Contacts of the strand formed by residues 566 - 570 (chain C) in PDB entry 1P4K
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 TYR 566 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ASN* 4.9 4.0 - - - -
306C ILE* 3.5 20.9 - - + -
308C LEU* 3.7 20.6 - - + -
528C PRO* 3.6 10.7 - - - +
529C GLN* 4.5 4.3 + - - +
559C ALA 3.2 13.7 - - - +
560C LEU* 3.9 2.9 - - + -
564C GLY 4.0 4.0 - - - -
565C GLU* 1.3 77.0 - - - +
567C GLY* 1.3 63.3 + - - +
577C PHE* 3.9 24.7 - + - -
579C VAL* 3.9 11.9 - - + -
581C ASP* 4.8 1.6 - - - -
586C ARG* 3.1 19.2 + - - -
588C GLU* 3.0 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 567 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C LEU* 4.3 1.7 - - - +
528C PRO* 3.6 1.2 - - - +
529C GLN* 3.9 19.7 - - - -
532C CYS* 4.2 5.4 - - - -
558C ILE* 3.4 2.1 - - - +
559C ALA 2.8 30.7 + - - +
566C TYR* 1.3 85.7 - - - +
568C ALA* 1.3 63.3 + - - +
577C PHE* 4.9 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 568 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C GLN* 3.8 16.4 + - - +
532C CYS* 3.8 6.5 - - - -
557C PHE 3.2 15.9 - - - +
558C ILE* 3.8 7.9 - - + -
567C GLY* 1.3 76.8 - - - +
569C TYR* 1.3 72.6 + - - +
575C PHE* 4.8 0.9 - - + -
577C PHE* 3.5 35.7 - - + -
590C PRO* 3.4 17.1 - - + +
591C GLY 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 569 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C GLN* 3.8 13.2 - - - +
532C CYS* 3.7 5.7 - - - +
533C LYS* 3.5 76.0 + - + +
536C VAL* 3.7 20.7 - - + +
537C GLU* 4.9 2.9 + - + -
556C GLY* 3.6 0.3 - - - -
557C PHE* 3.0 27.9 + - - +
568C ALA* 1.3 82.8 - - - +
570C CYS* 1.3 75.6 - - - +
575C PHE* 4.8 0.3 - - - -
590C PRO* 4.0 3.8 - - - -
591C GLY* 3.3 31.4 - - - -
592C PHE 3.5 14.1 + - - -
593C ALA* 3.7 23.2 + - + +
595C LYS* 4.0 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 570 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C VAL* 3.7 8.2 - - - +
554C GLN* 4.1 2.9 - - - +
555C VAL 3.1 15.0 - - - +
556C GLY* 3.8 1.6 - - - -
569C TYR* 1.3 81.6 - - - +
571C ILE* 1.3 60.8 + - - +
572C GLN 3.2 22.9 - - - -
573C ASP* 4.9 1.6 - - - -
575C PHE* 3.7 37.9 - - + -
590C PRO* 4.3 8.1 - - - -
591C GLY 3.1 13.5 + - - -
592C PHE* 3.1 11.0 - - - -
593C ALA 3.0 21.5 + - - -
----------------------------------------------------------
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