Contacts of the helix formed by residues 264 - 271 (chain A) in PDB entry 3OYM
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 264 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASN 3.6 8.1 - - - -
255A ASN* 3.4 24.7 - - + +
256A THR 3.4 14.6 - - - -
257A TYR* 3.6 20.0 - - + +
263A TYR* 1.3 75.1 - - - +
265A PRO* 1.3 74.6 - - - +
266A HIS* 3.5 6.1 + - - +
267A GLN* 2.9 42.0 + - - +
268A LEU* 3.1 23.1 + - - +
273A ASP* 4.3 1.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A THR* 3.3 26.7 - - - +
151A GLY* 3.9 11.7 - - - +
152A PHE* 3.6 24.4 - - - +
223A LYS* 4.9 6.7 - - - +
253A LEU 3.9 10.1 - - - +
254A ASN* 3.2 19.7 - - - +
256A THR 3.4 13.7 - - - +
258A SER* 5.6 2.0 - - - +
263A TYR 4.6 0.9 - - - +
264A THR* 1.3 83.7 - - - +
266A HIS* 1.3 55.5 + - - +
268A LEU* 3.1 5.2 + - + +
269A LEU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 3.9 16.1 - - + -
254A ASN 2.8 19.2 + - - +
255A ASN* 3.4 22.3 + - - +
264A THR* 3.7 2.7 - - - +
265A PRO* 1.3 77.1 - - - +
267A GLN* 1.3 59.0 + - - +
269A LEU 3.2 0.7 + - - -
270A PHE* 2.9 57.1 + + - +
272A ILE 2.9 28.7 + - - -
273A ASP* 3.8 14.1 - - - -
274A SER* 3.3 31.9 + - - -
122B PHE* 3.8 5.4 - + - -
176B ILE 3.9 14.6 + - - -
177B ALA* 4.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 3.0 31.7 + - - -
263A TYR* 3.4 25.1 - - + +
264A THR* 2.9 40.8 + - - +
266A HIS* 1.3 78.1 - - - +
268A LEU* 1.3 57.7 + - - +
271A GLY* 2.8 33.6 + - - +
272A ILE* 4.6 4.9 - - - +
273A ASP* 3.1 40.1 + - - +
280A ASN* 4.2 7.6 - - + +
295A LEU* 3.5 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 5.2 0.2 - - - +
149A MET* 4.4 8.7 - - + +
150A THR* 3.5 37.8 - - + +
261A LEU* 4.2 19.3 - - + -
263A TYR* 3.9 21.3 - - + -
264A THR 3.1 16.4 + - - +
265A PRO* 3.1 7.2 + - + +
267A GLN* 1.3 78.5 - - - +
269A LEU* 1.3 57.0 + - - +
295A LEU* 3.7 3.4 - - + +
298A ILE* 4.0 23.3 - - + -
299A ARG* 2.9 35.1 + - + -
302A LEU* 4.2 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 3.6 28.3 - - + -
122A PHE* 4.0 7.4 - - + -
147A ASP* 5.1 1.8 - - - +
150A THR* 3.5 11.2 - - + +
152A PHE* 3.6 37.2 - - + -
154A TRP* 4.6 10.8 - - + -
265A PRO 2.9 15.5 + - - +
266A HIS 3.7 3.6 - - - +
268A LEU* 1.3 78.7 - - - +
270A PHE* 1.3 78.7 + - + +
299A ARG* 2.9 18.8 + - - +
270B PHE* 3.7 36.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 4.2 9.2 - + - -
266A HIS* 2.9 54.6 + + - +
269A LEU* 1.3 95.6 - - + +
271A GLY* 1.3 59.6 + - - +
272A ILE* 3.2 15.8 + - + +
288A ARG* 2.7 33.6 + - - +
295A LEU* 4.1 6.4 - - - +
122B PHE* 3.7 15.9 - + + -
154B TRP* 5.8 2.9 - + - -
176B ILE* 4.3 19.1 - - + -
177B ALA* 5.1 0.4 - - + -
269B LEU* 3.6 41.5 - - + +
270B PHE* 3.5 24.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLN* 2.8 27.9 + - - -
269A LEU 3.8 0.4 - - - -
270A PHE* 1.3 72.4 - - - +
272A ILE* 1.3 60.5 + - - +
283A THR* 4.6 5.2 + - - +
288A ARG* 4.1 3.8 - - - -
291A GLU* 3.6 19.2 - - - +
295A LEU* 3.8 24.0 - - - +
----------------------------------------------------------
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