Contacts of the strand formed by residues 293 - 306 (chain B) in PDB entry 2QVS
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 SER 293 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP* 1.3 83.2 - - - +
294B PHE* 1.3 57.8 + - - +
295B TYR* 3.8 14.0 + - - -
333B GLY 3.7 4.2 - - - +
336B ALA* 3.8 1.3 - - - +
343B ARG* 2.7 32.2 + - - +
357B VAL* 3.6 21.8 - - - +
358B MET 2.8 28.0 - - - -
359B ASP* 3.8 4.5 - - - -
360B VAL* 3.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ILE* 6.0 0.2 - - + -
258B PHE* 3.6 33.4 - + - -
269B ILE* 5.7 3.1 - - + -
273B ILE* 5.3 3.1 - - + -
293B SER* 1.3 77.0 - - - +
295B TYR* 1.3 73.8 + - - +
296B ILE* 4.3 15.9 - - + -
331B TYR* 5.4 6.5 - + + -
332B PHE 3.7 8.7 - - - +
333B GLY 3.8 15.7 - - - +
334B GLU* 4.2 6.5 - - + +
337B LEU* 3.6 40.2 - - + -
356B LEU 3.6 1.6 - - - +
357B VAL* 3.6 2.4 - - - -
358B MET* 3.0 64.2 + - + -
360B VAL* 4.6 2.5 - - + -
363B PHE* 4.1 10.8 - + + -
----------------------------------------------------------
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 LYS* 5.2 1.6 + - + -
278B TYR* 3.6 13.2 + - - -
284B ILE* 3.5 39.1 + - + -
285B ILE* 3.6 21.4 - - + +
293B SER* 3.8 28.6 + - - -
294B PHE* 1.3 79.5 - - - +
296B ILE* 1.3 59.9 + - - +
297B ILE 4.2 0.4 - - - -
331B TYR* 2.8 35.9 - - - +
332B PHE* 2.9 44.3 + + + +
343B ARG* 4.4 1.6 - - - -
355B CYS* 4.1 11.7 - - + -
356B LEU 3.2 4.3 - - - +
357B VAL* 3.6 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 3.9 26.7 - - + +
252B ILE* 3.6 31.6 - - + -
255B VAL* 4.0 18.8 - - + -
258B PHE* 4.5 4.3 - - + -
273B ILE* 5.0 1.6 - - + -
294B PHE* 4.3 22.0 - - + -
295B TYR* 1.3 78.7 - - - +
297B ILE* 1.3 71.0 + - - +
298B GLU* 3.4 1.9 + - - +
329B GLY 4.3 9.4 - - - +
330B GLN 3.4 9.2 - - - +
331B TYR* 4.1 7.9 - - + -
355B CYS* 4.3 1.6 - - - -
356B LEU* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 3.8 3.6 - - - -
296B ILE* 1.3 72.3 - - - +
298B GLU* 1.3 58.7 + - - +
299B SER 3.4 24.9 - - - +
300B GLY 3.7 15.0 - - - +
302B VAL* 3.7 19.3 - - + -
326B CYS* 3.3 44.4 - - + +
327B HIS 3.5 15.5 - - - +
329B GLY* 2.7 30.3 + - - -
330B GLN 2.7 14.4 + - - +
332B PHE* 3.6 22.0 - - + -
353B VAL* 4.7 4.5 - - + -
354B LYS 3.8 5.2 - - - +
355B CYS* 4.3 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B MET* 3.6 24.3 - - - +
248B PHE* 4.4 0.5 - - - -
251B PHE* 3.4 32.1 - - + -
275B GLU* 2.9 28.0 - - - +
296B ILE 3.4 2.0 + - - +
297B ILE* 1.3 73.9 - - - +
299B SER* 1.3 64.8 + - - +
328B LYS* 3.6 21.5 - - - +
354B LYS* 2.8 38.4 + - + +
355B CYS 3.5 13.2 - - - +
356B LEU* 3.3 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 3.4 11.7 - - - +
298B GLU* 1.3 83.5 - - - +
300B GLY* 1.3 65.2 + - - +
328B LYS* 4.5 8.7 - - - -
352B ASP 4.3 2.1 + - - -
353B VAL* 3.5 4.0 - - - +
354B LYS* 3.1 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 3.7 3.5 - - - +
299B SER* 1.3 79.2 - - - +
301B GLU* 1.3 71.1 + - - +
327B HIS* 3.7 0.7 - - - +
328B LYS* 3.5 21.5 + - - +
350B VAL 4.9 1.6 - - - -
352B ASP 3.4 18.2 - - - -
353B VAL* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 5.1 0.2 - - - -
300B GLY* 1.3 80.2 - - - +
302B VAL* 1.3 60.1 + - - +
325B HIS* 2.8 34.6 + - + -
326B CYS 3.2 11.7 - - - +
327B HIS* 3.8 18.3 + - + +
350B VAL* 2.7 49.9 + - + +
353B VAL* 3.2 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ILE* 4.0 16.8 - - + -
297B ILE* 3.7 26.9 - - + -
301B GLU* 1.3 81.2 - - - +
303B SER* 1.3 62.5 + - - +
304B ILE* 3.8 23.3 + - + +
325B HIS* 3.4 5.8 - - - -
326B CYS* 2.9 32.4 + - + +
332B PHE* 3.7 19.7 - - + -
347B ALA* 3.9 14.1 - - + -
348B TYR 3.4 13.2 - - - +
350B VAL* 3.6 3.8 - - - -
353B VAL* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B VAL* 1.3 72.7 - - - +
304B ILE* 1.3 62.3 + - - +
305B LEU* 3.6 15.2 + - - +
322B GLU* 3.2 32.0 + - - +
324B ALA 4.0 3.6 - - - -
325B HIS* 4.6 1.6 - - - -
347B ALA* 3.3 2.9 - - - -
348B TYR* 2.8 45.8 + - - -
350B VAL* 3.2 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B VAL* 3.8 16.2 - - + +
303B SER* 1.3 74.0 + - - +
305B LEU* 1.3 57.8 + - - +
322B GLU* 3.2 4.3 - - - -
323B ILE* 2.7 40.9 + - + -
324B ALA* 3.1 34.3 + - + +
326B CYS* 4.7 8.5 - - - -
332B PHE* 4.4 18.8 - - + -
345B ALA* 4.0 18.6 - - + -
346B SER 3.4 8.5 - - - +
347B ALA* 3.5 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLN* 4.1 0.3 - - - +
303B SER* 3.6 16.4 - - - +
304B ILE* 1.3 73.9 - - - +
306B ILE* 1.3 59.9 + - - +
320B GLU* 3.5 38.8 - - + +
321B VAL* 3.0 9.0 - - - +
322B GLU* 3.3 38.6 - - + +
323B ILE* 4.7 0.2 - - - -
345B ALA* 2.8 5.4 - - - +
346B SER* 2.8 37.6 + - - +
348B TYR* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLN* 3.4 14.6 - - - +
305B LEU* 1.3 74.3 - - - +
307B ARG* 1.3 68.3 + - - +
308B SER* 3.2 12.2 + - - +
310B THR* 6.0 7.6 - - - +
320B GLU* 4.2 0.7 - - - -
321B VAL* 2.7 39.4 + - + +
323B ILE* 3.3 38.8 - - + -
344B ALA* 3.8 18.6 - - + +
345B ALA* 3.9 1.1 - - + -
----------------------------------------------------------
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