Contacts of the helix formed by residues 260 - 275 (chain B) in PDB entry 6Y2G
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TYR* 3.8 0.2 - - - -
224B THR* 4.4 9.6 - - + +
254B SER* 3.7 7.2 - - - -
258B GLY 4.1 2.2 + - - -
259B ILE* 1.3 75.8 - - - +
261B VAL* 1.3 61.1 + - - +
262B LEU* 4.3 6.7 - - + +
263B ASP* 2.8 22.8 + - + +
264B MET 2.8 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.3 7.0 - - + -
209B TYR* 3.5 17.3 - - - +
242B LEU* 4.4 0.7 - - + -
247B VAL* 4.1 39.5 - - + +
250B LEU* 3.9 37.9 - - + +
251B GLY* 5.7 0.4 - - - -
254B SER* 4.2 14.8 + - - +
260B ALA* 1.3 72.3 - - - +
262B LEU* 1.3 57.7 + - + +
264B MET* 3.0 6.4 + - + +
265B CYS* 2.7 48.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B THR* 3.8 11.5 - - + +
225B THR* 3.3 44.5 + - + +
226B THR* 4.0 2.5 - - - -
227B LEU* 3.9 31.4 - - + +
242B LEU* 6.4 0.2 - - + -
247B VAL* 4.8 14.8 - - + -
260B ALA* 3.1 5.3 - - + -
261B VAL* 1.3 87.1 - - + +
263B ASP* 1.3 66.2 + - - +
265B CYS* 3.3 14.6 + - - +
266B ALA 3.3 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 6.0 1.1 - - - +
221B ASN* 2.8 41.5 + - - +
222B ARG* 4.5 4.8 - - - +
223B PHE 3.5 15.8 - - - +
224B THR* 4.0 9.0 + - - +
258B GLY 5.6 0.2 - - - +
259B ILE* 4.2 13.5 - - + +
260B ALA* 2.8 33.0 + - + +
262B LEU* 1.3 73.2 - - - +
264B MET* 1.3 63.7 - - - +
265B CYS 3.0 1.1 - - - -
266B ALA* 2.9 16.6 + - - +
267B SER* 3.2 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.6 22.9 - - + +
208B LEU* 3.8 26.4 - - + +
209B TYR* 3.1 64.4 - - + +
212B VAL* 4.2 11.7 - - + -
219B PHE* 4.5 3.4 - - - -
220B LEU* 4.1 17.5 - - + -
259B ILE* 4.0 10.2 - - + +
260B ALA 2.8 13.3 + - - +
261B VAL* 3.2 11.7 - - - +
263B ASP* 1.3 71.3 - - - +
265B CYS* 1.4 55.2 + - - +
267B SER* 3.1 11.2 + - - -
268B LEU* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.1 9.6 - - - -
225B THR* 4.0 7.4 - - + -
227B LEU* 6.2 0.4 - - - -
230B PHE* 4.0 43.9 - - + -
242B LEU* 4.0 16.2 - - - -
261B VAL* 2.7 34.6 + - - -
262B LEU* 3.5 17.7 - - - +
263B ASP 3.0 0.6 + - - -
264B MET* 1.4 73.8 - - - +
266B ALA* 1.3 50.9 + - - +
268B LEU* 3.1 9.0 + - - +
269B LYS* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ASN* 3.8 11.4 - - - +
223B PHE* 3.4 32.5 - - + +
224B THR 4.8 0.4 - - - +
225B THR* 4.5 12.7 - - - +
262B LEU 3.3 6.2 + - - +
263B ASP 2.9 3.3 + - - +
265B CYS* 1.3 71.9 - - - +
267B SER* 1.3 66.4 + - - +
269B LYS* 3.4 12.5 - - + +
270B GLU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 5.4 1.3 - - - -
219B PHE* 3.0 35.1 + - - +
220B LEU* 3.6 15.9 - - - +
221B ASN* 3.8 12.3 + - - +
263B ASP* 3.2 10.4 + - - -
264B MET* 3.1 21.4 + - - -
266B ALA* 1.3 74.7 - - - +
268B LEU* 1.3 61.7 + - - +
270B GLU* 3.0 15.4 + - - +
271B LEU* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B THR* 4.7 2.2 - - + -
204B VAL* 3.8 21.3 - - + -
205B LEU* 4.0 23.3 - - + -
208B LEU* 4.3 10.0 - - + +
230B PHE* 4.0 19.7 - - + -
239B TYR* 4.0 20.9 - - + +
264B MET 2.9 12.5 + - - +
265B CYS* 3.1 8.7 + - - +
267B SER* 1.3 72.0 - - - +
269B LYS* 1.3 68.4 + - - +
271B LEU* 2.9 11.5 + - + +
272B LEU* 2.8 36.5 + - + +
287B LEU* 3.5 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 6.1 2.2 - - + +
229B ASP 6.2 0.2 - - - -
230B PHE* 4.9 3.1 - - + -
233B VAL* 3.9 31.4 - - + -
265B CYS 2.7 20.1 + - - +
266B ALA* 3.4 15.5 - - + +
268B LEU* 1.3 71.9 - - - +
270B GLU* 1.3 76.7 + - - +
272B LEU* 3.0 26.8 + - - +
273B GLN* 3.0 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ASN* 4.8 9.2 - - - +
266B ALA 3.0 14.5 + - - +
267B SER* 3.0 11.1 + - - +
269B LYS* 1.3 89.2 + - + +
271B LEU* 1.3 64.0 + - + +
272B LEU 3.3 0.2 + - - -
273B GLN* 3.4 13.8 + - - +
274B ASN* 2.6 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 4.5 8.3 - - + -
218B TRP* 4.5 15.3 - - + -
219B PHE* 4.0 28.7 - - + -
267B SER* 3.1 23.7 + - - +
268B LEU* 2.9 11.4 + - - +
270B GLU* 1.3 76.7 - - + +
272B LEU* 1.3 63.0 + - - +
274B ASN* 5.0 0.7 - - - -
275B GLY* 3.3 31.2 + - - +
276B MET* 4.0 26.6 - - - +
279B ARG* 5.2 2.0 - - - +
281B ILE* 4.5 7.4 - - + -
287B LEU* 4.2 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 4.9 4.3 - - + -
233B VAL* 4.6 14.4 - - + +
234B ALA* 5.2 0.7 - - - -
237B TYR* 3.6 51.7 - - + -
239B TYR* 3.6 45.3 - - + +
268B LEU* 2.8 32.4 + - + +
269B LYS* 3.0 12.5 + - - +
271B LEU* 1.3 78.3 - - - +
273B GLN* 1.3 60.5 + - - +
275B GLY* 4.5 2.4 + - - -
287B LEU* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B VAL* 4.7 3.6 - - - +
237B TYR* 3.2 28.0 + - + +
269B LYS* 3.0 59.3 + - - +
270B GLU* 3.6 15.6 - - - +
272B LEU* 1.3 77.7 - - - +
274B ASN* 1.3 71.1 + - - +
275B GLY* 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 2.6 50.7 + - - +
271B LEU* 5.0 0.9 - - - -
273B GLN* 1.3 83.5 - - - +
275B GLY* 1.3 65.1 + - - +
277B ASN* 3.3 17.1 + - - +
279B ARG* 5.0 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.3 22.3 + - - +
272B LEU 4.5 2.4 + - - -
273B GLN 3.4 2.6 - - - -
274B ASN* 1.3 81.7 - - - +
276B MET* 1.3 63.3 + - - +
277B ASN* 3.6 11.7 - - - -
279B ARG* 3.2 19.1 + - - -
----------------------------------------------------------
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