Contacts of the strand formed by residues 561 - 566 (chain A) in PDB entry 3CKM
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 THR 561 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A SER* 3.3 4.7 - - - -
488A ASP 2.9 39.2 + - - +
490A PRO* 3.3 28.9 - - - +
493A LYS* 4.1 17.7 - - + +
559A ASP 5.2 0.5 + - - -
560A MSE 1.3 75.9 + - - +
562A TRP* 1.3 71.0 + - - +
563A TYR* 3.6 28.2 - - + +
572A PRO* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A SER* 3.9 11.9 + - - -
369A ALA* 3.5 42.4 - - + -
372A LYS* 3.7 42.9 - - + +
436A TYR* 4.9 0.2 - + - -
461A TYR* 4.0 19.1 - + + -
462A ALA 3.8 11.9 - - - -
485A GLN* 3.9 13.9 - - + -
486A PHE* 3.3 40.2 - - - -
487A SER* 3.5 18.2 - - - -
560A MSE 3.9 13.0 + - - -
561A THR* 1.3 82.7 - - - +
563A TYR* 1.3 57.3 + - - +
572A PRO* 3.6 4.5 - - - +
573A VAL* 2.8 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLN* 3.2 6.9 - - - +
486A PHE* 2.8 57.3 + + + +
488A ASP* 3.6 30.3 - - + -
489A ILE 2.8 21.3 + - - -
490A PRO* 3.7 1.2 - - - +
492A PHE* 3.5 19.2 - - + -
493A LYS* 3.2 25.4 + - - +
561A THR* 3.6 28.3 - - + -
562A TRP* 1.3 72.7 - - - +
564A GLN* 1.3 63.2 + - - +
570A ILE* 4.1 6.7 - - + -
571A VAL 3.3 8.5 - - - +
572A PRO* 3.9 30.1 - - + -
573A VAL* 3.8 2.7 - - - -
583A BME 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLY* 2.9 25.4 + - - +
484A VAL 3.3 13.0 - - - +
485A GLN* 3.4 23.8 + - + +
486A PHE* 4.8 0.9 - - - -
563A TYR* 1.3 77.2 - - - +
565A TYR* 1.3 78.0 + - - +
566A GLN* 3.5 16.3 + - + -
570A ILE* 3.4 6.0 - - - -
571A VAL* 2.8 39.5 + - + +
573A VAL* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ALA* 3.6 17.0 + - + -
467A SER* 4.1 1.7 - - - -
472A ASN* 2.7 24.8 + - - -
477A PHE* 3.7 15.8 - + - -
478A ILE* 4.2 24.5 - - + +
481A MSE 3.4 52.0 - - + +
482A ASN* 4.0 3.6 - - - -
483A GLY* 2.8 26.8 + - - -
484A VAL* 3.1 20.9 + - + -
486A PHE* 3.6 29.2 - + - -
564A GLN* 1.3 75.2 - - - +
566A GLN* 1.3 60.2 + - - +
569A ALA 3.5 3.1 - - - +
570A ILE* 3.4 28.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
478A ILE* 5.4 0.2 - - - +
482A ASN* 3.5 2.9 - - - -
564A GLN* 3.5 15.5 + - + +
565A TYR* 1.3 75.1 - - - +
567A ASP* 1.3 88.6 + - + +
568A GLY 3.2 1.5 - - - +
569A ALA* 2.7 26.1 + - - +
571A VAL* 3.1 35.1 - - + +
----------------------------------------------------------
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