Contacts of the helix formed by residues 378 - 390 (chain A) in PDB entry 2V9V
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 378 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLY* 1.3 74.6 - - - -
379A PRO* 1.3 76.9 - - - +
380A GLU* 3.7 7.5 + - - +
381A LYS* 3.1 24.6 + - - +
382A ILE* 2.9 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLY 4.4 1.6 - - - +
378A SER* 1.3 88.2 - - - +
380A GLU* 1.3 61.2 + - - +
382A ILE* 3.3 13.7 + - + +
383A LEU* 3.0 23.7 + - - +
403A ALA* 5.1 2.6 - - - +
405A LEU* 3.8 32.5 - - + +
409A GLU* 4.2 10.8 - - - +
413A LEU* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A SER* 3.2 7.0 + - - +
379A PRO* 1.3 78.0 - - - +
381A LYS* 1.3 58.7 + - - +
383A LEU* 3.4 2.8 + - - +
384A ALA* 3.0 28.6 + - + +
409A GLU* 5.6 0.2 + - - -
413A LEU* 3.7 39.2 - - + +
416A SER* 4.8 6.3 + - - -
417A MET* 4.0 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLY* 4.0 27.5 - - - +
378A SER* 3.1 19.3 + - - +
380A GLU* 1.3 76.2 - - - +
382A ILE* 1.3 67.5 + - + +
384A ALA* 3.4 6.9 + - - +
385A GLN* 3.0 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLY* 3.6 29.2 - - - +
378A SER 2.9 14.5 + - - +
379A PRO* 3.3 13.2 + - + +
381A LYS* 1.3 79.2 - - + +
383A LEU* 1.3 64.0 + - - +
385A GLN* 3.4 8.8 + - - +
386A ILE* 3.1 37.8 + - + +
402A ARG 4.8 2.0 - - - +
403A ALA* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PRO 3.0 16.9 + - - +
380A GLU* 3.9 4.5 - - - +
382A ILE* 1.3 74.8 - - - +
384A ALA* 1.3 67.0 + - - +
386A ILE* 3.2 11.6 + - + +
387A ILE* 3.1 37.0 + - + +
399A ALA* 3.9 38.1 - - + +
403A ALA* 4.2 6.1 - - + -
405A LEU* 4.2 9.6 - - + -
410A THR* 4.2 22.2 - - + +
413A LEU* 3.8 34.5 - - + -
414A LEU* 4.9 2.0 - - + -
417A MET* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLU* 3.0 19.4 + - + +
381A LYS* 3.7 7.4 - - + +
382A ILE 3.4 0.2 - - - -
383A LEU* 1.3 77.2 - - - +
385A GLN* 1.3 58.3 + - - +
387A ILE* 3.3 2.0 + - - +
388A GLN* 2.8 42.3 + - + +
417A MET* 3.9 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS* 3.0 23.8 + - + +
382A ILE* 3.8 8.9 - - - +
384A ALA* 1.3 74.2 - - - +
386A ILE* 1.3 68.0 + - + +
388A GLN* 4.5 2.7 - - - +
389A GLU* 2.9 69.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ILE* 3.1 26.3 + - + +
383A LEU* 3.2 8.0 + - + +
385A GLN* 1.3 78.9 - - + +
387A ILE* 1.3 63.1 + - - +
389A GLU* 4.2 1.5 - - - +
390A HIS* 3.4 21.9 + - + +
394A LEU* 3.9 26.7 - - + -
399A ALA* 4.3 12.8 - - + +
402A ARG* 3.7 26.5 - - + +
403A ALA* 3.7 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 3.1 35.3 + - + +
384A ALA* 4.1 2.5 - - - +
386A ILE* 1.3 77.5 - - + +
388A GLN* 1.3 68.4 + - - +
390A HIS* 3.1 21.6 + - + +
393A GLY* 5.6 0.7 - - - -
394A LEU* 4.3 15.5 - - + -
399A ALA* 4.7 3.6 - - + -
414A LEU* 3.5 32.1 - - + -
417A MET* 4.3 11.2 - - - -
423A VAL* 4.1 15.3 - - + -
434A ALA* 4.2 16.4 - - + +
435A ILE 4.0 6.1 - - - -
436A SER* 3.8 26.4 + - - +
----------------------------------------------------------
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 ALA* 2.8 34.0 + - + +
385A GLN* 4.4 2.7 - - - +
387A ILE* 1.3 72.9 - - - +
389A GLU* 1.3 58.6 + - + +
417A MET* 5.9 0.6 - - - -
422A GLN* 3.0 37.7 + - - +
423A VAL* 3.7 17.0 - - - +
436A SER* 3.0 28.3 + - - +
438A GLU* 5.2 6.1 + - - +
439A ARG* 3.0 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN* 2.9 56.7 + - + +
386A ILE* 4.2 1.9 - - - +
388A GLN* 1.3 78.3 - - + +
390A HIS* 1.3 62.7 + - - +
391A ARG* 3.3 8.0 + - - +
439A ARG* 3.7 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 3.4 17.9 + - + +
387A ILE 3.1 11.5 + - - +
389A GLU* 1.3 76.0 - - - +
391A ARG* 1.3 60.1 + - - +
392A GLU* 3.1 29.3 + - + -
393A GLY* 3.1 45.7 + - - +
394A LEU* 4.1 21.4 - - + +
402A ARG* 3.9 27.6 + - - -
436A SER* 5.0 0.7 + - - -
439A ARG* 3.0 19.9 - - - -
----------------------------------------------------------
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