Contacts of the helix formed by residues 379 - 391 (chain B) in PDB entry 4BVH
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 TRP 379 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 3.4 28.0 + - + -
132B ILE* 4.0 13.0 - - + -
133B ARG* 5.5 0.4 - - - +
135B ARG* 5.0 1.1 - - - -
212B PHE* 3.6 28.7 - + - -
215B LEU* 3.7 24.0 - - + -
216B LEU* 3.6 33.2 - - + -
219B LYS* 3.4 36.1 - - + +
221B LEU* 3.8 15.7 - - + -
374B VAL* 3.0 17.6 + - + +
377B LEU* 3.5 40.2 + - + +
378B GLY* 1.3 82.0 - - - +
380B THR* 1.3 58.9 + - - +
381B GLU 3.2 3.1 - - - -
382B GLU* 3.4 15.3 + - + +
383B MET* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU 5.1 0.3 + - - -
374B VAL* 3.7 11.9 - - + +
375B GLU* 2.7 42.6 + - - +
378B GLY 3.5 3.2 - - - -
379B TRP* 1.3 77.9 - - - +
381B GLU* 1.3 67.6 + - - +
383B MET* 3.4 3.3 + - + +
384B ARG* 2.8 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PRO* 6.1 5.6 - - + +
264A PRO* 5.9 6.5 - - + -
378B GLY 5.3 0.2 + - - -
379B TRP 3.2 0.2 - - - -
380B THR* 1.3 87.0 - - - +
382B GLU* 1.3 69.0 + - + +
384B ARG* 3.3 36.5 + - - +
385B ASP* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PRO* 3.8 36.0 - - + +
266A GLU* 4.7 4.9 - - - +
267A ASP* 5.0 4.0 - - - +
215B LEU* 4.3 16.5 - - + +
219B LYS* 3.0 37.0 + - - -
378B GLY 4.1 6.4 - - - +
379B TRP* 3.9 22.8 - - - +
381B GLU* 1.3 76.6 - - + +
383B MET* 1.3 63.0 + - - +
385B ASP* 3.4 7.4 + - - +
386B LEU* 2.9 24.9 + - - +
389B ARG* 5.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 3.7 31.2 - - + +
211B TYR* 3.8 24.9 - - + +
212B PHE* 3.9 23.3 - - - -
215B LEU* 3.6 22.1 - - + +
374B VAL* 3.6 30.3 - - + -
379B TRP 2.8 14.1 + - - +
380B THR* 3.5 8.7 - - + +
382B GLU* 1.3 72.3 - - - +
384B ARG* 1.3 64.3 - - - +
386B LEU* 3.3 4.7 + - - +
387B VAL* 3.0 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B THR* 2.8 23.3 + - + +
381B GLU* 3.3 41.4 + - - +
382B GLU 3.2 0.2 - - - -
383B MET* 1.3 73.0 - - - +
385B ASP* 1.3 86.2 + - - +
387B VAL* 3.9 4.4 - - - +
388B GLN* 3.1 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 3.0 21.1 + - - +
382B GLU* 3.7 6.3 - - - +
384B ARG* 1.3 101.5 + - - +
386B LEU* 1.3 61.2 + - - +
388B GLN* 3.4 10.0 + - - +
389B ARG* 2.9 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 3.5 37.7 - - + +
214B ARG* 4.0 25.6 - - + +
215B LEU* 4.1 21.8 - - + +
218B ASP* 4.6 5.6 - - - +
382B GLU 2.9 18.5 + - - +
383B MET* 3.6 8.1 - - - +
385B ASP* 1.3 76.8 - - - +
387B VAL* 1.3 62.3 + - - +
389B ARG* 3.3 30.5 + - - +
390B GLU* 2.9 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 4.7 9.4 - - + -
211B TYR* 3.9 20.6 - - + -
383B MET* 3.0 41.6 + - + +
384B ARG* 3.9 4.7 - - - +
386B LEU* 1.3 78.2 - - - +
388B GLN* 1.3 58.1 + - + +
390B GLU* 4.6 4.5 - - - -
391B THR* 2.6 57.2 + - + +
1397B CL 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ARG* 3.1 50.3 + - + +
385B ASP* 3.8 10.5 + - - +
387B VAL* 1.3 79.4 - - + +
389B ARG* 1.3 61.5 + - - +
391B THR* 3.2 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ARG* 5.9 1.6 - - - +
218B ASP* 5.3 4.0 + - - -
382B GLU 5.5 0.6 + - - -
385B ASP* 2.9 40.6 + - - +
386B LEU* 3.6 34.6 - - - +
388B GLN* 1.3 73.0 - - - +
390B GLU* 1.3 70.8 + - + +
391B THR 3.6 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 3.8 35.1 + - + +
214B ARG* 3.5 30.0 + - - -
236B VAL 5.6 0.5 - - - +
237B SER* 5.1 2.2 - - - +
386B LEU* 2.9 35.9 + - + +
387B VAL 4.0 2.5 - - - +
389B ARG* 1.3 87.2 + - - +
391B THR* 1.3 61.0 - - - +
1395B EDO 4.0 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS* 6.5 0.9 - - + -
206B PRO 5.9 0.4 - - - +
211B TYR* 3.7 25.4 - - + +
387B VAL* 2.6 40.9 + - + +
388B GLN* 3.2 17.6 + - - +
389B ARG 3.7 3.6 - - - +
390B GLU* 1.3 80.3 - - - +
----------------------------------------------------------
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