Contacts of the helix formed by residues 453 - 468 (chain A) in PDB entry 2VIF
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 453 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 3.4 18.6 + - - -
440A PHE* 3.7 13.7 - - - -
451A HIS* 3.3 4.0 + - - +
452A THR* 1.3 80.7 + - - +
454A ILE* 1.3 59.4 + - - +
455A VAL* 3.5 5.0 + - - +
456A ASP* 2.6 35.1 + - - +
457A LEU* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 3.7 12.1 - - + -
375A GLU* 3.0 21.5 + - + +
376A LEU* 3.4 24.5 - - + -
379A LEU* 4.3 13.0 - - + -
408A VAL* 4.5 13.2 - - + -
418A LEU* 3.4 29.8 - - + -
433A ILE* 4.9 9.6 - - + -
440A PHE* 3.9 22.9 - - + -
453A SER* 1.3 67.8 - - - +
455A VAL* 1.3 66.3 + - - +
457A LEU* 3.2 9.5 + - + +
458A ILE* 2.9 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 2.8 22.0 + - + +
379A LEU* 3.9 28.0 - - + -
384A TRP* 4.2 13.5 - - + -
453A SER* 3.3 3.1 - - - +
454A ILE* 1.3 75.4 - - - +
456A ASP* 1.3 62.2 + - - +
458A ILE* 3.3 5.5 + - - +
459A GLU* 2.8 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A HIS* 4.0 17.8 + - + +
452A THR* 3.5 18.4 + - - +
453A SER* 2.6 29.8 + - - +
455A VAL* 1.3 80.6 - - - +
457A LEU* 1.3 56.6 + - - +
459A GLU* 3.8 6.8 - - - +
460A HIS* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ILE* 4.1 19.7 - - + -
440A PHE* 4.2 6.3 - - + -
441A SER* 3.9 31.4 - - - +
442A PHE* 3.8 43.3 - - + +
445A GLN* 5.8 0.4 - - - +
451A HIS* 3.6 32.6 - - + +
453A SER 3.0 14.1 + - - +
454A ILE* 3.5 10.8 - - - +
456A ASP* 1.3 76.4 - - - +
458A ILE* 1.3 62.7 + - + +
460A HIS* 3.4 3.4 + - + +
461A SER* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A TRP* 3.3 36.8 - - + -
406A PHE* 3.7 32.5 - - + -
408A VAL* 3.7 18.4 - - + -
420A LEU* 4.6 10.1 - - + -
442A PHE* 5.3 5.4 - - + -
454A ILE* 2.9 26.3 + - + +
455A VAL* 3.9 3.8 - - - +
457A LEU* 1.3 78.9 - - + +
459A GLU* 1.3 60.5 + - - +
461A SER* 3.1 9.8 + - - -
462A ILE* 2.8 36.2 + - + +
487A LEU* 5.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A VAL* 2.8 28.4 + - + +
456A ASP* 3.8 9.0 - - - +
458A ILE* 1.3 72.7 - - - +
460A HIS* 1.3 63.0 + - - +
462A ILE* 3.3 21.3 + - - +
463A GLY* 3.0 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A HIS* 3.4 35.3 + + + -
456A ASP 2.9 18.3 + - - +
457A LEU* 3.6 6.1 - - + +
459A GLU* 1.3 77.1 - - - +
461A SER* 1.3 61.2 + - - +
463A GLY* 3.3 2.5 + - - -
464A ASP* 2.9 50.4 + - - +
574P THR* 3.2 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A PHE* 3.2 25.7 - - - -
457A LEU* 2.9 16.0 + - - +
458A ILE* 3.1 10.6 + - - -
460A HIS* 1.3 77.3 - - - +
462A ILE* 1.3 61.1 + - - +
464A ASP* 3.3 10.8 + - - +
465A SER* 2.8 28.4 + - - -
470A PHE* 3.8 26.5 - - - +
487A LEU* 4.0 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A PHE* 4.2 15.7 - - + -
458A ILE* 2.8 36.6 + - + +
459A GLU* 3.7 22.9 - - - +
461A SER* 1.3 75.9 - - - +
463A GLY* 1.3 58.3 + - - +
465A SER* 3.1 8.8 + - - -
466A GLU* 2.9 43.6 + - + +
487A LEU* 4.2 26.0 - - + +
488A THR 4.2 10.5 - - - +
490A PRO* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLU* 3.0 15.9 + - - -
460A HIS* 3.3 3.8 + - - -
461A SER 3.2 0.2 - - - -
462A ILE* 1.3 78.4 - - - +
464A ASP* 1.3 62.1 + - - +
466A GLU* 3.2 18.6 + - - +
467A ASN* 3.2 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A HIS* 2.9 35.1 + - - +
461A SER* 3.6 10.3 - - - +
463A GLY* 1.3 75.2 - - - +
465A SER* 1.3 63.2 + - - +
467A ASN* 3.1 7.2 + - - +
468A GLY 3.0 5.0 + - - -
469A ALA* 2.8 33.6 + - - +
470A PHE* 3.7 19.5 - - + +
574P THR* 2.6 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A SER 2.8 14.3 + - - -
462A ILE* 3.1 13.2 + - - -
464A ASP* 1.3 76.5 - - - +
466A GLU* 1.3 62.4 + - - +
468A GLY* 3.3 11.5 + - - -
470A PHE* 3.5 18.1 - - - +
485A VAL 3.9 3.7 - - - +
486A ARG* 2.9 23.5 - - - +
487A LEU* 2.7 36.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ILE* 2.9 36.2 + - + +
463A GLY* 3.2 11.6 + - - +
465A SER* 1.3 77.7 + - - +
467A ASN* 1.3 62.6 + - - +
468A GLY 3.5 0.4 + - - -
486A ARG* 5.6 9.1 + - - +
487A LEU 4.6 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A GLY 3.2 16.9 + - - +
464A ASP* 3.1 11.9 + - - +
466A GLU* 1.3 81.4 - - - +
468A GLY* 1.3 60.4 + - - +
469A ALA* 4.7 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ASP 3.0 3.0 + - - -
465A SER* 3.3 10.4 + - - -
466A GLU 3.5 0.6 - - - -
467A ASN* 1.3 79.9 - - - +
469A ALA* 1.3 58.4 + - - +
470A PHE 3.7 3.5 - - - +
471A CYS* 5.9 1.6 - - - +
484A PRO* 5.3 9.2 - - - +
----------------------------------------------------------
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