Contacts of the helix formed by residues 255 - 276 (chain A) in PDB entry 3V4R
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 LYS 255 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 3.5 16.2 + - + +
254A GLU* 1.3 75.1 - - + +
256A MET* 1.4 58.8 + - - +
257A GLU 3.7 1.6 - - - -
258A LYS* 4.2 4.8 + - - -
259A ALA* 3.8 13.2 + - - +
313A LEU 4.4 5.2 - - - +
315A LEU* 3.5 39.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 5.7 7.2 - - - -
252A ARG 3.8 8.2 + - - +
253A ALA* 3.5 19.1 - - - +
254A GLU 3.1 2.8 + - - -
255A LYS* 1.4 76.0 - - - +
257A GLU* 1.3 65.2 + - - +
259A ALA* 3.4 8.1 - - - +
260A ILE* 3.2 34.2 + - + +
313A LEU* 5.7 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ALA 5.0 0.2 + - - -
254A GLU 4.2 7.1 + - - +
255A LYS 3.7 0.2 - - - -
256A MET* 1.3 74.1 - - - +
258A LYS* 1.4 58.9 + - - +
260A ILE* 3.4 11.7 + - - +
261A GLN* 3.1 25.9 + - - +
----------------------------------------------------------
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 GLU 5.5 0.4 + - - -
255A LYS* 4.2 5.5 + - - +
256A MET 3.4 0.2 - - - -
257A GLU* 1.4 74.3 - - - +
259A ALA* 1.3 60.2 + - - +
261A GLN* 3.3 8.6 + - - +
262A ASN* 2.9 37.4 + - - +
315A LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LYS 3.8 13.6 + - - +
256A MET* 3.4 12.3 - - - +
258A LYS* 1.3 78.4 - - - +
260A ILE* 1.4 56.4 + - - +
262A ASN* 3.2 8.4 + - - +
263A ILE* 3.0 34.4 + - - +
312A HIS* 3.3 30.5 - - - +
313A LEU* 3.9 20.6 - - + -
315A LEU* 4.8 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A MET* 3.2 23.1 + - + +
257A GLU* 3.4 10.3 + - - +
259A ALA* 1.4 74.8 - - + +
261A GLN* 1.4 60.9 + - - +
263A ILE* 3.5 2.3 + - + -
264A GLU* 3.3 24.0 + - + +
294A LEU* 3.7 31.4 - - + +
297A MET* 4.3 37.5 - - + +
298A ARG* 4.5 17.3 - - + +
313A LEU* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU 3.1 13.2 + - - +
258A LYS* 3.5 11.9 - - - +
259A ALA 3.3 0.2 - - - -
260A ILE* 1.4 76.2 - - - +
262A ASN* 1.4 59.6 + - - +
264A GLU* 3.5 6.5 + - - +
265A LYS* 3.1 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 2.9 26.0 + - - +
259A ALA* 3.2 8.0 + - - +
261A GLN* 1.4 74.6 - - - +
263A ILE* 1.4 64.3 + - - +
265A LYS* 3.4 10.8 + - - +
266A GLU* 3.1 16.8 + - - +
312A HIS* 3.6 27.9 + - + +
315A LEU* 4.8 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA 3.0 26.6 + - - +
260A ILE* 4.0 5.2 - - - +
262A ASN* 1.4 71.4 - - - +
264A GLU* 1.4 55.2 + - - +
266A GLU* 2.9 8.0 + - - +
267A LEU* 2.8 32.1 + - - +
290A THR* 4.0 8.5 - - + -
294A LEU* 3.8 24.5 - - + -
297A MET* 4.5 6.3 - - + -
309A TYR* 3.8 34.5 - - + -
312A HIS* 3.6 34.8 - - + -
313A LEU* 4.7 6.7 - - + -
368A LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 3.3 11.9 + - + +
261A GLN* 3.7 10.8 - - - +
262A ASN 3.4 0.2 - - - -
263A ILE* 1.4 76.9 - - - +
265A LYS* 1.4 56.7 + - - +
267A LEU* 3.4 9.0 + - - +
268A GLU* 3.0 38.7 + - - +
291A ARG* 4.3 20.1 + - - +
294A LEU* 4.8 6.2 - - + +
----------------------------------------------------------
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 GLN 3.1 13.4 + - - +
262A ASN* 3.4 15.7 - - - +
263A ILE 3.2 0.2 - - - -
264A GLU* 1.4 76.0 - - - +
266A GLU* 1.4 59.3 + - - +
268A GLU* 3.7 8.3 + - - +
269A GLU* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASN 3.1 10.9 + - - +
263A ILE 2.9 8.5 + - - +
265A LYS* 1.4 72.6 - - - +
267A LEU* 1.4 59.8 + - - +
269A GLU* 3.4 7.0 + - + +
270A GLN* 2.9 28.7 + - + +
311A ARG* 4.1 6.7 + - - +
312A HIS* 3.2 15.0 + - + +
368A LEU* 3.4 25.6 - - + +
369A PRO* 3.6 11.8 - - + +
370A SER* 2.7 49.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
263A ILE 2.8 18.4 + - - +
264A GLU* 3.6 5.8 - - - +
266A GLU* 1.4 69.3 - - - +
268A GLU* 1.3 65.2 + - - +
270A GLN* 3.3 1.9 + - - +
271A LEU* 3.0 51.3 + - + +
286A LEU* 3.8 22.0 - - + +
287A GLU* 4.3 2.9 - - + -
290A THR* 3.6 42.2 - - + +
291A ARG* 3.7 43.1 - - + +
294A LEU* 4.5 3.8 - - + -
368A LEU* 3.7 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLU* 3.0 22.7 + - - +
265A LYS* 4.0 7.7 - - - +
267A LEU* 1.3 73.4 - - - +
269A GLU* 1.3 62.0 + - - +
271A LEU* 3.2 11.9 + - + +
272A LYS* 3.2 21.1 + - - +
291A ARG* 4.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LYS 3.3 15.8 + - - +
266A GLU* 3.6 8.3 - - + +
267A LEU 3.3 0.6 - - - -
268A GLU* 1.3 78.4 - - - +
270A GLN* 1.3 57.4 + - - +
272A LYS* 3.5 7.9 + - - +
273A VAL* 3.2 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 2.9 18.2 + - + +
267A LEU 3.7 4.7 - - - +
269A GLU* 1.3 73.2 - - - +
271A LEU* 1.3 60.8 + - - +
273A VAL* 3.4 22.5 - - - +
274A MET* 2.9 44.7 + - + +
286A LEU* 3.7 20.9 - - + -
362A VAL* 4.4 10.1 - - - +
367A ARG 5.6 0.4 + - - -
368A LEU* 4.0 8.5 - - + -
369A PRO* 3.5 36.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.0 44.0 + - + +
268A GLU* 3.2 9.2 + - + +
270A GLN* 1.3 76.1 - - - +
272A LYS* 1.4 64.7 + - - +
273A VAL 3.2 0.2 - - - -
274A MET* 3.4 2.6 + - + +
275A HIS* 3.0 43.1 + - + +
283A ALA* 3.5 36.3 - - + +
286A LEU* 3.9 20.9 - - + -
287A GLU* 4.4 13.7 - - + -
291A ARG* 5.5 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU 3.2 12.0 + - - +
269A GLU* 3.5 10.3 + - - +
270A GLN 3.5 0.2 - - - -
271A LEU* 1.4 74.1 - - - +
273A VAL* 1.4 53.6 + - + +
275A HIS* 3.8 5.4 - - - +
276A GLU* 2.9 55.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 3.2 16.6 - - + +
270A GLN* 3.4 29.2 - - - +
272A LYS* 1.4 74.5 - - + +
274A MET* 1.3 65.8 - - + +
275A HIS 3.4 0.3 + - - -
276A GLU* 3.5 7.7 + - - +
277A ASN* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLN* 2.9 36.5 + - + +
271A LEU* 3.4 5.4 + - + +
273A VAL* 1.3 76.3 - - + +
275A HIS* 1.3 60.8 + - - +
277A ASN* 3.6 6.4 + - - +
278A GLY 3.3 2.6 + - - -
279A LYS* 3.0 38.8 + - + +
282A GLU* 3.7 13.9 - - + +
283A ALA* 3.7 36.6 - - + -
286A LEU* 3.8 22.7 - - + -
362A VAL 4.0 11.4 - - - +
363A ASP 5.1 2.9 - - - +
365A GLY* 3.7 26.9 - - - +
367A ARG 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.0 33.4 + - + +
272A LYS* 3.8 5.6 - - - +
274A MET* 1.3 73.0 + - - +
276A GLU* 1.3 54.5 + - + +
277A ASN 2.8 14.7 + - - -
278A GLY* 3.0 14.0 + - - -
279A LYS 5.1 0.7 - - - +
280A LEU* 4.7 14.7 - - + +
283A ALA* 3.4 29.6 - - + +
284A GLN 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 2.9 39.7 + - - +
273A VAL* 3.5 6.5 + - - +
275A HIS* 1.3 73.5 - - + +
277A ASN* 1.4 58.6 + - - +
----------------------------------------------------------
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