Contacts of the helix formed by residues 379 - 392 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 4.2 9.9 - - + -
133A ARG* 5.6 2.9 - - - +
212A PHE* 3.5 30.3 - + - -
215A LEU* 3.7 23.3 - - + -
216A LEU* 3.9 23.3 - - + -
219A LYS* 3.4 44.1 - - + +
221A LEU* 3.8 24.7 - - + -
374A VAL* 2.8 17.9 + - + +
377A LEU* 3.4 45.1 + - + +
378A GLY* 1.3 80.7 - - - +
380A THR* 1.3 65.5 + - - +
381A GLU 3.2 2.6 + - - -
382A GLU* 3.3 11.2 + - + +
383A MET* 2.8 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU 4.8 0.7 + - - -
374A VAL* 3.7 10.5 - - + +
375A GLU* 2.6 46.9 + - - +
378A GLY 3.4 2.8 - - - -
379A TRP* 1.3 79.8 - - - +
381A GLU* 1.3 63.6 + - - +
383A MET* 3.3 2.8 + - - +
384A ARG* 2.9 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLY 5.2 0.4 + - - -
379A TRP 3.3 0.4 - - - -
380A THR* 1.3 79.4 - - + +
382A GLU* 1.3 62.0 + - - +
384A ARG* 3.3 33.3 + - - +
385A ASP* 2.8 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 3.5 24.3 - - + +
219A LYS* 2.9 38.0 + - - +
379A TRP* 3.3 15.4 + - - +
381A GLU* 1.3 79.3 - - - +
383A MET* 1.3 57.2 + - - +
385A ASP* 3.4 8.4 + - + +
386A LEU* 2.9 30.2 + - + +
389A ARG* 5.2 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 3.6 32.5 - - + +
211A TYR* 3.9 15.0 - - + +
212A PHE* 3.7 24.7 - - + -
215A LEU* 3.7 22.9 - - + -
374A VAL* 3.6 26.7 - - + -
379A TRP 2.8 22.2 + - - +
380A THR 3.6 4.3 - - - +
382A GLU* 1.3 70.3 - - - +
384A ARG* 1.4 62.8 + - + +
386A LEU* 3.6 5.6 - - + +
387A VAL* 3.0 55.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A THR* 2.9 37.8 + - - +
381A GLU* 3.3 31.0 + - - +
383A MET* 1.4 78.1 - - + +
385A ASP* 1.3 64.6 + - - +
387A VAL* 3.4 4.3 + - - +
388A GLN* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU* 2.8 31.4 + - - +
382A GLU* 3.6 7.7 - - + +
384A ARG* 1.3 77.6 - - - +
386A LEU* 1.3 62.8 + - - +
388A GLN* 3.4 10.3 + - - +
389A ARG* 3.0 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 3.5 42.4 - - + +
214A ARG* 4.0 25.4 - - + +
215A LEU* 4.3 20.4 - - + +
218A ASP* 5.3 3.6 - - - +
382A GLU* 2.9 18.2 + - + +
383A MET* 3.6 8.7 - - - +
385A ASP* 1.3 76.2 - - - +
387A VAL* 1.3 58.4 + - - +
389A ARG* 3.4 26.8 - - - +
390A GLU* 2.9 56.4 + - + +
122B LYS 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL* 4.8 15.9 - - + +
211A TYR* 4.0 22.7 - - + -
383A MET* 3.0 40.9 + - + +
384A ARG* 4.0 5.2 - - - +
386A LEU* 1.3 78.4 - - - +
388A GLN* 1.3 59.4 + - - +
390A GLU* 4.5 3.8 - - - +
391A THR* 2.8 48.9 + - - +
392A GLY* 3.4 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ARG* 3.0 19.7 + - - +
385A ASP* 3.7 10.8 - - - +
387A VAL* 1.3 78.9 - - - +
389A ARG* 1.3 56.5 + - - +
392A GLY* 2.8 38.1 + - - +
358B ARG* 2.9 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 5.2 1.8 + - - +
385A ASP* 3.0 38.8 + - - +
386A LEU* 3.4 39.6 - - - +
388A GLN* 1.3 76.4 - - - +
390A GLU* 1.3 59.6 + - + +
121B GLY* 3.3 42.2 + - - -
122B LYS 3.9 9.9 + - - +
123B LEU* 3.8 27.6 - - + +
357B SER* 3.5 38.1 + - - +
358B ARG* 2.8 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 3.6 39.3 + - + +
214A ARG* 3.4 14.3 + - - -
236A VAL 5.5 0.7 - - - +
386A LEU* 2.9 34.8 + - + +
387A VAL 4.0 2.2 - - - +
389A ARG* 1.3 78.0 + - - +
391A THR* 1.3 63.4 + - - +
122B LYS 5.0 0.3 - - - +
123B LEU* 3.4 17.9 - - + +
127B ASP* 2.8 42.1 - - - +
131B LEU* 4.9 13.3 - - - +
358B ARG* 4.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 3.6 50.6 + - + +
206A PRO* 4.5 4.7 - - + +
211A TYR* 3.7 28.1 - - + +
387A VAL* 2.8 37.4 + - - +
390A GLU* 1.3 78.4 - - - +
392A GLY* 1.3 64.3 + - - +
358B ARG* 4.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A VAL* 3.4 2.5 + - - -
388A GLN* 2.8 31.0 + - - +
391A THR* 1.3 82.7 - - - +
358B ARG* 2.6 29.2 + - - +
----------------------------------------------------------
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