Contacts of the helix formed by residues 260 - 275 (chain C) in PDB entry 6XHU
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 ALA 260 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C TYR* 3.7 0.2 + - - -
254C SER* 3.6 8.1 - - - -
258C GLY 4.1 2.6 + - - -
259C ILE* 1.3 76.5 - - - +
261C VAL* 1.3 66.9 + - - +
262C LEU* 4.4 3.6 - - + +
263C ASP* 2.9 35.2 + - - +
264C MET 2.9 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU* 4.8 2.2 - - + -
209C TYR* 3.3 18.3 + - + +
242C LEU* 4.9 0.7 - - + -
247C VAL* 4.1 42.4 - - + +
250C LEU* 4.0 41.3 - - + +
251C GLY* 4.9 1.1 - - - +
254C SER* 4.0 13.6 + - - +
259C ILE 3.6 0.2 + - - -
260C ALA* 1.3 70.8 - - - +
262C LEU* 1.3 59.7 + - + +
264C MET* 2.9 5.4 + - + +
265C CYS* 2.8 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C THR* 4.1 6.0 + - - +
225C THR* 3.7 22.6 - - - +
226C THR* 4.2 6.7 - - - -
227C LEU* 3.9 43.3 - - + +
247C VAL* 5.6 5.8 - - + -
260C ALA* 3.3 4.6 - - + +
261C VAL* 1.3 80.6 - - + +
263C ASP* 1.3 63.3 + - - +
265C CYS* 3.3 14.7 + - + +
266C ALA* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ASN* 4.7 2.7 - - - +
223C PHE 4.0 6.9 - - - +
224C THR* 3.0 28.3 + - - -
259C ILE* 4.1 12.0 - - + -
260C ALA* 2.9 26.1 + - - +
262C LEU* 1.3 76.0 - - - +
264C MET* 1.3 67.2 + - - +
266C ALA* 3.1 14.1 + - - +
267C SER* 3.2 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU* 3.9 19.1 - - + -
208C LEU* 3.9 28.3 - - + +
209C TYR* 3.8 52.3 - - + +
212C VAL* 3.9 25.1 - - + -
219C PHE* 4.1 11.4 - - - -
220C LEU* 4.1 14.1 - - + -
259C ILE* 4.1 10.2 - - + +
260C ALA 2.9 7.4 + - - +
261C VAL* 3.4 8.7 - - + +
263C ASP* 1.3 76.2 - - - +
265C CYS* 1.3 63.2 + - - +
267C SER* 3.1 11.4 + - - -
268C LEU* 3.0 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU* 4.1 19.3 - - - +
225C THR* 4.2 7.2 - - + -
227C LEU* 5.2 0.7 - - - -
230C PHE* 3.5 30.7 - - + -
242C LEU* 3.7 30.7 - - - -
261C VAL* 2.8 20.8 + - - -
262C LEU* 3.4 23.1 - - + +
264C MET* 1.3 77.3 - - - +
266C ALA* 1.3 57.2 + - - +
268C LEU* 3.2 3.4 + - - +
269C LYS 2.8 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ASN* 3.5 13.3 + - - +
223C PHE* 3.9 11.6 - - + +
224C THR* 3.5 41.5 - - - +
225C THR* 3.8 9.3 - - + +
262C LEU 3.1 9.1 + - - +
263C ASP 3.1 8.0 + - - +
265C CYS* 1.3 72.8 - - - +
267C SER* 1.3 65.6 + - - +
269C LYS* 3.5 9.1 + - + +
270C GLU* 3.2 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C LEU* 5.5 0.7 - - - -
219C PHE* 3.4 38.8 + - - +
220C LEU* 3.7 10.4 - - - +
221C ASN* 3.5 22.6 + - - +
263C ASP 3.2 9.3 + - - -
264C MET* 3.1 15.0 + - - -
266C ALA* 1.3 77.1 - - - +
268C LEU* 1.3 65.1 + - - +
270C GLU* 3.1 4.9 + - - +
271C LEU* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C THR* 4.1 12.3 - - + -
204C VAL* 4.1 22.9 - - + -
205C LEU* 3.9 17.0 - - + -
208C LEU* 4.2 13.0 - - + +
230C PHE* 3.7 26.9 - - + -
239C TYR* 4.4 6.3 - - + -
264C MET 3.0 12.0 + - - +
265C CYS* 3.2 10.3 + - - +
267C SER* 1.3 78.0 - - - +
269C LYS* 1.3 64.3 + - - +
271C LEU* 3.0 10.3 + - + +
272C LEU* 2.8 31.7 + - + +
287C LEU* 4.1 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PHE* 6.6 0.2 - - - -
224C THR 5.1 3.9 + - - -
225C THR* 4.1 21.1 + - - +
229C ASP* 3.5 27.9 + - - +
230C PHE* 4.1 18.6 - - + -
233C VAL* 4.2 20.1 - - + +
265C CYS 2.8 19.8 + - - +
266C ALA* 3.8 8.5 - - - +
267C SER 3.3 0.2 - - - -
268C LEU* 1.3 72.2 - - - +
270C GLU* 1.3 66.7 + - - +
272C LEU* 3.3 9.7 + - - +
273C GLN* 3.1 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ASN* 3.8 19.9 + - + +
223C PHE* 4.6 17.3 - - + -
266C ALA 3.2 11.9 + - - +
267C SER 3.1 8.4 + - - +
268C LEU 3.1 0.8 - - - -
269C LYS* 1.3 83.0 - - - +
271C LEU* 1.3 59.9 + - - +
273C GLN* 3.9 15.8 - - - +
274C ASN* 2.5 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C LEU* 4.2 12.6 - - + -
218C TRP* 3.4 36.8 - - + -
219C PHE* 4.2 12.8 - - + +
267C SER 3.0 16.8 + - - +
268C LEU* 3.0 14.9 + - + +
270C GLU* 1.3 78.7 - - - +
272C LEU* 1.3 58.0 + - - +
275C GLY* 2.7 43.4 + - - +
276C MET* 4.4 9.4 - - + +
281C ILE* 4.1 13.0 - - + -
287C LEU* 3.9 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 4.8 4.5 - - + -
233C VAL* 4.4 16.8 - - + -
234C ALA* 4.5 13.7 - - - -
237C TYR* 3.7 41.0 - - + -
239C TYR* 3.5 46.4 - - + +
268C LEU* 2.8 31.4 + - + +
269C LYS* 3.7 9.2 - - - +
271C LEU* 1.3 79.6 - - - +
273C GLN* 1.3 61.9 + - - +
275C GLY* 4.1 2.9 + - - -
287C LEU* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C VAL* 3.4 30.8 - - + +
237C TYR* 3.8 25.1 + - + +
269C LYS* 3.1 37.0 + - - +
270C GLU* 3.3 19.9 + - - +
272C LEU* 1.3 80.0 - - - +
274C ASN* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C GLU* 2.5 46.2 + - + +
273C GLN* 1.3 85.6 + - - +
275C GLY* 1.3 62.5 + - - +
277C ASN* 3.1 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C TRP* 5.1 1.0 - - - -
271C LEU* 2.7 39.8 + - - +
272C LEU 4.1 3.3 + - - -
273C GLN 3.7 1.2 - - - -
274C ASN* 1.3 79.4 - - - +
276C MET* 1.3 62.7 + - - -
277C ASN* 4.4 2.0 - - - +
----------------------------------------------------------
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