Contacts of the strand formed by residues 560 - 563 (chain A) in PDB entry 2DB3
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 560 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE* 3.9 10.9 - - + +
485A LEU* 6.2 0.2 - - - +
488A GLN 5.3 4.0 + - - -
490A ASP 5.4 1.6 - - - +
491A GLY 2.9 3.6 + - - +
492A THR* 3.2 15.0 + - - -
493A ILE* 2.9 28.8 + - - +
558A ILE* 3.5 2.8 - - - +
559A LYS* 1.3 83.0 - - + +
561A VAL* 1.3 75.6 + - - +
562A ILE* 3.7 25.2 - - + +
580A THR* 3.6 0.4 + - - -
588A ARG* 3.0 64.7 + - + +
589A ALA 4.2 0.2 - - - -
590A THR* 2.6 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A ILE* 3.5 17.7 - - + -
495A PHE* 3.7 22.9 - - + -
558A ILE* 4.0 0.2 - - + -
560A HIS* 1.3 75.8 - - - +
562A ILE* 1.3 66.0 + - - +
563A ASN* 4.1 3.0 + - - +
576A ARG* 3.5 32.3 - - + +
577A ILE* 4.1 15.3 - - + +
579A ARG* 4.0 7.4 - - + -
580A THR* 3.4 26.5 - - - +
588A ARG 3.1 6.5 + - - +
589A ALA* 3.2 4.1 - - + +
590A THR 2.8 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LEU* 4.2 19.3 - - + -
484A ILE* 3.8 29.8 - - + -
485A LEU* 4.5 3.1 - - + -
492A THR* 3.7 20.4 - - - +
493A ILE 2.8 12.5 + - - +
494A VAL* 4.2 12.8 - - + -
495A PHE* 2.7 29.8 + - - +
560A HIS* 3.7 18.6 - - + +
561A VAL* 1.3 77.9 - - - +
563A ASN* 1.3 64.5 + - - +
564A TYR* 3.2 11.8 + - - +
590A THR* 3.1 10.8 - - - +
592A PHE* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A PHE* 3.8 7.5 - - - +
561A VAL* 4.8 4.9 + - - +
562A ILE* 1.3 73.2 - - - +
564A TYR* 1.3 63.0 + - - +
565A ASP 3.1 11.2 - - - +
566A MET* 4.4 4.0 - - - -
567A PRO* 4.7 2.5 - - - -
573A TYR* 3.6 23.4 - - - -
576A ARG* 3.0 41.2 + - - +
577A ILE* 3.8 14.1 - - - +
589A ALA* 5.5 0.4 - - - +
590A THR 2.8 9.3 + - - -
591A SER* 2.9 30.1 + - - +
592A PHE* 2.9 27.5 + - - +
----------------------------------------------------------
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