Contacts of the helix formed by residues 583 - 592 (chain A) 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 583 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LEU 5.6 0.2 - - - -
572A ASP* 4.6 23.6 - - - -
575A THR* 5.9 1.3 - - - -
576A THR* 5.5 4.0 - - - +
582A VAL* 1.3 75.8 - - - +
584A ALA* 1.3 54.9 + - - -
585A ALA 3.2 3.1 - - - -
586A THR* 2.8 9.6 + - - +
587A LEU* 2.6 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A VAL* 6.5 1.8 - - - +
571A LEU 5.4 2.8 + - - -
572A ASP* 5.3 3.0 - - - +
575A THR* 6.3 0.4 - - - +
582A VAL 3.9 0.4 + - - -
583A GLY* 1.3 69.4 - - - -
585A ALA* 1.3 59.5 + - - +
587A LEU* 3.2 4.1 + - - +
588A VAL* 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A PRO 6.1 1.1 - - - -
572A ASP* 6.0 1.4 - - - +
583A GLY* 3.2 1.0 - - - -
584A ALA* 1.3 77.2 - - - +
586A THR* 1.3 55.3 + - - +
588A VAL* 3.2 2.5 + - - +
589A ASP* 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A VAL* 5.5 1.6 - - - -
583A GLY* 2.8 15.6 + - - +
585A ALA* 1.3 74.5 - - - +
587A LEU* 1.3 59.2 + - - +
589A ASP* 3.5 4.4 - - - +
590A GLU* 2.8 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A VAL 5.3 0.2 - - - -
583A GLY 2.6 17.2 + - - -
584A ALA* 3.2 6.7 + - - +
585A ALA 3.1 0.2 - - - -
586A THR* 1.3 74.6 - - - +
588A VAL* 1.3 57.3 + - - +
590A GLU* 3.2 2.2 + - - +
591A VAL* 3.1 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A ALA 2.9 14.1 + - - -
585A ALA* 3.2 3.5 + - - +
587A LEU* 1.3 76.6 - - - +
589A ASP* 1.3 57.8 + - - +
590A GLU 3.2 1.5 + - - -
591A VAL* 4.1 6.0 + - - +
592A GLY 4.1 12.1 + - - -
593A VAL* 4.8 3.8 + - - -
629A GLY* 6.0 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ALA 2.9 16.0 + - - -
586A THR* 3.5 6.3 - - - +
588A VAL* 1.3 76.1 - - - +
590A GLU* 1.3 57.6 + - - +
592A GLY* 4.6 3.5 + - - +
629A GLY* 5.8 4.0 - - - -
630A ARG* 4.7 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A THR 2.8 15.8 + - - -
587A LEU* 3.2 4.4 + - - +
589A ASP* 1.3 80.2 - - - +
591A VAL* 1.3 62.2 + - - +
592A GLY 3.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LEU 3.1 13.5 + - - -
588A VAL* 4.1 2.1 + - - +
589A ASP 3.7 0.2 - - - -
590A GLU* 1.3 77.4 - - - +
592A GLY* 1.3 64.6 + - - +
595A VAL* 5.4 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A VAL 4.1 8.7 + - - -
589A ASP 4.6 3.1 + - - -
590A GLU 3.4 4.2 + - - +
591A VAL* 1.3 82.4 - - - +
593A VAL* 1.3 64.4 + - - -
594A ASP 3.2 4.2 + - - -
595A VAL 3.6 3.7 + - - -
596A ALA* 3.6 14.6 + - - -
629A GLY* 6.0 0.4 - - - -
630A ARG 5.9 4.5 - - - -
----------------------------------------------------------
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