Contacts of the strand formed by residues 652 - 656 (chain A) in PDB entry 5ZE3
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 HIS 652 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ASN 4.5 4.5 + - - +
579A CYS* 3.1 36.0 + - - -
580A LEU* 3.8 17.5 + - - -
581A SER* 3.9 7.8 - - - -
636A THR 3.7 0.3 - - - +
637A HIS* 3.5 4.2 - - - +
638A TYR* 2.8 42.3 + - + +
639A ASP* 4.5 1.1 + - - +
650A GLU* 5.9 0.2 - - - -
651A GLY* 1.3 87.5 + - - -
653A LYS* 1.3 72.0 + - - +
654A ALA* 3.8 3.8 - - + +
695A CYS 5.9 1.3 - - - +
697A TRP* 3.6 22.6 + + - +
698A VAL* 3.6 12.3 - - + +
699A ASP* 3.1 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A GLU 4.1 5.0 - - - +
634A VAL* 3.7 18.6 - - + -
636A THR 3.2 5.8 - - - -
637A HIS* 3.5 45.0 - - + -
639A ASP* 5.6 1.3 - - - -
647A LYS* 3.4 27.4 - - - +
650A GLU 5.4 1.2 + - - -
651A GLY 5.7 0.8 - - - -
652A HIS* 1.3 79.8 - - - +
654A ALA* 1.3 66.7 + - - +
655A SER* 3.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A GLU 3.9 0.4 - - - -
634A VAL* 3.4 3.5 - - - -
635A PHE 2.9 24.5 + - - -
636A THR* 3.1 26.5 + - - +
638A TYR* 4.0 17.0 - - + -
652A HIS* 3.8 5.2 - - + +
653A LYS* 1.3 78.9 - - - +
655A SER* 1.3 60.6 + - - +
656A PHE* 4.0 15.9 - - + -
695A CYS* 5.0 11.9 - - + +
696A GLN* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A HIS* 4.0 10.4 + - - -
626A HIS* 5.1 0.9 - - - -
630A HIS* 2.6 42.4 + - - +
632A MET 3.2 11.0 - - - -
633A GLU* 3.3 24.9 - - - -
635A PHE 4.4 0.2 - - - +
653A LYS 3.7 1.0 + - - -
654A ALA* 1.3 75.1 - - - +
656A PHE* 1.3 70.0 + - - +
689A TYR* 4.0 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 656 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A SER* 4.4 4.7 - - - -
603A ILE* 4.3 12.1 - - + -
630A HIS* 3.4 5.8 + - - -
631A SER* 3.2 21.5 + - - -
632A MET* 3.0 13.1 + - + +
635A PHE* 3.4 43.3 - + + -
636A THR* 3.8 18.2 - - + -
638A TYR* 3.5 24.7 - - - -
654A ALA* 4.0 13.5 - - + -
655A SER* 1.3 86.6 - - - +
657A CYS* 1.3 68.8 + - - +
658A LEU* 3.8 6.1 + - + +
687A ASP* 4.5 7.2 - - - -
689A TYR* 3.2 51.4 - + + -
696A GLN* 4.4 0.4 - - - -
----------------------------------------------------------
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