Contacts of the helix formed by residues 461 - 469 (chain D) in PDB entry 5VOT
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 ASN 461 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D ASP* 4.2 10.3 + - - +
449D LYS* 5.0 2.4 - - - +
451D GLY* 3.1 12.9 - - - -
452D ALA* 2.3 53.9 + - - +
454D ASP* 5.7 4.6 - - + +
459D ILE* 3.9 3.3 + - + +
460D TRP* 1.3 73.9 - - - +
462D GLY* 1.3 69.7 + - - +
464D VAL* 3.3 2.3 - - - +
465D GLY* 3.0 11.7 + - - -
652D SER* 3.8 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 462 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D VAL* 3.8 7.6 - - - -
447D ASP* 3.2 30.5 + - - -
449D LYS 4.0 3.4 - - - -
451D GLY* 4.0 8.3 - - - -
461D ASN* 1.3 77.5 - - - +
463D MET* 1.3 60.2 + - - -
465D GLY* 3.0 3.5 + - - -
466D GLU* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 463 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D THR* 3.2 39.3 - - + +
399D THR* 3.8 23.8 - - - +
400D ILE* 4.5 17.3 - - + -
445D VAL* 3.6 15.5 - - + +
449D LYS 3.9 14.8 + - - +
450D TYR* 3.3 23.5 + - + +
462D GLY* 1.3 69.5 - - - -
464D VAL* 1.3 65.9 + - + +
466D GLU* 2.9 18.8 + - - +
467D LEU* 3.0 19.5 + - - +
475D ALA* 5.2 7.4 - - + -
477D ALA* 4.4 18.4 - - + -
478D PRO 6.4 0.4 - - - -
479D LEU* 5.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 464 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D TYR 3.7 4.9 + - - +
451D GLY* 3.6 29.4 - - - +
460D TRP* 3.5 38.1 - - + -
461D ASN 3.3 8.1 - - - +
462D GLY 3.1 0.2 - - - -
463D MET* 1.3 78.1 - - + +
465D GLY* 1.3 57.8 + - - +
467D LEU* 3.3 3.9 + - - +
468D VAL* 2.9 37.0 + - + +
479D LEU* 5.2 14.1 - - + +
485D ARG* 5.1 15.5 - - + +
488D VAL* 4.6 9.4 - - + -
489D ILE* 4.9 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 465 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D TRP 3.3 21.5 + - - -
461D ASN 3.0 11.9 + - - -
462D GLY 3.0 2.9 + - - -
464D VAL* 1.3 76.8 - - - +
466D GLU* 1.3 57.1 + - - +
468D VAL* 3.9 3.1 - - - -
469D TYR* 2.6 51.1 + - - +
471D LYS* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 466 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D THR* 4.6 6.9 - - - +
445D VAL* 4.2 15.7 - - + +
446D GLY 5.1 3.1 + - - -
462D GLY 2.9 20.2 + - - +
463D MET* 2.9 22.2 + - + +
465D GLY* 1.3 75.4 - - - +
467D LEU* 1.3 54.7 + - - +
471D LYS* 2.8 49.5 + - - +
472D ALA* 2.7 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 467 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D THR* 5.3 0.7 - - + -
463D MET 3.0 15.6 + - - +
464D VAL 4.0 2.5 - - - +
466D GLU* 1.3 73.4 - - - +
468D VAL* 1.3 67.2 + - - +
470D GLY* 3.5 8.7 + - - -
472D ALA* 3.2 30.3 - - + +
473D ASP 3.6 3.8 - - - -
474D ILE* 3.4 23.6 - - - +
475D ALA* 3.7 18.6 - - + -
489D ILE* 4.2 19.7 - - + -
735D ALA* 3.5 37.5 - - + +
736D THR* 3.8 5.6 - - - +
737D PRO* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 468 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D TRP* 4.7 11.2 - - + -
464D VAL* 2.9 28.5 + - + +
465D GLY* 3.7 7.0 - - - +
467D LEU* 1.3 78.9 - - - +
469D TYR* 1.3 81.7 + - + +
470D GLY 3.2 4.7 + - - -
488D VAL* 4.2 22.0 - - + +
489D ILE* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 469 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D LYS 4.4 2.8 + - - -
459D ILE* 3.5 31.2 - - + +
460D TRP* 3.3 30.6 + - - +
465D GLY* 2.6 37.3 + - - +
468D VAL* 1.3 86.1 - - + +
470D GLY* 1.3 55.2 + - - +
471D LYS* 3.0 43.1 + - + +
----------------------------------------------------------
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