Contacts of the strand formed by residues 265 - 273 (chain A) in PDB entry 5IXC
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 VAL 265 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.5 23.6 - - + +
169A ASP* 6.1 0.9 - - + -
185A LEU* 5.0 2.9 - - + -
202A GLY* 6.1 2.7 - - - -
223A LEU* 4.2 22.2 - - + +
255A MET 3.7 0.7 - - - +
256A ASP* 3.2 5.8 - - - +
257A VAL* 2.7 48.7 + - + +
263A PRO 5.4 0.7 - - - +
264A GLY* 1.3 77.0 - - - +
266A ARG* 1.3 62.8 + - - +
267A LEU* 4.1 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU 2.5 33.9 + - - +
169A ASP* 3.5 19.1 - - + +
254A THR* 3.2 24.3 - - + +
255A MET 3.8 1.3 - - - -
256A ASP* 2.9 40.4 + - - +
265A VAL* 1.3 74.4 - - - +
267A LEU* 1.3 64.5 + - - +
268A GLN* 3.7 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 4.1 13.0 - - + -
167A HIS 3.2 17.0 - - - +
168A LEU* 4.1 14.6 - - + -
185A LEU* 4.3 11.2 - - + -
187A LEU* 4.2 24.2 - - + -
207A PHE* 5.8 0.2 - - + -
219A LEU* 5.8 1.1 - - + -
253A VAL 3.6 0.7 - - - +
254A THR* 3.3 8.8 - - - +
255A MET* 2.9 47.7 + - + +
257A VAL* 3.9 21.1 - - + -
265A VAL* 4.1 16.4 - - + -
266A ARG* 1.3 82.1 - - - +
268A GLN* 1.3 64.4 + - - +
269A LEU* 3.5 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASP 3.3 1.6 - - - +
166A VAL* 3.2 6.8 - - - -
167A HIS* 2.9 55.1 + - + +
169A ASP 3.4 21.4 + - - +
252A GLU* 3.2 27.6 - - - +
253A VAL 3.5 2.2 - - - -
254A THR* 3.8 14.5 + - - +
266A ARG* 3.7 27.7 - - - +
267A LEU* 1.3 75.2 + - - +
269A LEU* 1.3 64.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
164A LEU* 4.4 10.8 - - + -
165A ASP 3.2 4.0 - - - +
166A VAL* 4.1 21.1 - - + -
219A LEU* 3.6 26.0 - - + -
242A VAL* 4.3 25.4 - - + -
244A LEU* 6.4 1.3 - - + -
251A LYS 3.4 1.8 - - - +
252A GLU* 3.3 3.6 + - - +
253A VAL* 2.8 46.7 + - + +
255A MET* 4.1 11.9 - - + -
267A LEU* 3.5 30.3 - - + +
268A GLN* 1.3 84.3 - - - +
270A LYS* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A CYS 3.8 0.3 - - - +
164A LEU* 3.3 5.0 - - - +
165A ASP* 2.8 40.4 + - + +
250A GLY 3.4 18.9 + - - -
251A LYS* 3.3 26.2 - - - +
252A GLU* 3.9 15.8 - - + +
269A LEU* 1.3 73.7 - - - +
271A ALA* 1.3 74.4 + - - +
272A GLU* 4.3 10.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 5.4 3.4 - - - -
163A CYS 3.2 5.4 - - - +
164A LEU* 4.1 7.6 - - + +
211A TYR* 3.7 22.9 - - - +
244A LEU* 5.4 5.8 - - + -
248A THR 6.0 0.2 - - - +
250A GLY* 3.8 30.7 + - - +
251A LYS 4.2 3.6 + - - -
270A LYS* 1.3 85.9 - - - +
272A GLU* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 3.3 6.5 - - - -
163A CYS* 2.5 42.8 + - + +
270A LYS* 5.2 10.8 - - + -
271A ALA* 1.3 76.2 - - - +
273A GLY* 1.3 80.2 + - - +
275A PRO* 5.4 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU 3.7 11.9 - - - -
162A SER* 4.1 2.7 - - - -
163A CYS* 4.7 0.5 - - - +
272A GLU* 1.3 99.4 + - - +
274A CYS* 1.3 67.7 + - - -
275A PRO* 3.4 3.8 - - - +
----------------------------------------------------------
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