Contacts of the helix formed by residues 377 - 391 (chain A) in PDB entry 2VKT
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 377 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 2.7 36.6 + - - -
340A ILE* 3.8 11.8 - - - +
343A GLU* 3.5 19.0 + - - -
375A ILE 3.3 2.0 + - - -
376A ARG* 1.3 75.9 - - - +
378A THR* 1.3 64.2 + - - +
379A LEU 3.3 2.5 - - - -
380A GLY 3.4 0.5 + - - -
381A LYS* 3.1 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY 3.7 6.8 + - - -
375A ILE* 2.8 45.2 + - + +
376A ARG 3.2 1.7 + - - -
377A GLY* 1.3 77.0 - - - +
379A LEU* 1.3 64.9 + - + +
381A LYS* 3.3 12.4 + - - +
382A LEU* 3.1 31.6 + - + +
400A LEU* 5.1 1.7 - - - +
404A LEU* 3.9 25.5 - - + +
424A PHE* 4.3 10.2 - - + -
425A ARG* 4.7 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU* 3.6 23.5 + - + +
377A GLY 3.3 0.4 - - - -
378A THR* 1.3 81.2 - - + +
380A GLY* 1.3 60.4 + - - +
382A LEU* 3.3 19.7 + - + +
383A GLN* 3.1 31.9 + - + +
411A ARG* 6.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 3.3 27.1 - - - -
342A LEU* 3.7 15.3 - - - +
343A GLU* 3.3 17.4 + - - +
377A GLY 3.4 1.2 + - - -
378A THR 3.4 0.4 - - - -
379A LEU* 1.3 75.6 - - - +
381A LYS* 1.3 60.1 + - - +
383A GLN* 3.3 10.7 + - - +
384A ALA* 3.0 22.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
304A VAL* 4.0 24.7 - - + +
305A GLY* 4.2 10.3 - - - -
339A SER* 2.9 26.7 - - - +
369A VAL* 4.1 21.2 - - + +
370A PRO 4.8 8.7 + - - -
372A GLY* 4.7 12.9 + - - +
373A PHE 5.5 2.4 + - - -
374A GLY 5.5 1.0 + - - -
376A ARG 4.3 11.9 + - - -
377A GLY 3.1 17.1 + - - +
378A THR* 3.3 8.3 + - - +
380A GLY* 1.3 75.0 - - - +
382A LEU* 1.3 57.5 + - - +
384A ALA* 3.1 4.0 + - - +
385A ILE* 3.0 34.1 + - + +
400A LEU* 4.6 16.9 - - + +
404A LEU* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A THR* 3.1 31.7 + - + +
379A LEU* 3.3 20.2 + - + +
381A LYS* 1.3 76.3 - - - +
383A GLN* 1.3 55.6 + - - +
385A ILE* 3.2 6.1 + - + +
386A SER* 3.0 33.0 + - - -
404A LEU* 3.4 44.6 - - + +
407A ILE* 4.4 7.9 - - + -
408A GLU* 4.0 21.0 - - + +
411A ARG* 3.7 26.7 - - - +
425A ARG* 6.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.6 13.6 - - + +
343A GLU* 5.0 2.0 - - + -
344A LYS* 4.7 20.2 + - - +
358A TRP* 4.2 31.1 - - + -
379A LEU* 3.1 24.8 + - + +
380A GLY* 3.4 13.2 - - - +
382A LEU* 1.3 75.9 - - + +
384A ALA* 1.3 62.5 + - - +
386A SER* 3.6 8.5 + - - -
387A TRP* 3.2 21.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
304A VAL* 4.0 32.1 - - + -
342A LEU* 4.2 3.3 - - + +
361A LEU* 4.0 22.6 - - + +
367A ILE* 4.7 9.1 - - + +
369A VAL* 5.0 3.6 - - + -
380A GLY 3.0 13.8 + - - +
381A LYS 3.1 8.5 + - - +
383A GLN* 1.3 76.3 - - - +
385A ILE* 1.3 58.3 + - - +
387A TRP* 3.4 4.2 + - - +
388A ALA* 3.1 27.2 + - - +
395A PHE* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL* 4.3 10.3 - - + -
381A LYS* 3.0 22.7 + - + +
382A LEU* 3.2 8.5 + - - +
384A ALA* 1.3 74.1 - - - +
386A SER* 1.3 65.0 + - - +
388A ALA* 3.4 6.2 + - - +
389A ARG* 2.9 22.7 + - - +
395A PHE* 3.7 23.6 - - + -
401A GLY 4.1 7.2 - - - +
404A LEU* 3.9 18.4 - - + +
405A ALA* 3.8 32.8 - - + +
408A GLU* 4.0 22.9 - - + +
520A PHE* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU 3.0 17.5 + - - -
383A GLN* 3.8 10.8 + - - -
385A ILE* 1.3 75.4 - - - +
387A TRP* 1.3 57.4 + - - +
389A ARG* 3.2 4.0 + - - +
390A THR* 2.8 40.6 + - - +
408A GLU* 2.5 31.3 + - - +
412A ASN* 3.8 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TRP* 4.2 17.9 - + + -
361A LEU* 4.1 28.7 + - + -
362A CYS* 3.5 36.8 + - + +
367A ILE* 3.9 19.1 - - + -
383A GLN 3.2 11.3 + - - +
384A ALA 3.5 8.7 - - - +
385A ILE 3.3 0.2 - - - -
386A SER* 1.3 79.9 - - - +
388A ALA* 1.3 58.9 + - - +
390A THR* 4.0 3.4 - - - -
391A LYS* 2.9 72.7 + - + +
393A ILE* 4.0 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 3.8 16.2 - - + -
384A ALA 3.1 14.5 + - - +
385A ILE 3.4 4.0 + - - +
387A TRP* 1.3 79.0 - - - +
389A ARG* 1.3 60.0 + - - +
392A LYS 3.3 0.5 + - - -
393A ILE* 3.0 36.2 + - - +
395A PHE* 3.9 25.4 - - + -
517A HIS* 3.0 22.2 - - - -
520A PHE* 4.8 0.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
385A ILE 2.9 18.5 + - - +
386A SER* 3.6 4.9 - - - +
388A ALA* 1.3 77.1 - - - +
390A THR* 1.3 88.6 + - - +
391A LYS 3.4 0.2 + - - -
392A LYS* 3.5 14.9 + - - -
408A GLU* 2.5 51.6 + - - +
409A PHE* 4.3 19.7 - - - -
412A ASN* 4.0 17.6 + - - +
413A CYS* 3.6 25.5 - - - -
514A LEU* 3.7 25.8 - - + +
517A HIS* 3.8 10.7 + - - -
520A PHE* 4.0 17.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A SER* 2.8 30.7 + - - +
387A TRP* 3.6 5.5 + - - -
389A ARG* 1.3 99.8 - - - +
391A LYS* 1.3 75.3 + - - +
392A LYS* 3.4 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TRP* 2.9 61.7 + - + +
390A THR* 1.3 86.5 - - - +
392A LYS* 1.3 70.7 + - - +
393A ILE* 3.3 24.8 + - + +
----------------------------------------------------------
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