Contacts of the helix formed by residues 592 - 605 (chain E) 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 GLY 592 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588E VAL 4.1 8.9 + - - +
589E ASP 4.6 2.9 + - - -
590E GLU 3.4 4.0 + - - +
591E VAL* 1.3 81.9 - - - +
593E VAL* 1.3 64.7 + - - -
594E ASP 3.2 4.1 + - - -
595E VAL 3.6 3.9 + - - -
596E ALA* 3.6 14.7 + - - -
629E GLY* 6.0 0.7 - - - -
630E ARG 5.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 593 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588E VAL 4.8 5.2 + - - -
592E GLY* 1.3 72.4 - - - -
594E ASP* 1.3 60.8 + - - +
596E ALA* 3.5 11.7 + - - +
597E LYS 4.2 3.3 + - - -
628E LEU 5.2 4.3 + - - -
629E GLY* 5.1 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 594 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592E GLY 3.2 1.0 - - - -
593E VAL* 1.3 79.1 - - - +
595E VAL* 1.3 59.9 + - - +
596E ALA 3.4 0.7 + - - -
597E LYS* 3.9 7.1 + - - -
598E HIS 4.3 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 595 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591E VAL 5.4 2.2 + - - -
592E GLY 3.6 6.8 + - - -
593E VAL 3.5 0.2 - - - -
594E ASP* 1.3 75.1 - - - +
596E ALA* 1.3 59.3 + - - +
597E LYS 3.3 0.4 - - - -
598E HIS* 3.3 4.6 + - - +
599E VAL* 2.9 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 596 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592E GLY 3.6 9.2 + - - -
593E VAL* 3.5 9.2 + - - +
594E ASP 3.2 1.8 - - - -
595E VAL* 1.3 75.1 - - - +
597E LYS* 1.3 59.6 + - - +
599E VAL* 3.6 1.7 - - - +
600E ALA* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 597 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593E VAL 4.2 4.4 + - - -
594E ASP 3.9 5.7 + - - -
595E VAL 3.3 0.6 - - - -
596E ALA* 1.3 75.7 - - - +
598E HIS* 1.3 56.1 + - - +
600E ALA* 3.2 2.8 + - - +
601E GLU* 2.9 24.4 + - - -
619E LEU 6.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 598 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E ASP 4.3 3.4 + - - -
595E VAL* 3.3 9.8 + - - +
597E LYS* 1.3 76.5 - - - +
599E VAL* 1.3 58.3 + - - +
600E ALA 3.1 0.2 - - - -
601E GLU* 3.1 1.9 + - - +
602E ASP* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 599 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478E ALA* 6.4 2.5 - - - +
552E ALA* 5.2 9.5 - - - -
595E VAL 2.9 16.2 + - - -
596E ALA* 3.6 3.1 - - - +
598E HIS* 1.3 73.5 - - - +
600E ALA* 1.3 59.7 + - - +
602E ASP* 4.4 3.4 + - - +
603E LEU 5.1 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 600 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596E ALA 2.9 15.0 + - - -
597E LYS* 3.6 4.7 - - - +
598E HIS 3.1 0.2 - - - -
599E VAL* 1.3 81.0 - - - +
601E GLU* 1.3 60.4 + - - +
602E ASP 3.4 0.6 + - - -
603E LEU 4.9 0.2 - - - -
604E GLY* 3.6 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 601 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597E LYS 2.9 14.7 + - - -
598E HIS* 3.1 3.1 + - - +
600E ALA* 1.3 75.9 - - - +
602E ASP* 1.3 59.9 + - - +
603E LEU 3.6 0.2 - - - -
604E GLY* 4.6 1.6 - - - +
605E LYS* 2.8 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 602 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478E ALA* 6.5 1.1 - - - +
598E HIS 2.9 15.7 + - - -
599E VAL* 4.4 2.2 - - - +
600E ALA 3.4 1.4 - - - -
601E GLU* 1.3 80.4 - - - +
603E LEU* 1.3 59.9 + - - +
605E LYS* 3.4 8.8 + - - -
606E VAL* 4.0 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543E PRO 6.1 0.9 - - - -
599E VAL 5.1 3.4 + - - -
600E ALA 4.5 1.6 + - - -
602E ASP* 1.3 71.7 - - - +
604E GLY* 1.3 56.1 + - - +
605E LYS 3.1 1.6 - - - -
606E VAL* 2.8 4.6 + - - +
607E PHE 2.6 16.7 + - - +
608E GLY* 2.5 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 604 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600E ALA 3.6 18.8 + - - -
601E GLU* 3.7 2.9 - - - -
602E ASP 3.4 0.4 - - - -
603E LEU* 1.3 75.1 - - - +
605E LYS* 1.3 61.9 + - - +
606E VAL 4.6 1.2 - - - -
608E GLY* 3.5 22.9 + - - +
609E GLU* 4.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 605 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601E GLU 2.8 17.4 + - - -
602E ASP 3.4 5.1 + - - -
603E LEU 3.1 0.8 - - - -
604E GLY* 1.3 79.6 - - - +
606E VAL* 1.3 57.1 + - - +
----------------------------------------------------------
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