Contacts of the helix formed by residues 438 - 448 (chain D) in PDB entry 5ZRV
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 VAL 438 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D GLY 3.2 8.4 + - - -
435D CYS* 4.9 1.0 - - - +
436D ARG 3.0 1.2 + - - -
437D LEU* 1.3 78.4 - - - +
439D MET* 1.3 57.5 + - - +
441D ALA* 3.1 3.9 + - - +
442D ALA* 2.8 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLY* 6.0 6.7 - - - +
436D ARG 3.3 6.8 + - - -
438D VAL* 1.3 77.1 - - - +
440D ALA* 1.3 56.7 + - - +
441D ALA 3.1 0.2 - - - -
442D ALA* 3.0 3.4 + - - +
443D ASN* 2.9 30.1 + - - +
444D ARG 4.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D ARG 3.4 9.1 + - - -
437D LEU* 3.3 10.0 + - - +
438D VAL 3.2 0.8 - - - -
439D MET* 1.3 75.8 - - - +
441D ALA* 1.3 58.9 + - - +
444D ARG* 4.3 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D LEU 2.9 13.4 + - - -
438D VAL* 3.1 4.2 + - - +
440D ALA* 1.3 78.2 - - - +
442D ALA* 1.3 58.5 + - - +
444D ARG* 3.5 1.4 + - - -
445D LEU* 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D LYS 5.6 7.7 - - - +
438D VAL 2.8 14.0 + - - -
439D MET* 3.0 3.5 + - - +
441D ALA* 1.3 73.9 - - - +
443D ASN* 1.3 65.6 + - - +
445D LEU 3.3 1.4 + - - -
446D ARG* 3.0 20.6 + - - -
470D GLU 6.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 443 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D MET* 2.9 14.8 + - - +
442D ALA* 1.3 73.0 - - - +
444D ARG* 1.3 55.8 + - - +
446D ARG* 3.5 2.2 + - - +
447D LYS* 3.0 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 444 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D MET 4.2 2.2 + - - -
440D ALA* 4.3 9.4 + - - +
441D ALA 3.5 7.1 + - - -
442D ALA 3.1 1.0 - - - -
443D ASN* 1.3 76.5 - - - +
445D LEU* 1.3 58.1 + - - +
447D LYS* 2.9 17.0 + - - -
448D GLU 3.3 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D ALA 2.9 19.0 + - - -
442D ALA 3.9 0.4 - - - -
444D ARG* 1.3 70.1 - - - +
446D ARG* 1.3 60.5 + - - +
448D GLU 2.9 17.4 - - - +
449D GLY 3.1 16.6 - - - +
450D GLY 4.0 7.8 - - - +
471D ALA* 6.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 446 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D ALA 3.0 16.4 + - - -
443D ASN* 3.8 2.7 - - - +
445D LEU* 1.3 78.8 - - - +
447D LYS* 1.3 59.3 + - - +
448D GLU 2.8 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 447 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443D ASN 3.0 11.5 + - - -
444D ARG* 2.9 9.2 + - - +
446D ARG* 1.3 78.3 - - - +
448D GLU* 1.3 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 448 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D ARG 3.3 9.3 + - - -
445D LEU* 2.9 9.1 - - - +
446D ARG* 2.8 17.3 - - - +
447D LYS* 1.3 75.7 - - - +
449D GLY* 1.3 63.8 + - - +
----------------------------------------------------------
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