Contacts of the helix formed by residues 252 - 265 (chain A) in PDB entry 6Q2J
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 ASN 252 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ALA* 3.2 4.5 - - - +
251A ALA* 1.3 79.5 + - - +
253A MET* 1.3 62.6 + - - +
254A HIS* 3.7 13.5 - - - +
255A ALA* 3.1 30.9 + - - +
256A GLN 3.8 2.9 + - - -
308A ILE* 3.4 21.2 - - + +
279B TYR* 3.0 41.1 + - + -
299B ASP* 3.2 24.1 + - + +
591F VAL* 3.8 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 1.3 71.0 - - - +
254A HIS* 1.3 59.9 + - - +
255A ALA 3.2 0.2 - - - -
256A GLN* 3.1 11.3 + - + +
257A ILE* 3.0 36.0 + - + +
225B TRP* 4.8 16.4 - - + -
228B TRP* 4.5 7.6 - - + -
297B TYR* 3.6 47.8 - - + -
299B ASP* 3.0 30.9 + - - +
300B LEU* 4.9 3.6 - - + -
590F ILE 5.1 3.6 - - - +
591F VAL* 3.7 12.1 - - + +
592F GLY* 3.6 41.3 - - - +
593F GLY 4.4 1.1 - - - +
594F HIS* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 3.2 13.6 - - - +
253A MET* 1.3 77.0 - - - +
255A ALA* 1.3 56.0 + - - +
257A ILE* 3.8 9.9 - - + +
258A LYS* 2.9 48.6 + - + +
308A ILE* 4.7 7.2 - - - -
237B VAL* 4.6 8.1 - - + +
238B THR 3.7 23.8 - - - -
239B MET* 3.8 24.5 - - + +
240B CYS 5.3 0.4 + - - -
276B PRO* 4.4 13.8 - - + +
279B TYR* 4.1 17.9 - + + -
299B ASP 3.3 20.4 + - - +
300B LEU 3.5 17.4 + - - +
302B ALA* 4.6 5.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ALA* 3.8 21.5 - - + -
252A ASN* 3.1 25.3 + - - +
253A MET 3.2 0.4 - - - -
254A HIS* 1.3 78.7 - - - +
256A GLN* 1.3 53.1 + - - +
258A LYS* 3.4 6.2 + - - +
259A THR* 2.7 38.0 + - - -
272A PRO* 4.7 9.1 - - + +
307A CYS* 4.4 10.3 - - + +
308A ILE* 4.4 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLN* 5.5 5.6 - - + +
250A ALA* 4.3 11.7 - - + -
253A MET* 3.1 15.1 + - + +
255A ALA* 1.3 75.0 - - - +
257A ILE* 1.3 60.3 + - + +
259A THR* 3.3 7.5 + - - -
260A SER* 2.9 34.0 + - - +
225B TRP* 6.1 2.2 - - + -
591F VAL* 3.3 38.8 + - + +
592F GLY* 3.9 14.8 - - - -
619F PHE* 3.7 21.4 - - - +
620F CYS 5.2 0.2 - - - +
621F GLU* 3.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A MET* 3.0 21.2 + - + +
254A HIS* 3.9 7.4 - - + +
256A GLN* 1.3 76.2 - - + +
258A LYS* 1.3 56.8 + - - +
260A SER* 3.3 5.0 + - - -
261A LEU* 2.9 50.1 + - + +
223B LEU* 3.9 13.0 - - + -
225B TRP* 3.6 38.8 - - + -
237B VAL* 4.4 18.6 - - + -
239B MET* 5.1 0.9 - - + -
300B LEU* 3.7 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A HIS* 2.9 37.3 + - + +
255A ALA* 3.7 4.9 - - - +
257A ILE* 1.3 76.3 - - - +
259A THR* 1.3 57.5 + - - +
261A LEU* 4.7 0.7 - - - -
262A HIS* 2.9 30.8 + - - +
269A VAL* 3.7 14.3 - - + +
270A PRO* 3.3 48.8 - - - +
271A ALA 4.3 7.1 + - - -
272A PRO* 4.6 13.2 - - + +
273A CYS* 5.5 0.8 - - - +
308A ILE* 4.3 21.5 + - - +
239B MET* 5.0 10.8 - - + -
240B CYS* 4.4 11.3 + - - +
274B CYS 4.5 11.7 + - - -
275B VAL* 5.8 1.6 - - - +
276B PRO* 5.4 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO 5.5 2.3 + - - +
246A SER* 3.8 33.1 - - - +
247A GLN 5.3 2.8 + - - +
255A ALA* 2.7 22.7 + - - +
256A GLN* 3.6 8.0 - - - -
257A ILE 3.3 0.2 - - - -
258A LYS* 1.3 76.9 - - - +
260A SER* 1.3 58.4 + - - +
262A HIS* 3.3 7.3 + - + +
263A ARG* 2.9 42.1 + - + +
272A PRO* 4.0 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLN* 2.9 17.2 + - - +
257A ILE* 3.8 6.0 - - - -
259A THR* 1.3 77.4 - - - +
261A LEU* 1.3 60.0 + - - +
263A ARG* 3.2 13.4 + - - +
264A LEU* 2.9 26.0 + - - +
222B ASP 4.7 5.3 - - - +
223B LEU* 4.3 29.6 + - - -
225B TRP* 5.6 1.8 + - - -
621F GLU* 5.1 6.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
257A ILE* 2.9 32.5 + - + +
260A SER* 1.3 74.4 - - - +
262A HIS* 1.3 60.1 + - - +
264A LEU* 3.7 12.1 - - + +
265A LYS* 2.7 56.5 + - - +
269A VAL* 3.9 21.6 - - + +
216B VAL* 5.0 6.3 - - + +
218B ALA* 4.1 17.9 - - + -
222B ASP* 4.8 3.1 - - + +
223B LEU* 3.8 19.5 - - + -
237B VAL* 4.8 6.3 - - + -
239B MET* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS 2.9 19.7 + - - +
259A THR* 3.3 7.4 + - + +
261A LEU* 1.3 73.9 - - - +
263A ARG* 1.3 68.6 + - + +
265A LYS 3.7 4.3 - - - -
266A PRO* 3.3 44.5 + - + +
269A VAL* 2.9 23.5 + - - +
270A PRO* 4.3 5.6 - - + +
271A ALA* 3.6 32.9 + - + +
272A PRO* 5.7 0.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
246A SER* 4.2 15.2 + - - +
259A THR* 2.9 31.1 + - + +
260A SER* 3.2 13.9 + - - +
262A HIS* 1.3 82.0 - - + +
264A LEU* 1.3 60.8 + - - +
266A PRO* 5.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER 2.9 15.4 + - - +
261A LEU* 3.9 8.5 - - + +
262A HIS 3.3 0.2 - - - -
263A ARG* 1.3 80.0 - - - +
265A LYS* 1.3 90.3 + - + +
266A PRO* 3.4 9.2 - - - +
222B ASP* 3.6 46.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 2.7 38.4 + - - +
262A HIS* 3.7 3.8 - - - -
264A LEU* 1.3 103.0 - - + +
266A PRO* 1.3 68.0 - - - +
267A ASP 3.5 1.6 - - - -
268A THR* 4.3 22.4 - - + +
269A VAL* 3.6 20.4 + - + +
216B VAL* 3.8 27.6 - - - +
217B ARG 4.3 10.4 + - - -
218B ALA* 4.9 1.4 - - - +
222B ASP* 5.4 0.4 + - - -
----------------------------------------------------------
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