Contacts of the helix formed by residues 293 - 305 (chain B) in PDB entry 2VZI
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 GLY 293 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE 3.2 13.4 + - - -
291B ALA 3.2 2.2 + - - -
292B ASP* 1.3 76.7 + - - +
294B VAL* 1.3 62.8 + - - +
295B TYR 3.5 1.6 - - - -
296B LEU* 3.5 8.5 + - - +
297B VAL* 3.2 28.8 + - - +
326B ASN* 3.7 16.3 - - - +
327B VAL* 3.7 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP* 3.1 18.1 + - - +
293B GLY* 1.3 77.7 - - - +
295B TYR* 1.3 65.7 + - + +
297B VAL* 3.2 2.4 + - - +
298B LEU* 3.1 44.4 + - + +
313B PHE* 4.4 9.0 - - + -
314B PHE 3.4 18.2 - - - +
315B LEU* 3.4 36.6 - - + +
317B PRO* 3.8 10.1 - - + -
326B ASN* 4.0 2.7 - - - +
1375B PGE 3.7 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 4.0 12.5 - - + +
281B LEU* 3.8 46.3 - - + +
282B GLU 3.7 24.9 + - - -
283B VAL* 3.6 17.7 - - + -
289B GLN* 3.5 18.6 + - + +
290B PHE* 3.7 21.6 - - + +
292B ASP* 4.4 2.0 + - - -
293B GLY 3.5 0.6 - - - +
294B VAL* 1.3 81.0 - - + +
296B LEU* 1.3 55.8 - - - +
298B LEU* 3.9 6.2 - - + -
299B LEU* 2.9 31.9 + - - +
1375B PGE 3.6 51.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE* 3.8 21.0 + - + +
293B GLY* 3.5 12.5 + - - +
294B VAL 3.2 0.4 - - - -
295B TYR* 1.3 78.1 - - - +
297B VAL* 1.3 60.7 + - - +
299B LEU* 3.7 4.7 + - + +
300B MET* 3.3 28.1 + - - +
327B VAL* 4.5 7.4 - - + -
330B ALA* 3.8 9.5 - - + +
331B PHE* 4.4 9.9 - - + -
334B MET* 3.9 18.8 - - + -
349B ILE* 4.3 26.0 - - + -
360B VAL* 4.0 23.1 - - + -
361B LEU* 3.8 29.2 - - + -
364B LEU* 4.4 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLY 3.2 16.4 + - - +
294B VAL 3.6 6.7 - - - +
296B LEU* 1.3 73.9 - - - +
298B LEU* 1.3 64.8 + - - +
300B MET* 3.3 14.2 + - - +
301B GLY 3.3 8.5 + - - -
308B VAL* 3.8 32.3 - - + +
313B PHE* 3.8 30.3 - - + -
326B ASN* 3.3 26.5 - - + +
329B PHE* 4.0 13.7 - - + -
330B ALA* 3.9 13.2 - - + +
333B LEU* 4.3 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 4.6 3.6 - - + -
279B LEU* 4.0 19.6 - - + +
281B LEU* 3.5 27.6 - - + -
294B VAL* 3.1 34.6 + - + +
295B TYR* 4.0 7.6 - - + +
297B VAL* 1.3 76.2 - - + +
299B LEU* 1.3 57.1 + - - +
301B GLY* 3.2 4.2 + - - +
302B LEU* 3.0 31.5 + - - +
308B VAL* 5.0 9.9 - - + +
310B LEU* 5.2 4.0 - - + -
313B PHE* 3.9 24.2 - - + -
315B LEU* 5.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 4.9 2.7 - - + -
272B VAL* 4.0 37.0 - - + +
275B HIS* 3.7 34.3 - - + -
276B LEU* 4.3 8.7 - - + +
290B PHE* 4.5 9.4 - - + -
295B TYR 2.9 17.0 + - - +
296B LEU* 3.8 7.6 - - + +
298B LEU* 1.3 72.9 - - - +
300B MET* 1.3 61.2 + - - +
302B LEU* 3.2 7.3 + - + +
303B LEU* 2.8 52.3 + - + +
361B LEU* 4.4 7.0 - - + -
364B LEU* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU 3.3 14.1 + - - +
297B VAL 3.3 9.3 + - - +
299B LEU* 1.3 76.2 - - - +
301B GLY* 1.3 58.4 + - - +
303B LEU* 4.6 3.8 - - + -
304B GLU* 2.9 40.2 + - + +
306B TYR* 3.9 3.5 - - - +
330B ALA* 3.9 18.8 - - + +
333B LEU* 3.8 24.9 - - + +
334B MET* 3.5 41.5 - - + -
364B LEU* 3.6 22.0 - - - -
368B TYR* 3.7 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B VAL 3.3 5.5 + - - -
298B LEU 3.2 7.6 + - - -
300B MET* 1.3 77.1 - - - +
302B LEU* 1.3 57.7 + - - +
305B GLY* 2.9 9.7 + - - -
306B TYR* 2.8 58.9 + - - +
308B VAL* 3.8 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B HIS* 3.4 48.7 + - + +
276B LEU* 4.0 10.1 - - + +
278B LYS* 4.1 21.8 + - + +
279B LEU* 3.7 38.6 - - + -
298B LEU 3.0 18.9 + - - +
299B LEU* 3.2 16.1 + - - +
301B GLY* 1.3 78.2 - - - +
303B LEU* 1.3 60.7 + - - +
305B GLY* 3.9 6.6 + - - -
371B VAL* 4.3 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 4.1 12.8 - - + -
275B HIS* 3.5 45.8 - - + +
299B LEU* 2.8 41.0 + - + +
300B MET* 4.1 5.2 - - - +
302B LEU* 1.3 72.7 - - - +
304B GLU* 1.3 63.0 + - - +
305B GLY 3.3 0.6 + - - -
364B LEU* 4.2 13.9 - - + -
368B TYR* 3.6 54.8 - - + -
371B VAL* 3.8 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B MET* 2.9 17.1 + - + +
303B LEU* 1.3 76.5 - - - +
305B GLY* 1.3 63.3 + - - +
306B TYR* 3.2 35.9 - - + +
333B LEU 5.1 0.7 - - - +
336B ASP 5.4 0.3 - - - +
337B GLY* 3.7 25.0 - - - +
367B LYS* 4.7 1.0 - - - -
368B TYR* 2.6 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B GLY 2.9 13.1 + - - -
302B LEU 4.3 6.1 - - - -
303B LEU 3.3 3.4 - - - -
304B GLU* 1.3 80.9 - - - +
306B TYR* 1.3 58.0 + - - +
----------------------------------------------------------
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