Contacts of the helix formed by residues 460 - 475 (chain A) in PDB entry 5VR6
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 460 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ASP* 3.4 8.1 - - - -
458A SER* 3.1 7.9 + - - -
459A PRO* 1.3 79.6 - - - +
461A LEU* 1.3 66.7 + - - +
462A ARG* 3.9 19.1 + - - -
463A CYS* 3.0 27.3 + - - +
464A VAL* 3.1 10.2 + - - +
489A PHE* 3.2 30.1 - - - -
503A TRP* 3.8 4.8 + - - -
565A HIS* 3.3 10.3 - - - -
704A SO4 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PRO* 5.0 8.3 - - + -
417A ARG* 3.9 6.7 - - - +
424A TYR* 3.6 33.4 - - + +
427A ASP* 2.9 29.5 + - - +
428A ALA 4.3 0.4 - - - +
429A PRO* 4.0 17.5 - - + -
459A PRO 3.3 4.8 + - - -
460A SER* 1.3 69.9 - - - +
462A ARG* 1.3 58.1 + - - +
464A VAL* 3.1 5.5 + - + +
465A GLN* 2.8 53.2 + - + +
504A ILE* 4.1 12.3 - - + -
509A LEU* 4.1 24.7 - - + -
514A LEU* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A HIS* 3.4 18.6 + - + +
383A ARG* 3.6 42.0 - - + +
427A ASP* 4.4 13.9 + - - +
428A ALA 3.6 21.4 + - - +
429A PRO 4.6 0.4 - - - -
430A ILE* 3.6 23.6 - - + +
460A SER* 3.9 13.3 + - - -
461A LEU* 1.3 79.5 - - - +
463A CYS* 1.3 55.5 + - - +
465A GLN* 4.1 3.4 - - - -
466A THR* 2.6 37.4 + - - -
490A GLU* 3.1 19.6 + - - -
565A HIS* 3.4 12.8 + - - -
701A SO4 2.8 29.3 + - - -
704A SO4 3.1 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A HIS* 4.1 7.2 - - - -
457A CYS* 4.1 2.2 - - - +
458A SER* 3.5 33.2 - - - +
460A SER* 3.0 20.7 + - - +
462A ARG* 1.3 80.2 - - - +
464A VAL* 1.3 59.7 - - - +
466A THR 3.4 0.3 + - - -
467A ALA* 2.9 30.3 + - - +
563A VAL* 3.5 22.0 - - - +
564A ALA* 3.4 26.9 - - - -
565A HIS* 3.8 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A CYS* 3.6 24.9 - - - -
458A SER 3.7 4.7 - - - +
459A PRO* 4.1 9.4 - - + +
460A SER 3.1 13.6 + - - +
461A LEU* 3.1 9.4 + - - +
463A CYS* 1.3 75.6 - - - +
465A GLN* 1.3 57.9 + - - +
467A ALA* 3.1 3.8 + - - +
468A HIS* 2.9 27.9 + - - +
482A ILE* 4.1 2.4 - - + +
484A VAL* 4.6 1.1 - - + -
509A LEU* 3.8 23.8 - - + -
514A LEU* 3.9 22.0 - - + -
516A VAL* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A PRO* 6.1 1.0 - - - +
414A LEU* 4.8 8.5 - - - +
415A PRO* 5.2 6.5 - - - +
429A PRO* 3.2 20.0 - - - +
430A ILE* 2.8 48.2 + - + +
435A CYS* 5.8 0.2 - - - -
461A LEU* 2.8 43.6 + - + +
462A ARG* 4.1 1.1 - - - +
464A VAL* 1.3 71.9 - - - +
466A THR* 1.3 63.4 + - - +
468A HIS* 3.4 1.2 + - - +
469A ASN* 2.9 34.2 + - - +
514A LEU* 4.2 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A HIS* 3.8 4.7 - - - -
381A GLY* 2.9 31.2 + - - +
430A ILE* 3.6 9.8 - - - +
438A ALA* 3.5 20.4 - - + +
462A ARG 2.6 23.6 + - - -
463A CYS 3.7 4.3 - - - -
464A VAL 3.3 0.2 - - - -
465A GLN* 1.3 77.2 - - - +
467A ALA* 1.3 55.5 + - - +
469A ASN 3.3 1.2 + - - -
470A ILE* 2.9 30.7 + - + +
563A VAL* 3.7 17.9 - - + -
597A LEU* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A VAL* 4.3 4.8 - - + +
457A CYS* 4.3 2.5 - - + -
463A CYS 2.9 18.0 + - - +
464A VAL 3.1 2.2 + - - +
466A THR* 1.3 75.1 - - - +
468A HIS* 1.3 63.1 + - - +
470A ILE* 3.3 6.1 + - - +
471A LEU* 3.0 26.2 + - - +
482A ILE* 3.6 33.0 - - + -
561A LEU* 6.0 0.2 - - - +
563A VAL* 3.8 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ARG* 5.6 0.6 + - - -
464A VAL 2.9 11.6 + - - +
465A GLN 3.6 2.7 - - - +
466A THR 3.3 0.2 - - - -
467A ALA* 1.3 76.7 - - - +
469A ASN* 1.3 69.3 + - - +
471A LEU* 3.1 9.3 + - - +
472A LYS* 3.0 53.9 + - + +
477A GLU* 4.5 4.7 - - + +
482A ILE* 3.5 12.0 - - + +
513A ASN 3.2 23.1 + - - -
514A LEU* 3.6 29.1 - - + -
515A SER* 3.2 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE* 4.2 1.2 - - - +
435A CYS* 3.8 32.0 - - - +
438A ALA* 3.5 24.5 - - + -
439A ARG* 2.9 47.8 + - + -
465A GLN* 2.9 30.1 + - - +
468A HIS* 1.3 82.8 - - - +
470A ILE* 1.3 64.8 + - - +
472A LYS* 3.3 9.3 - - - +
473A GLY 3.1 17.0 + - - -
514A LEU* 5.7 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A CYS* 4.0 27.6 - - - -
438A ALA* 3.5 23.6 - - + +
441A VAL* 4.5 6.5 - - + -
442A GLY* 3.4 17.3 - - - +
445A LEU* 4.3 7.4 - - + -
466A THR* 2.9 22.6 + - + +
467A ALA* 3.5 7.4 - - - +
469A ASN* 1.3 76.5 - - - +
471A LEU* 1.3 63.8 + - + +
473A GLY 3.2 2.3 + - - -
474A LEU* 2.9 29.3 + - + +
561A LEU* 3.9 20.6 - - + -
563A VAL* 4.0 14.6 - - + -
597A LEU* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ILE* 5.7 0.7 - - + -
455A VAL* 4.0 15.0 - - + -
467A ALA 3.0 18.2 + - - +
468A HIS* 3.1 7.2 + - - +
470A ILE* 1.3 77.0 - - + +
472A LYS* 1.3 57.3 + - - +
474A LEU* 3.2 13.9 + - + -
475A GLN 2.9 8.7 + - - -
476A GLN* 2.8 28.3 + - + +
477A GLU* 3.8 15.7 - - + +
480A LEU* 3.5 58.8 - - + +
482A ILE* 3.8 24.0 - - + -
515A SER* 4.0 13.7 - - - -
561A LEU* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ARG* 3.3 35.2 - - + +
468A HIS* 3.0 38.2 + - + +
469A ASN* 3.3 24.5 - - - +
470A ILE 3.2 0.2 - - - -
471A LEU* 1.3 75.7 - - - +
473A GLY* 1.3 63.2 + - - +
475A GLN* 3.0 19.4 + - - +
477A GLU* 3.3 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ARG* 3.5 27.4 - - - +
442A GLY 3.5 6.7 - - - +
443A GLU* 3.6 24.4 - - - +
446A LEU* 3.8 11.3 - - - +
469A ASN 3.1 8.3 + - - -
470A ILE 3.2 3.7 + - - -
472A LYS* 1.3 78.8 - - - +
474A LEU* 1.3 60.8 + - - +
475A GLN* 3.1 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A GLY* 3.5 10.5 + - - +
445A LEU* 3.5 30.7 - - + -
446A LEU* 3.7 28.9 - - + +
450A THR 4.2 11.2 - - - +
452A ILE* 3.6 31.2 - - + +
470A ILE* 2.9 28.4 + - + +
471A LEU* 3.2 24.0 + - + +
473A GLY* 1.3 73.3 - - - +
475A GLN* 1.3 67.7 + - - +
476A GLN* 3.4 20.1 + - + +
480A LEU* 4.4 4.0 - - + -
561A LEU* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLU* 6.2 1.2 - - - +
446A LEU* 3.6 23.7 - - + +
471A LEU 2.9 2.8 + - - -
472A LYS 3.0 17.4 + - - +
473A GLY 4.0 3.9 + - - +
474A LEU* 1.3 79.9 - - - +
476A GLN* 1.3 63.3 + - - +
477A GLU* 3.4 12.8 - - - -
478A ASN 5.4 0.3 + - - -
----------------------------------------------------------
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