Contacts of the helix formed by residues 437 - 458 (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 THR 437 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLY* 3.4 25.1 + - - +
422A GLN* 3.0 11.7 + - - -
423A VAL 3.0 21.5 + - - -
424A THR* 2.8 25.4 + - - +
435A ILE 3.2 0.8 + - - -
436A SER* 1.3 71.0 - - - +
438A GLU* 1.3 62.7 + - - +
440A TYR* 3.2 2.5 + - + +
441A GLN* 2.9 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLN* 5.2 4.3 + - - +
422A GLN 4.8 0.4 + - - -
436A SER* 3.2 8.7 + - - +
437A THR* 1.3 77.8 - - - +
439A ARG* 1.3 65.6 + - + +
441A GLN* 3.5 10.0 + - - +
442A ALA* 3.0 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLN 3.0 23.2 + - - -
389A GLU* 3.7 13.9 + - - +
390A HIS 3.0 29.3 + - - -
391A ARG* 3.8 36.3 + - - +
435A ILE* 4.8 7.0 - - + -
436A SER* 3.1 21.8 + - - +
438A GLU* 1.3 79.8 - - + +
440A TYR* 1.3 56.6 + - - +
442A ALA* 3.1 8.0 + - - +
443A TRP* 2.9 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A THR* 3.8 33.7 - - + +
426A LEU* 5.6 1.1 - - + -
435A ILE* 4.3 10.3 - - + +
436A SER 3.0 12.7 + - - +
437A THR* 3.6 7.6 - - + +
439A ARG* 1.3 77.5 - - - +
441A GLN* 1.3 68.3 + - + +
443A TRP* 3.2 20.7 + + - +
444A TRP* 3.1 19.4 + - - +
485A LEU* 3.7 30.1 - - + -
488A GLU* 2.6 32.0 + - - +
489A TRP* 3.0 32.0 + + - -
492A GLU* 4.3 1.9 + - - -
494A ARG* 4.0 8.3 + - - -
1514A CL 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A THR* 2.9 40.8 + - + +
438A GLU* 3.9 7.5 - - - +
440A TYR* 1.3 78.2 - - + +
442A ALA* 1.3 57.2 + - - +
444A TRP* 3.3 4.0 + - - +
445A GLN* 3.0 34.7 + - + +
1514A CL 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLU* 3.0 19.0 + - + +
439A ARG* 3.1 6.7 + - - +
441A GLN* 1.3 74.9 - - - +
443A TRP* 1.3 65.8 + - + +
445A GLN* 3.4 7.6 + - - +
446A ALA* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ARG 3.7 23.4 + - - -
392A GLU* 3.6 21.5 - - - -
435A ILE* 3.9 26.7 - - + -
439A ARG* 2.9 21.2 + - + +
440A TYR* 3.2 20.4 + + - +
442A ALA* 1.3 78.4 - - + +
444A TRP* 1.3 62.3 + - - +
446A ALA* 3.2 7.1 + - - +
447A VAL* 3.0 26.6 + - - +
473A TYR* 4.4 12.8 + - + -
474A PHE* 3.5 32.2 - + + -
477A LEU* 3.9 24.6 - - + +
481A VAL* 5.7 0.4 - - + -
485A LEU* 3.6 33.7 - - + -
489A TRP* 4.0 5.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A TYR 3.1 9.8 + - - +
441A GLN 3.3 6.5 + - - +
443A TRP* 1.3 78.4 - - - +
445A GLN* 1.3 77.1 + - - +
447A VAL* 3.1 20.1 + - + -
448A THR* 2.9 59.5 + - - +
489A TRP* 3.6 34.0 - + + -
494A ARG* 3.1 60.5 - - + +
495A LEU* 3.7 26.0 - - + -
504A LEU* 4.5 4.3 - - + -
1514A CL 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN* 3.0 20.9 + - + +
442A ALA* 3.9 7.4 - - - +
443A TRP 3.3 0.4 - - - -
444A TRP* 1.3 94.7 + - - +
446A ALA* 1.3 61.1 + - - +
448A THR* 3.6 13.4 - - - +
449A ARG* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ALA 3.1 13.6 + - - +
443A TRP* 3.5 9.2 - - - +
445A GLN* 1.3 75.0 - - - +
447A VAL* 1.3 64.9 + - + +
449A ARG* 3.6 3.5 + - - +
450A ALA* 3.0 25.5 + - - +
473A TYR* 3.9 38.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A TRP 3.0 20.1 + - - +
444A TRP* 3.7 26.5 - - + +
446A ALA* 1.3 74.6 - - + +
448A THR* 1.3 67.5 + - - +
450A ALA* 3.2 4.9 + - - +
451A LEU* 2.9 42.1 + - + +
469A LEU* 4.2 23.1 - - + -
473A TYR* 5.2 0.7 - - + -
474A PHE* 3.6 31.4 - - + -
489A TRP* 4.0 12.8 - - + -
495A LEU* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A TRP* 2.9 49.7 + - - +
445A GLN* 3.6 22.9 - - - +
447A VAL* 1.3 75.2 - - - +
449A ARG* 1.3 67.0 + - + +
451A LEU* 3.9 0.5 - - - +
452A GLU* 2.7 53.7 + - - +
504A LEU* 3.7 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN 3.2 19.0 + - - +
446A ALA* 4.1 3.8 - - - +
448A THR* 1.3 80.6 - - + +
450A ALA* 1.3 61.6 + - - +
452A GLU* 3.3 15.9 + - - +
453A GLU* 2.9 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA 3.0 19.9 + - - +
447A VAL 3.7 4.0 - - - +
449A ARG* 1.3 75.1 - - - +
451A LEU* 1.3 59.9 + - - +
453A GLU* 3.5 5.5 + - - +
454A PHE* 2.9 29.2 + - - +
464A LEU* 4.9 3.3 - - + +
469A LEU* 4.5 10.8 - - + -
472A ARG* 4.1 24.1 + - - +
473A TYR* 4.1 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A VAL* 2.9 30.9 + - + +
450A ALA* 1.3 75.9 - - + +
452A GLU* 1.3 57.9 + - - +
454A PHE* 3.2 4.1 + - + +
455A HIS* 2.8 43.8 + - + +
464A LEU* 3.8 30.5 - - + +
469A LEU* 5.1 2.5 - - + -
495A LEU* 3.5 31.4 - - + -
502A VAL* 3.6 32.1 - - + +
503A ALA* 4.0 9.4 - - - -
504A LEU* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A THR* 2.7 49.7 + - - +
449A ARG* 3.6 17.1 - - - +
451A LEU* 1.3 75.5 - - - +
453A GLU* 1.3 70.6 + - - +
455A HIS* 3.5 3.5 + - - +
456A SER* 3.1 27.3 + - - -
504A LEU* 3.6 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ARG* 2.9 60.3 + - + +
450A ALA* 3.8 5.6 - - - +
452A GLU* 1.3 86.8 - - - +
454A PHE* 1.3 56.8 + - - +
456A SER* 3.3 9.6 + - - -
457A ARG* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ALA 2.9 18.6 + - - +
451A LEU* 3.2 7.6 + - + +
453A GLU* 1.3 76.3 - - - +
455A HIS* 1.3 69.9 + + - +
457A ARG* 3.3 1.1 + - - +
458A TYR* 2.8 54.2 + + + +
461A ARG* 3.6 42.2 - - + -
463A GLY* 3.4 31.9 - - - -
464A LEU* 3.7 39.9 - - + -
472A ARG* 5.1 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 2.8 25.6 + - + +
452A GLU* 4.0 4.0 - - - +
454A PHE* 1.3 84.8 - + - +
456A SER* 1.3 60.1 + - - +
458A TYR 4.5 3.1 + - - -
459A PRO* 3.2 27.7 - - - +
461A ARG 4.9 0.2 + - - -
463A GLY* 4.3 11.6 - - - -
502A VAL 4.5 1.1 - - - -
503A ALA* 3.5 26.1 - - + +
504A LEU* 3.0 45.2 + - + +
507A PHE* 3.5 46.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A GLU 3.1 19.0 + - - -
453A GLU* 3.6 10.7 + - - -
454A PHE 3.2 0.2 - - - -
455A HIS* 1.3 77.7 - - - +
457A ARG* 1.3 60.8 + - - +
459A PRO* 3.6 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A GLU 2.9 17.3 + - - +
454A PHE* 4.7 0.4 - - - -
456A SER* 1.3 78.2 - - - +
458A TYR* 1.3 103.0 + - + +
459A PRO* 3.5 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A PHE* 2.8 41.9 + + + +
455A HIS* 4.1 2.9 - - - +
457A ARG* 1.3 123.2 + - + +
459A PRO* 1.3 63.0 - - - +
460A LEU 3.1 6.7 + - - -
461A ARG* 3.2 73.5 + - + +
507A PHE* 4.6 0.5 - - - -
----------------------------------------------------------
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