GLN* 2.9 20.9 + - + +
448A ASP* 3.6 28.9 + - - +
478A PHE* 2.8 65.1 + - + -
479A PHE* 3.6 21.6 - - + +
480A LYS 5.8 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ASN* 3.2 20.0 + - - +
261A LEU* 3.3 16.0 + - + +
263A ARG* 1.3 76.9 - - + +
265A PHE* 1.3 62.1 + - - +
267A GLN* 3.5 9.6 + - - +
268A GLN* 3.0 39.6 + - - +
301A SER* 3.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 4.2 16.4 - - + -
248A LEU* 3.7 31.6 - - + -
257A VAL* 4.3 4.0 - - + -
261A LEU* 3.0 45.7 + - + -
262A THR* 3.6 10.3 - - - +
264A LYS* 1.3 76.0 - - - +
266A ALA* 1.3 63.2 + - - +
268A GLN* 3.5 1.1 + - - +
269A MET* 3.0 30.0 + - + +
295A LEU* 4.0 11.0 - - + -
301A SER 3.5 25.8 - - - -
303A ILE* 3.6 33.2 - - + +
351A LEU* 4.4 8.5 - - + -
354A MET* 4.1 18.8 - - + -
----------------------------------------------------------
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 THR* 2.8 18.1 + - + +
263A ARG* 3.1 8.5 + - - +
265A PHE* 1.3 77.2 - - - +
267A GLN* 1.3 56.3 + - - +
269A MET* 3.4 3.6 + - - +
270A CYS* 2.9 36.2 + - - -
351A LEU* 3.6 31.8 - - + +
455A LEU* 5.1 2.0 - - + -
478A PHE* 4.5 8.3 - - + -
479A PHE* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ARG* 2.9 11.8 + - + +
264A LYS* 4.0 9.7 + - - +
265A PHE 3.3 0.4 - - - -
266A ALA* 1.3 76.1 - - - +
268A GLN* 1.3 55.6 + - + +
270A CYS 3.6 0.2 + - - -
271A THR* 2.7 38.7 + - - +
474A LEU* 3.7 20.3 - - + +
479A PHE* 3.6 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 3.5 42.8 - - + +
264A LYS* 3.0 30.4 + - - +
265A PHE 3.9 3.7 - - - +
267A GLN* 1.3 79.8 - - + +
269A MET* 1.3 56.6 + - - +
271A THR* 3.3 5.5 + - - -
272A ALA* 2.9 27.5 + - - +
301A SER* 3.0 26.0 + - - -
302A ALA* 3.3 8.5 - - - +
303A ILE* 2.8 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 5.8 0.9 - - - +
265A PHE* 3.0 23.2 + - + +
266A ALA 3.9 1.8 - - - +
268A GLN* 1.3 74.4 - - - +
270A CYS* 1.3 59.6 + - - +
272A ALA* 3.3 3.0 + - - +
273A LEU* 2.8 36.9 + - + +
288A LEU* 4.0 21.1 - - + -
293A ILE* 3.5 30.3 - - + -
303A ILE* 3.8 20.9 - - + +
304A LYS* 6.1 0.2 - - - -
305A ILE* 3.5 40.2 - - + -
347A LEU* 3.6 29.8 - - + -
351A LEU* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ALA 2.9 23.4 + - - +
269A MET* 1.3 74.9 - - - +
271A THR* 1.3 57.9 + - - +
273A LEU* 3.2 7.2 + - - +
274A LEU* 2.8 25.5 + - - +
344A MET* 4.8 3.1 - - - -
347A LEU* 3.8 6.5 - - - -
459A MET* 3.7 23.1 - - - -
470A PRO* 3.5 11.6 - - + +
473A ALA* 3.7 26.5 - - + -
474A LEU* 3.5 26.9 - - + -
479A PHE* 4.5 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A MET* 3.6 27.3 - - + +
220A TYR* 3.6 28.3 - - + -
267A GLN* 2.7 26.7 + - - +
268A GLN* 3.5 5.8 - - - -
269A MET 3.2 0.2 - - - -
270A CYS* 1.3 72.2 - - - +
272A ALA* 1.3 59.2 + - - +
274A LEU* 3.2 8.0 + - + +
275A PHE* 2.9 27.5 + - - +
474A LEU* 3.7 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A MET 4.8 0.9 - - - -
220A TYR* 3.8 22.1 - - + +
221A ILE* 4.0 8.9 - - + +
268A GLN 2.9 19.7 + - - +
269A MET* 3.6 6.1 - - - +
271A THR* 1.3 71.3 - - - +
273A LEU* 1.3 59.6 + - - +
275A PHE* 3.1 9.0 + - - +
276A LEU* 2.9 31.7 + - - +
305A ILE* 3.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A MET* 2.8 25.9 + - + +
270A CYS* 3.6 4.5 - - - +
272A ALA* 1.3 73.8 - - - +
274A LEU* 1.3 62.8 + - - +
276A LEU* 3.5 22.5 + - + +
277A ALA* 3.1 23.7 + - - +
288A LEU* 4.2 13.2 - - + -
305A ILE* 4.6 6.7 - - + -
340A LEU* 5.2 1.4 - - - +
343A ASP* 4.1 23.1 - - + +
344A MET* 4.0 34.1 - - + +
347A LEU* 4.0 23.8 - - + -
470A PRO* 3.7 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A MET* 3.7 24.7 - - + +
270A CYS 2.8 14.0 + - - +
271A THR* 3.2 10.1 + - - +
273A LEU* 1.3 73.1 - - - +
275A PHE* 1.3 66.4 + - - +
277A ALA* 3.2 14.0 + - + +
278A THR* 3.4 9.5 + - - -
470A PRO* 3.4 10.0 - - + +
471A TYR* 3.9 41.1 - - + +
474A LEU* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 3.7 38.1 - - + -
213A HIS* 3.7 13.5 - + + -
215A THR* 3.5 32.5 - - + -
217A MET* 3.9 19.3 - - + +
218A LYS* 3.3 29.8 - - + -
221A ILE* 3.8 22.9 - - + -
271A THR 2.9 13.1 + - - +
272A ALA* 3.1 8.9 + - - +
274A LEU* 1.3 76.4 - - - +
276A LEU* 1.3 63.1 + - + +
278A THR* 2.4 37.5 + - - -
281A LEU* 3.6 20.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
210A MET* 3.9 27.1 - - - -
221A ILE* 4.2 11.7 - - + -
272A ALA 2.9 20.5 + - - +
273A LEU* 3.8 24.2 - - + +
274A LEU 3.4 0.2 - - - -
275A PHE* 1.3 80.7 - - + +
277A ALA* 1.3 56.1 + - - +
278A THR 3.5 0.2 + - - -
281A LEU* 3.8 5.0 - - - +
282A SER* 3.1 10.0 + - - -
283A ILE* 3.0 55.0 + - + +
285A HIS* 4.5 13.5 - - + +
305A ILE* 5.0 4.3 - - + -
308A PHE* 4.1 25.6 - - + -
340A LEU* 4.1 2.9 - - + -
343A ASP* 4.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU 3.1 16.4 + - - +
274A LEU* 3.7 12.3 - - + +
275A PHE 3.1 0.8 - - - -
276A LEU* 1.3 72.5 - - - +
278A THR* 1.3 69.8 + - - +
279A PRO* 3.0 9.2 - - - +
282A SER* 4.5 3.4 + - - -
340A LEU* 3.5 21.9 - - + +
470A PRO* 5.0 10.3 - - + -
----------------------------------------------------------
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