Contacts of the helix formed by residues 258 - 276 (chain K) in PDB entry 6X5A
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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K PHE 2.5 23.6 + - - +
252K LEU 3.3 0.4 - - - -
253K GLU* 2.7 50.6 + - - +
256K VAL 3.4 0.6 + - - -
257K LEU* 1.3 69.2 - - - +
259K ALA* 1.3 65.2 + - - +
260K THR* 3.2 4.9 - - - -
261K LYS* 4.1 16.1 - - - -
262K MET* 3.1 20.4 + - - +
361K GLU* 3.7 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257K LEU* 3.2 7.0 + - - -
258K SER* 1.3 73.1 - - - +
260K THR* 1.3 57.0 + - - +
262K MET* 4.7 3.8 - - - -
263K LEU* 2.8 46.8 + - + +
349K PRO* 5.2 1.3 - - + -
360K GLY 3.1 30.7 - - - +
361K GLU* 4.1 5.6 - - - +
363K TRP* 3.5 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253K GLU* 5.0 4.3 + - - -
258K SER* 4.3 4.3 - - - -
259K ALA* 1.3 77.0 - - - +
261K LYS* 1.3 66.2 + - - +
263K LEU* 3.4 7.3 + - - +
264K SER* 2.9 29.7 + - - -
359K GLN 3.5 25.4 - - - +
360K GLY* 4.0 10.1 - - - -
361K GLU* 4.0 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250K HIS* 3.2 27.9 + - + +
251K PHE* 4.1 9.8 - - + -
252K LEU 3.7 18.8 + - - -
253K GLU* 4.7 10.0 - - - +
258K SER* 3.3 21.9 + - - +
260K THR* 1.3 81.9 + - - +
262K MET* 1.3 63.6 + - - +
264K SER* 3.0 13.2 + - - +
265K LYS* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 262 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188K GLU* 5.5 1.1 - - + +
189K PHE* 3.6 28.4 - - + -
218K LEU* 3.9 17.5 - - + -
248K LEU* 3.5 30.1 - - + -
251K PHE* 3.4 42.8 - - + -
257K LEU* 4.4 16.6 - - + -
258K SER 3.1 15.4 + - - +
259K ALA* 4.0 4.7 - - - +
261K LYS* 1.3 77.9 - - - +
263K LEU* 1.3 58.9 + - + +
265K LYS* 3.2 2.4 + - - +
266K PHE* 2.8 28.6 + - + +
310K LEU* 5.9 4.5 - - + -
312K LEU* 5.6 8.1 - - + -
363K TRP* 5.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259K ALA* 2.8 37.2 + - + +
260K THR* 3.8 6.1 - - - +
262K MET* 1.3 72.3 - - + +
264K SER* 1.3 57.6 + - - +
266K PHE* 3.7 6.1 - - + +
267K ARG* 2.8 31.1 + - - +
292K PRO* 3.5 35.9 - - + +
294K VAL* 5.4 1.8 - - + +
310K LEU* 3.5 29.6 - - + -
349K PRO* 3.7 28.7 - - + -
360K GLY* 5.5 2.9 - - - +
363K TRP* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 264 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260K THR 2.9 18.1 + - - -
261K LYS* 3.0 15.3 + - - +
263K LEU* 1.3 75.9 - - - +
265K LYS* 1.3 61.3 + - - +
267K ARG* 3.4 7.8 + - - +
268K LYS* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K SER* 5.6 7.5 - - - -
188K GLU* 5.1 7.7 + - + +
189K PHE* 4.9 6.3 - - + -
250K HIS* 4.8 13.0 + - - -
251K PHE* 3.6 36.7 - - + -
261K LYS 3.0 4.5 + - - +
262K MET 3.2 2.0 + - - +
264K SER* 1.3 80.9 + - - +
266K PHE* 1.3 58.3 - - - +
268K LYS* 3.3 31.0 + - - +
269K ILE* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178K LEU* 6.3 0.2 - - + -
182K MET* 6.5 1.1 - - - -
189K PHE* 3.3 38.2 - + + -
192K VAL* 4.8 13.0 - - + -
216K PHE* 4.5 7.2 - + - -
218K LEU* 6.4 1.1 - - + -
262K MET 2.8 16.9 + - - +
263K LEU* 3.7 5.8 - - + +
264K SER 3.4 0.2 - - - -
265K LYS* 1.3 73.8 - - - +
267K ARG* 1.3 68.1 + - - +
269K ILE* 3.1 3.6 - - + +
270K ILE* 2.9 47.9 + - + +
294K VAL* 4.0 27.6 - - + -
308K ILE* 4.2 14.8 - - + -
310K LEU* 3.3 50.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263K LEU 2.8 21.5 + - - +
264K SER* 3.7 7.6 - - - +
266K PHE* 1.3 72.3 - - - +
268K LYS* 1.3 65.0 + - - +
270K ILE* 3.1 10.3 - - + +
271K LYS* 2.9 51.5 + - - +
284K VAL* 4.7 4.8 - - + +
285K GLU 4.0 4.8 + - - -
286K LYS* 3.1 65.0 - - - +
287K GLU* 5.1 2.2 + - - +
291K SER 5.1 1.2 + - - -
292K PRO* 4.9 3.2 - - - +
293K ALA 3.0 30.1 + - - +
294K VAL* 3.4 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K ARG* 5.1 4.9 - - - +
264K SER 3.0 18.3 + - - +
265K LYS* 3.6 36.7 - - - +
267K ARG* 1.3 76.9 - - - +
269K ILE* 1.3 65.1 + - - +
271K LYS* 3.0 28.8 - - + +
272K GLU* 3.0 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K ARG* 3.3 25.4 - - - +
187K SER* 3.1 33.0 - - - +
189K PHE* 3.5 28.7 - - + -
265K LYS* 2.9 22.8 + - + +
266K PHE* 3.1 13.9 - - + +
268K LYS* 1.3 83.4 - - - +
270K ILE* 1.3 66.7 + - - +
272K GLU* 3.1 20.2 - - - +
273K GLU* 2.8 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178K LEU* 4.3 22.0 - - + -
182K MET* 5.3 2.0 - - - -
266K PHE* 2.9 46.8 + - + +
267K ARG* 3.1 14.4 - - + +
269K ILE* 1.3 74.0 - - + +
271K LYS* 1.3 68.6 + - + +
273K GLU* 3.2 9.7 + - - +
274K VAL* 3.0 42.2 + - + +
294K VAL* 3.7 22.4 - - + -
296K LEU* 5.1 4.5 - - + -
308K ILE* 3.7 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267K ARG* 2.9 51.7 + - - +
268K LYS* 3.0 26.0 - - + +
270K ILE* 1.3 77.8 - - + +
272K GLU* 1.3 59.3 + - + +
274K VAL* 3.5 2.1 + - - -
275K LYS* 2.9 37.8 + - + +
284K VAL* 3.6 40.6 - - + -
286K LYS* 4.7 13.3 - - - +
296K LEU* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 272 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K ARG* 3.2 28.3 + - - -
268K LYS* 3.0 35.3 + - - +
269K ILE* 3.1 40.3 - - - +
271K LYS* 1.3 79.8 - - + +
273K GLU* 1.3 58.2 + - + +
275K LYS* 3.1 9.7 + - - +
276K GLU* 3.0 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181K ARG* 5.2 1.5 - - + -
182K MET* 3.1 51.0 - - + +
185K ARG* 3.1 33.2 - - + +
187K SER* 5.3 0.2 + - - -
269K ILE* 2.8 48.8 + - - +
270K ILE* 3.5 5.5 + - - +
272K GLU* 1.3 78.3 - - + +
274K VAL* 1.3 64.8 + - + +
276K GLU* 3.1 29.1 + - - +
277K ILE* 3.2 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 274 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174K VAL* 5.3 2.5 - - + -
177K ARG* 5.1 8.3 - - - +
178K LEU* 3.6 31.6 - - + -
270K ILE* 3.0 22.1 + - + +
271K LYS 4.1 2.2 - - - +
273K GLU* 1.3 77.5 - - + +
275K LYS* 1.3 66.4 + - - +
276K GLU 3.3 0.2 + - - -
277K ILE* 3.3 19.6 - - - +
278K LYS* 5.4 1.2 - - - +
282K VAL* 3.6 46.2 - - + +
296K LEU* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271K LYS* 2.9 27.0 + - + +
272K GLU* 3.1 11.9 + - - +
274K VAL* 1.3 84.2 - - - +
276K GLU* 1.3 58.4 + - - +
277K ILE 3.4 2.4 + - - -
278K LYS* 5.5 11.0 - - + +
282K VAL 4.0 6.0 + - - +
283K SER* 3.2 28.4 - - - +
284K VAL* 2.9 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K ARG* 4.6 5.7 + - - -
272K GLU* 3.0 27.3 + - + +
273K GLU* 3.1 39.2 + - - +
275K LYS* 1.3 77.8 - - - +
277K ILE* 1.3 70.7 + - + +
----------------------------------------------------------
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