Contacts of the helix formed by residues 258 - 269 (chain A) in PDB entry 1RL3
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 ASP 258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 4.6 6.2 - - - +
190A THR* 4.1 8.1 - - - +
257A LEU* 1.3 79.0 - - - +
259A LYS* 1.3 66.2 + - - +
260A TRP 3.2 5.3 + - - +
261A GLU* 2.5 44.6 + - + +
262A ARG* 3.3 9.9 + - - +
401A PCG 4.8 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 3.3 35.2 + - - +
258A ASP* 1.3 73.2 - - - +
260A TRP* 1.3 57.9 + - - +
262A ARG* 3.7 23.8 + - - +
263A LEU* 3.2 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A THR* 4.0 14.8 - - - -
192A VAL* 4.1 17.9 - - + -
197A SER 3.6 25.1 - - - -
198A PHE* 4.7 0.7 - - + -
200A GLU* 3.5 18.8 + - - -
201A LEU* 4.1 12.1 - - + -
241A ARG* 4.8 3.8 - - - +
258A ASP* 3.2 2.7 - - + +
259A LYS* 1.3 74.1 - - - +
261A GLU* 1.3 67.8 + - + +
262A ARG 3.1 2.0 - - - -
263A LEU* 3.1 13.8 + - + +
264A THR* 2.7 65.1 + - + -
401A PCG 3.3 84.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A THR* 2.9 31.3 - - + +
256A SER 4.0 3.5 - - - +
257A LEU* 3.1 24.5 - - + +
258A ASP* 2.5 49.5 + - + +
260A TRP* 1.3 84.7 - - + +
262A ARG* 1.3 58.1 + - - +
264A THR* 3.0 26.0 - - - -
265A VAL* 3.0 14.0 + - - +
356A VAL 4.5 2.5 - - - +
359A PRO* 3.1 31.2 - - + +
401A PCG 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 3.8 32.3 + - - +
248A LEU* 3.7 31.1 - - + +
249A SER* 4.1 20.2 - - - +
254A LEU* 3.6 21.8 - - + +
255A GLU 5.9 0.2 + - - -
257A LEU* 3.7 32.4 + - + -
258A ASP 3.3 3.0 + - - +
259A LYS* 3.8 30.9 + - - +
260A TRP 3.1 0.6 - - - -
261A GLU* 1.3 74.7 - - - +
263A LEU* 1.3 55.2 + - - +
264A THR 3.1 1.1 - - - -
265A VAL* 2.7 11.9 + - + +
266A ALA* 2.6 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 5.4 3.6 - - + -
241A ARG* 3.7 60.1 - - + +
245A GLU* 3.7 28.3 - - + +
259A LYS* 3.2 34.3 - - + +
260A TRP* 3.1 17.6 + - + +
262A ARG* 1.3 74.3 - - - +
264A THR* 1.3 57.7 + - - +
266A ALA* 2.8 8.0 + - + +
267A ASP* 2.5 40.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 5.1 0.6 - - - +
260A TRP* 2.7 53.8 + - + -
261A GLU* 3.0 16.2 - - - +
263A LEU* 1.3 77.7 - - - +
265A VAL* 1.3 58.2 + - - +
267A ASP* 3.5 11.1 + - + +
268A ALA* 3.2 18.0 + - - +
355A ARG* 4.9 11.1 + - - +
356A VAL* 3.5 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.3 22.2 - - + -
254A LEU* 4.1 15.0 - - + -
257A LEU* 4.1 11.0 - - + -
261A GLU 3.0 15.3 + - - +
262A ARG* 2.7 13.4 + - - +
264A THR* 1.3 75.4 - - - +
266A ALA* 1.3 67.4 + - - +
268A ALA* 3.4 2.9 + - - +
269A LEU* 3.1 30.7 + - + +
292A ILE* 5.6 1.8 - - + -
348A LEU* 4.9 4.2 - - + +
356A VAL* 3.8 17.3 - - + -
357A LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LYS* 3.1 17.1 + - - +
241A ARG* 4.2 26.9 - - + -
244A TYR* 4.3 14.8 - - + -
245A GLU* 5.4 0.7 - - - +
248A LEU* 4.1 4.0 - - + -
262A ARG 2.6 14.5 + - - +
263A LEU* 2.8 15.9 + - + +
265A VAL* 1.3 72.3 - - - +
267A ASP* 1.3 66.1 + - - +
269A LEU* 2.8 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.6 12.3 - - - +
135A LEU* 3.6 33.2 - - + +
197A SER* 5.3 4.2 + - - -
237A THR* 4.7 5.2 + - - +
240A LYS* 3.2 18.9 + - - +
241A ARG* 2.9 48.4 + - - +
263A LEU 2.5 19.9 + - - +
264A THR* 3.6 11.0 - - + +
266A ALA* 1.3 72.6 - - - +
268A ALA* 1.3 58.6 + - - +
269A LEU 3.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.6 7.2 - - - -
135A LEU* 5.7 0.4 - - - -
264A THR 3.2 4.9 + - - +
265A VAL 3.4 2.9 + - - +
267A ASP* 1.3 76.8 - - - +
269A LEU* 1.3 51.8 + - - +
348A LEU* 3.6 6.2 - - + +
352A ARG* 2.2 63.5 + - + +
355A ARG* 4.4 7.9 - - - +
356A VAL* 3.8 28.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
134A VAL* 3.7 9.4 - - - +
240A LYS* 2.6 26.5 + - - +
244A TYR* 4.0 30.7 - - + -
248A LEU* 4.2 16.8 - - + -
265A VAL* 3.1 27.8 + - + +
266A ALA* 2.8 24.1 + - - +
267A ASP 3.1 0.4 + - - -
268A ALA* 1.3 73.0 - - - +
270A GLU* 1.3 58.3 + - - +
271A PRO* 3.9 3.2 - - - +
290A PHE* 6.6 0.2 - - + -
292A ILE* 5.2 7.6 - - + -
346A VAL* 3.4 42.0 - - + +
347A LYS 4.1 8.7 - - - +
348A LEU* 4.1 12.3 - - + -
352A ARG* 4.0 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