Contacts of the helix formed by residues 261 - 268 (chain B) in PDB entry 4X3G
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 THR 261 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ASN* 5.5 5.8 - - - +
195B LYS* 3.5 19.1 - - - +
203B GLN* 3.4 44.4 + - + +
205B PHE* 4.3 8.3 - - + -
260B ASP* 1.3 73.6 - - - +
262B SER* 1.4 64.4 + - - +
264B ALA* 3.3 4.4 + - - +
265B GLN* 3.2 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A MET 4.5 8.9 + - - -
253A ASN* 3.9 20.4 - - - +
254A SER* 4.2 7.9 - - - -
260B ASP* 3.4 12.9 + - - -
261B THR* 1.4 81.7 + - - +
263B ILE* 1.4 61.2 + - - +
265B GLN* 3.4 17.8 + - - +
266B LEU* 3.7 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 5.2 4.0 - - + -
254A SER* 3.7 22.2 - - - +
256A CYS 5.6 1.1 - - - +
258A VAL* 4.0 30.3 - - + +
234B LEU* 4.1 12.8 - - + -
258B VAL 5.0 0.4 - - - +
259B PHE* 3.8 27.4 - - + -
260B ASP* 3.3 35.1 + - - +
261B THR 3.4 0.2 - - - -
262B SER* 1.4 70.8 - - - +
264B ALA* 1.4 64.6 + - - +
266B LEU* 3.0 23.0 + - + +
267B PHE* 3.3 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 4.3 15.3 - - + -
205B PHE* 3.9 21.5 - - + -
227B LEU* 6.1 0.2 - - - -
259B PHE* 4.1 17.8 - - + -
260B ASP 3.1 14.3 + - - +
261B THR 3.3 10.1 + - - +
263B ILE* 1.4 75.0 - - - +
265B GLN* 1.4 51.8 + - - +
267B PHE* 3.2 5.6 + - - +
268B ALA* 2.8 36.9 + - - +
273B LEU* 4.1 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 4.0 10.3 - - - +
171B ASN* 2.7 41.5 + - - +
261B THR* 3.2 21.5 + - - +
262B SER* 3.5 10.5 - - - +
263B ILE 3.2 0.4 - - - -
264B ALA* 1.4 76.0 - - - +
266B LEU* 1.3 61.4 + - - +
267B PHE 3.3 1.0 + - - -
268B ALA* 3.6 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 5.3 1.6 - - + -
253A ASN* 3.6 27.1 - - + +
254A SER 4.0 11.4 - - - +
255A ASP* 3.7 22.9 - - + +
229B GLY* 4.2 8.5 - - - -
230B HIS 4.6 1.2 + - - -
232B ARG* 3.7 49.3 + - - +
262B SER 3.7 12.3 - - - +
263B ILE* 3.0 21.1 + - + +
265B GLN* 1.3 76.6 - - + +
267B PHE* 1.3 66.1 + - + +
268B ALA 5.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 3.6 27.6 - + - -
227B LEU* 3.2 38.6 - - + -
228B ASN 3.6 10.9 - - - +
229B GLY* 3.4 30.2 - - - -
232B ARG* 3.8 20.9 - - + -
233B ARG 3.8 0.2 - - - -
234B LEU* 3.9 15.3 - - + -
263B ILE* 3.3 43.7 - - + -
264B ALA* 3.2 2.3 + - - +
265B GLN 3.2 0.4 - - - -
266B LEU* 1.3 82.8 - - + +
268B ALA* 1.3 67.9 + - - +
269B GLU* 3.8 5.9 + - - +
273B LEU* 3.9 21.5 - - + +
274B GLY 5.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 3.8 19.7 - - + -
171B ASN* 5.8 0.7 - - - +
264B ALA 2.8 17.8 + - - +
265B GLN* 3.6 18.5 + - - +
266B LEU 5.1 0.3 - - - -
267B PHE* 1.3 79.5 - - - +
269B GLU* 1.3 63.1 + - - +
270B ASN 4.4 0.2 - - - -
271B GLY* 5.1 4.3 - - - +
272B ASN 3.2 18.2 - - - +
273B LEU* 4.1 3.6 - - + +
----------------------------------------------------------
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