Contacts of the strand formed by residues 386 - 390 (chain A) in PDB entry 1CK7
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 LYS 386 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ASN* 2.7 55.5 + - + +
344A SER* 3.1 16.7 + - - +
376A ALA* 3.3 10.4 - - - +
377A THR* 2.9 31.6 + - - +
378A THR* 4.2 15.4 + - + +
381A TYR* 4.0 3.3 - - - +
384A ASP* 3.3 25.8 - - + +
385A ARG* 1.3 80.6 - - - +
387A TRP* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.7 29.2 - + + +
38A PRO* 3.2 26.2 + - + +
40A ASP* 4.2 13.7 - - + -
342A GLY* 3.3 22.9 - - - -
343A ASN* 2.7 42.2 + - - +
344A SER* 2.8 14.3 + - - -
368A ARG* 3.8 9.0 - - - -
374A TRP* 3.5 28.0 - + + -
375A CYS 3.2 15.9 - - - +
377A THR* 3.9 3.8 - - - +
381A TYR* 3.9 17.7 - + + -
385A ARG 4.0 1.6 - - - -
386A LYS* 1.3 74.8 - - - +
388A GLY* 1.3 85.2 + - - +
389A PHE* 3.4 49.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A THR* 3.7 24.8 + - - -
341A GLY 4.0 5.6 - - - -
374A TRP* 3.2 2.9 - - - +
375A CYS* 2.9 30.5 + - - +
377A THR* 4.6 0.2 - - - +
387A TRP* 1.3 89.6 - - - +
389A PHE* 1.3 64.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 4.2 7.2 - - - -
41A VAL* 6.4 0.9 - - + -
187A LYS* 6.5 0.4 - - - -
339A THR* 3.2 6.9 - - - -
340A VAL* 2.7 51.9 + - + +
341A GLY* 4.8 1.6 - - - -
342A GLY 4.5 4.5 - - - -
368A ARG* 2.8 39.7 - - - -
372A LYS* 3.3 48.7 - - + +
373A MET 3.3 17.9 - - - +
374A TRP* 4.0 5.2 - - + -
387A TRP* 3.4 25.8 - + - -
388A GLY* 1.3 73.4 - - - -
390A CYS* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS* 5.8 0.7 + - - -
338A SER 4.0 3.4 - - - +
340A VAL* 5.0 2.7 - - - +
349A CYS* 4.4 2.0 - - - -
363A CYS* 2.4 52.7 - - + -
373A MET* 3.1 13.9 + - + +
374A TRP* 3.6 17.7 - - - -
375A CYS* 3.9 10.1 - - - -
389A PHE* 1.3 78.6 - - - +
391A PRO* 1.3 81.3 - - + +
392A ASP* 3.3 6.1 + - - +
----------------------------------------------------------
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