Contacts of the strand formed by residues 365 - 372 (chain A) in PDB entry 5KFG
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 GLN 365 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A THR* 1.3 81.2 - - - +
366A LEU* 1.3 63.9 + - - +
367A VAL* 4.0 7.9 - - + +
384A CYS* 3.7 35.1 - - + +
385A CYS 3.7 10.8 - - - +
387A LEU* 3.7 6.2 - - - +
425A CYS 3.7 0.2 - - - +
426A ALA* 3.5 4.0 - - - -
427A THR* 2.9 51.9 + - - +
428A LYS* 3.2 38.6 + - + +
1P A 4.7 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.8 29.4 - - + -
365A GLN* 1.3 73.2 - - - +
367A VAL* 1.3 61.2 + - - +
368A VAL* 4.1 16.5 + - + +
383A ARG 4.0 0.3 - - - +
384A CYS* 3.3 2.9 - - - +
385A CYS* 2.9 59.8 + - - +
386A ALA 5.5 0.7 - - - +
387A LEU* 3.7 17.8 - - + +
395A MET* 3.7 44.6 - - + +
398A ASP* 4.8 0.9 - - + +
399A ALA* 4.6 2.0 - - + -
424A LEU* 4.4 8.3 - - + -
425A CYS 3.5 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLN* 4.0 10.8 - - - +
366A LEU* 1.3 78.0 - - - +
368A VAL* 1.3 65.3 + - - +
369A SER* 5.0 1.6 - - - +
382A ARG* 4.0 27.6 - - + +
383A ARG 3.7 8.3 - - - +
384A CYS* 4.4 7.6 - - + -
423A PHE 3.6 1.4 - - - +
424A LEU* 3.5 5.2 - - - +
425A CYS* 2.7 47.0 + - + +
427A THR* 4.0 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 4.9 5.8 - - + -
366A LEU* 4.2 13.5 - - + +
367A VAL* 1.3 78.2 - - - +
369A SER* 1.3 65.7 + - - +
370A ILE* 4.9 2.2 - - + -
381A LEU* 3.8 2.8 - - - +
382A ARG* 3.4 2.1 - - - -
383A ARG* 2.7 43.7 + - - +
385A CYS* 5.0 2.5 - - - -
399A ALA* 3.6 37.5 - - + -
402A VAL* 3.8 14.4 - - + -
403A ILE* 3.5 27.4 - - + -
423A PHE 3.4 4.5 - - - +
424A LEU* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 4.2 2.4 - - - -
368A VAL* 1.3 76.2 - - - +
370A ILE* 1.3 67.7 + - - +
379A SER* 2.7 34.1 + - - -
381A LEU 3.1 6.5 - - - -
382A ARG* 3.7 18.0 + - - -
421A MET* 3.8 6.4 - - - +
422A LEU 3.6 0.5 - - - -
423A PHE* 2.9 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 4.9 3.1 - - + -
369A SER* 1.3 80.3 + - - +
371A ARG* 1.3 65.0 + - - +
372A VAL* 4.8 6.7 - - + -
379A SER* 3.8 1.0 + - - -
380A SER* 2.8 23.8 + - - -
381A LEU* 3.1 31.8 + - + -
403A ILE* 4.3 26.5 - - + -
406A CYS* 3.9 32.5 - - + -
419A LEU* 4.0 24.0 - - + -
421A MET* 3.2 13.7 - - - +
422A LEU* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ASN* 5.6 6.7 - - - +
370A ILE* 1.3 74.8 - - - +
372A VAL* 1.3 68.6 + - - +
375A ASP 2.6 25.0 + - - +
376A LYS* 3.2 21.9 + - - +
377A ARG 2.8 20.6 + - - +
378A LEU* 3.4 19.9 - - - +
380A SER* 3.4 11.9 - - - +
419A LEU* 3.4 10.0 - - - +
420A THR* 2.9 40.8 + - - +
421A MET* 3.1 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 4.8 9.0 - - + -
371A ARG* 1.3 81.0 - - - +
373A GLN* 1.3 70.3 + - - +
374A GLY 3.2 0.2 + - - -
375A ASP* 3.2 22.4 + - + +
380A SER* 3.1 22.8 + - - +
406A CYS* 5.9 5.6 - - + +
417A PRO* 3.9 26.0 - - + +
418A PRO 3.7 3.8 - - - +
419A LEU* 4.0 17.0 - - + -
420A THR* 3.9 4.7 + - - -
----------------------------------------------------------
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