Contacts of the strand formed by residues 562 - 567 (chain A) in PDB entry 1P4J
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 LEU 562 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A SER* 1.3 70.9 - - - +
563A PHE* 1.3 76.7 + - - +
564A ASP* 3.2 12.7 + - + +
599A VAL* 4.6 6.1 - - + -
600A PRO 2.8 17.1 + - - +
601A ARG* 3.4 18.5 - - + +
602A THR 2.9 23.6 + - - -
661A ASP* 3.7 8.7 - - + -
662A LEU* 3.8 20.2 - - + -
787A VAL* 4.1 22.0 - - + +
788A SER* 5.0 1.6 - - - -
791A TYR* 3.6 50.5 - - + -
797A TRP* 4.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LYS* 3.7 41.7 - - + -
545A PHE* 4.5 9.9 - + - -
546A ALA* 4.8 0.2 - - + -
557A ILE* 4.0 18.8 - - + -
558A ASN 3.6 21.1 - - - -
559A PRO* 4.2 9.9 - - + -
561A SER* 3.6 13.9 - - - -
562A LEU* 1.3 73.6 - - - +
564A ASP* 1.3 60.9 + - - +
565A VAL* 3.6 4.8 + - + +
602A THR* 3.6 19.1 - - + -
604A MET* 3.5 22.4 - - + -
656A VAL* 6.6 0.2 - - + -
659A ALA* 3.2 29.4 - - + +
660A ALA* 4.2 2.9 - - - -
661A ASP* 2.8 21.3 + - - +
662A LEU 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A LEU* 3.2 10.4 + - + +
563A PHE* 1.3 69.4 - - - +
565A VAL* 1.3 57.5 + - - +
579A ASN* 4.8 1.2 + - - +
582A HIS* 4.8 2.6 + - - -
601A ARG* 2.5 37.4 + - + +
602A THR 2.9 13.3 + - - +
603A VAL* 3.2 26.4 - - + +
604A MET 2.6 33.4 + - - +
662A LEU* 3.9 9.0 - - - +
664A GLU* 2.5 34.4 - - - +
784A GLN* 3.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A PHE* 4.1 13.0 - - + +
564A ASP* 1.3 80.7 + - - +
566A GLN* 1.3 62.8 - - - +
567A VAL* 3.7 33.5 + - + -
604A MET* 3.3 32.1 - - + +
656A VAL* 4.0 17.5 - - + -
660A ALA* 4.1 18.2 - - + -
662A LEU 3.0 15.8 + - - +
663A SER* 3.9 2.3 - - - -
664A GLU* 3.1 26.4 + - - -
681A PHE* 4.1 10.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A VAL* 1.3 72.8 - - - +
567A VAL* 1.3 58.7 + - - +
568A LYS* 3.7 23.7 - - + +
574A LYS 3.4 21.5 - - - +
576A GLN* 3.6 28.1 + - + +
579A ASN* 3.1 39.1 + - - +
604A MET 2.8 10.7 + - - +
605A ILE* 3.3 11.0 - - + +
606A GLY 3.1 22.7 + - - +
664A GLU* 3.7 26.0 - - + +
666A ILE* 3.8 11.6 + - - +
681A PHE* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A VAL* 3.7 15.7 + - + -
566A GLN* 1.3 78.5 - - - +
568A LYS* 1.3 70.6 + - - +
605A ILE 4.8 0.2 - - - -
606A GLY* 3.4 12.3 - - - +
645A LEU* 3.8 23.6 - - + -
648A TYR* 3.5 44.9 + - + +
656A VAL* 4.5 8.1 - - + -
657A ILE* 4.9 1.3 - - + -
664A GLU 5.5 0.2 + - - -
665A GLN* 5.8 0.3 + - - -
677A GLY* 5.8 1.4 - - - -
681A PHE* 3.7 33.0 - - + -
999A PLP 3.9 7.4 + - - +
----------------------------------------------------------
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