Contacts of the helix formed by residues 279 - 300 (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 279 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 3.0 25.5 + - + +
277A ASN* 3.3 14.8 + - - +
278A GLY* 1.4 71.2 - - - +
280A LEU* 1.4 57.2 + - - +
282A GLU* 3.6 31.9 + - + +
283A ALA* 3.1 27.5 + - - +
363A ASP 5.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A HIS* 4.7 13.5 + - + +
278A GLY 3.0 14.0 + - - +
279A LYS* 1.4 68.0 - - - +
281A LEU* 1.3 61.2 + - - +
282A GLU* 3.3 0.6 + - - -
283A ALA* 3.7 7.0 - - - +
284A GLN* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LYS 3.6 0.4 - - - -
280A LEU* 1.3 76.5 - - - +
282A GLU* 1.3 65.9 + - - +
284A GLN* 3.3 7.9 + - - +
285A ARG* 3.0 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 3.7 14.6 - - - -
279A LYS* 3.6 32.1 - - + +
280A LEU 4.1 0.2 + - - -
281A LEU* 1.3 87.2 + - - +
283A ALA* 1.3 56.0 + - - +
285A ARG* 3.7 8.0 - - - +
286A LEU* 3.0 29.5 + - - +
363A ASP 4.0 7.4 - - - +
364A HIS* 3.5 48.4 + - + +
365A GLY* 3.6 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.5 18.0 - - + +
274A MET* 3.7 19.7 - - + -
275A HIS* 3.4 34.8 - - + +
279A LYS 3.1 19.0 + - - +
280A LEU 3.7 3.1 - - - +
281A LEU 3.3 0.6 - - - -
282A GLU* 1.3 74.8 - - - +
284A GLN* 1.3 62.3 + - - +
286A LEU* 3.6 0.4 + - - -
287A GLU* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU 3.1 13.5 + - - +
281A LEU* 3.5 11.0 - - - +
283A ALA* 1.3 76.1 - - - +
285A ARG* 1.4 56.5 + - - +
287A GLU* 3.4 5.9 + - - +
288A GLN* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 4.9 4.6 + - - -
106A ASP* 4.6 10.3 + - - -
281A LEU* 3.0 21.4 + - - +
282A GLU* 3.7 15.5 - - - +
284A GLN* 1.4 76.3 - - - +
286A LEU* 1.3 56.5 + - - +
288A GLN* 3.8 5.0 - - - +
289A ARG* 3.0 44.5 + - - +
364A HIS* 2.8 42.3 + - - +
365A GLY 3.4 10.5 - - - +
366A PHE* 3.3 40.6 - - + -
186B ILE* 3.1 27.9 + - - +
187B ASP* 4.6 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.8 21.5 - - + -
270A GLN* 3.7 30.1 - - + -
271A LEU* 3.9 11.4 - - + -
274A MET* 3.8 10.3 - - + -
282A GLU 3.0 19.1 + - - +
283A ALA 3.9 4.7 - - - +
284A GLN 3.3 0.4 - - - -
285A ARG* 1.3 73.5 - - - +
287A GLU* 1.3 59.8 + - - +
289A ARG* 4.1 1.3 - - + +
290A THR* 2.6 46.1 + - - +
365A GLY* 3.3 19.5 + - - +
366A PHE 4.5 1.6 - - - +
367A ARG* 3.7 32.3 - - - +
368A LEU* 4.0 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.3 11.4 - - + +
271A LEU* 4.4 15.7 - - + +
283A ALA 3.2 14.3 + - - +
284A GLN* 3.4 5.1 + - - +
286A LEU* 1.3 76.2 - - - +
288A GLN* 1.4 56.5 + - - +
291A ARG* 2.8 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLN 3.1 19.3 + - - +
285A ARG* 3.8 6.1 - - - +
287A GLU* 1.4 74.1 - - - +
289A ARG* 1.3 63.5 + - + +
291A ARG* 4.5 2.0 - - - +
292A TYR* 3.3 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 3.5 15.8 + - - -
108A PHE* 3.4 30.3 - - - -
285A ARG* 3.0 38.0 + - + +
286A LEU* 4.1 2.5 - - + +
288A GLN* 1.3 77.2 - - + +
290A THR* 1.3 64.0 + - - +
292A TYR* 3.7 4.1 - - - +
293A ASP* 3.2 32.2 + - - +
309A TYR* 5.0 0.9 - - - -
366A PHE* 2.6 53.0 + - - +
367A ARG* 3.9 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 4.0 7.4 - - + -
267A LEU* 3.6 24.4 - - + +
286A LEU* 2.6 37.9 + - - +
289A ARG* 1.3 71.9 - - - +
291A ARG* 1.4 62.0 + - - +
293A ASP* 3.1 6.2 + - - +
294A LEU* 3.0 40.9 + - + +
309A TYR* 4.0 15.4 + - + +
366A PHE 5.7 0.2 + - - -
368A LEU* 3.8 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLU* 4.3 18.6 + - - +
267A LEU* 3.7 27.5 - - + +
268A GLU* 4.1 24.2 - - - +
271A LEU* 5.5 3.0 - - - +
287A GLU* 2.8 33.9 + - + +
288A GLN* 4.5 2.2 - - - +
290A THR* 1.4 69.4 - - - +
292A TYR* 1.3 60.2 + - - +
294A LEU* 3.5 17.5 + - - +
295A GLU* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLN 3.3 20.5 + - - +
289A ARG* 3.7 4.7 - - - +
290A THR 3.2 0.8 - - - -
291A ARG* 1.3 75.8 - - - +
293A ASP* 1.3 77.2 + - - +
295A GLU* 3.1 17.0 + - + +
296A MET* 3.1 43.4 + - + +
303A CYS* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ARG* 3.2 13.7 + - - +
290A THR 3.1 5.7 + - - +
292A TYR* 1.3 94.5 - - - +
294A LEU* 1.3 56.1 + - - +
296A MET* 3.4 7.2 + - - +
297A MET* 2.9 35.3 + - - +
303A CYS* 3.8 12.5 - - - +
304A SER 3.9 10.8 + - - +
309A TYR* 2.9 44.3 + - + +
367A ARG* 3.4 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 3.7 38.8 - - + +
263A ILE* 3.8 33.7 - - + -
264A GLU* 4.9 5.8 - - + +
267A LEU* 4.5 3.4 - - + -
290A THR* 3.0 39.3 + - + +
291A ARG* 3.8 27.8 - - - +
292A TYR 3.2 0.2 - - - -
293A ASP* 1.3 73.0 - - - +
295A GLU* 1.3 61.2 + - - +
297A MET* 3.5 14.4 + - + +
298A ARG* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG 3.3 12.0 + - - +
292A TYR* 3.1 11.0 + - + +
294A LEU* 1.3 73.6 - - - +
296A MET* 1.3 64.9 + - - +
298A ARG* 3.3 12.1 + - - +
299A GLU* 3.1 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TYR* 3.1 49.9 + - + +
293A ASP 3.4 9.9 - - - +
295A GLU* 1.3 76.7 - - + +
297A MET* 1.3 56.6 + - - +
299A GLU* 4.9 1.6 - - - -
300A MET* 3.1 63.7 + - + +
302A PHE 3.0 19.9 - - - +
303A CYS* 3.8 19.3 - - + -
304A SER 5.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 4.3 28.9 - - + +
263A ILE* 4.5 7.4 - - + -
293A ASP 2.9 26.5 + - - +
294A LEU* 3.6 17.5 - - + +
295A GLU 3.3 0.2 - - - -
296A MET* 1.3 76.3 - - - +
298A ARG* 1.4 61.4 + - - +
301A GLY* 2.8 33.1 + - - +
302A PHE 3.9 4.5 - - - -
303A CYS* 3.8 9.2 - - + -
306A ILE* 3.9 24.5 - - + -
309A TYR* 3.6 44.0 - - + -
313A LEU* 4.8 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 4.5 13.4 - - + +
294A LEU 3.1 17.4 + - - +
295A GLU* 3.3 17.4 + - - +
297A MET* 1.4 75.8 - - - +
299A GLU* 1.4 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 3.1 16.9 + - + +
298A ARG* 1.4 78.6 - - - +
300A MET* 1.4 89.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A MET* 3.1 46.5 + - + +
299A GLU* 1.4 95.9 - - + +
301A GLY* 1.3 57.6 + - - +
302A PHE* 3.4 13.9 - - + +
----------------------------------------------------------
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