Contacts of the helix formed by residues 422 - 437 (chain A) in PDB entry 5KX8
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 ASP 422 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TRP* 4.6 3.8 + - - -
420A ASP 3.5 5.3 + - - +
421A ALA* 1.3 72.7 - - - +
423A SER* 1.3 62.5 + - - +
424A THR* 3.3 13.4 + - - +
425A SER* 2.9 41.0 + - - -
426A VAL* 3.2 22.0 + - - +
206C ASN* 3.6 31.4 + - + +
207C ASN* 3.5 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLU* 3.0 32.1 + - - -
414A ILE* 5.2 3.8 - - - +
421A ALA 3.9 1.6 + - - -
422A ASP* 1.3 69.2 - - - +
424A THR* 1.3 60.6 + - - +
426A VAL* 3.9 5.5 - - - +
427A GLU* 2.9 48.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASP* 3.3 11.2 + - - -
423A SER* 1.3 80.0 - - - +
425A SER* 1.3 59.5 + - - +
427A GLU* 3.3 8.5 + - - +
428A ALA* 2.9 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TRP* 2.8 31.7 + - - -
289A CYS* 5.2 1.3 - - - -
422A ASP* 2.9 27.6 + - - -
424A THR* 1.3 76.4 - - - +
426A VAL* 1.3 60.6 + - - +
428A ALA* 3.2 9.6 + - - +
429A MET* 2.9 25.3 + - - +
457A MET* 3.7 29.7 - - - +
458A THR* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TRP* 3.6 31.0 - - + -
381A ILE* 3.9 19.7 - - + +
410A ILE* 4.4 9.6 - - + -
414A ILE* 3.6 38.8 - - + -
421A ALA* 4.0 18.2 - - + -
422A ASP 3.2 17.3 + - - +
423A SER 3.9 3.6 - - - +
425A SER* 1.3 76.5 + - - +
427A GLU* 1.3 52.5 + - - +
429A MET* 3.0 5.4 + - - +
430A TYR* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR* 5.8 0.3 + - - -
410A ILE* 3.8 23.3 - - + +
411A GLU* 5.2 4.7 - - - +
423A SER* 2.9 35.6 + - - +
424A THR* 3.6 7.1 - - - +
426A VAL* 1.3 75.2 - - + +
428A ALA* 1.3 57.3 + - - +
430A TYR* 3.3 10.0 + - + +
431A SER* 2.8 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A THR* 2.9 16.1 + - + +
425A SER* 3.4 10.3 - - - +
426A VAL 3.2 0.4 - - - -
427A GLU* 1.3 76.8 - - - +
429A MET* 1.4 60.5 + - - +
431A SER* 3.4 9.3 + - - -
432A VAL* 3.3 24.1 + - - +
453A LEU 5.7 0.6 - - - +
457A MET* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TRP* 3.6 31.4 - - + -
288A ARG 4.3 2.9 - - - +
289A CYS* 4.1 10.1 - - - -
292A ALA* 3.7 22.9 - - + -
377A LEU* 4.1 24.3 - - + +
380A ILE* 3.8 19.3 - - + -
381A ILE* 3.8 14.8 - - + -
425A SER 2.9 9.2 + - - +
426A VAL 3.5 6.7 - - - +
428A ALA* 1.4 72.2 - - - +
430A TYR* 1.3 65.7 + - - +
432A VAL* 3.2 9.8 + - - +
433A ALA* 3.0 19.6 + - - +
454A LEU* 4.4 4.0 - - + -
457A MET* 3.7 32.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 3.7 27.4 - - + -
381A ILE* 3.7 9.1 - - + +
399A ILE* 5.0 1.3 - - + -
400A LYS* 3.5 29.1 + - + +
403A ILE* 3.3 44.5 - - + +
404A GLU* 5.2 1.3 - - + +
410A ILE* 3.5 43.1 - - + -
426A VAL 2.8 15.0 + - - +
427A GLU* 3.6 8.3 - - - +
429A MET* 1.3 76.5 - - - +
431A SER* 1.4 54.8 + - - +
433A ALA* 3.0 3.8 + - - +
434A SER* 2.8 47.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLU 2.8 20.9 + - - -
428A ALA* 3.5 9.9 - - - -
429A MET 3.2 0.4 - - - -
430A TYR* 1.4 74.5 - - - +
432A VAL* 1.3 62.6 + - - +
434A SER* 3.2 8.3 + - - -
435A GLN* 3.0 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 3.6 21.1 - - + -
428A ALA 3.3 13.2 + - - +
429A MET 3.2 7.7 + - - +
431A SER* 1.3 76.5 - - - +
433A ALA* 1.3 56.5 + - - +
435A GLN* 3.3 11.2 + - - +
436A CYS* 2.9 31.2 + - - -
445A PRO* 6.1 0.7 - - + -
450A VAL* 4.0 29.4 - - + +
453A LEU* 3.6 36.6 - - + +
454A LEU* 4.2 17.7 - - + -
457A MET* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY* 3.8 20.0 - - - +
377A LEU* 3.9 17.0 - - + +
378A LEU* 3.8 23.6 - - + +
381A ILE* 4.9 0.2 - - + -
429A MET 3.0 12.7 + - - +
430A TYR* 3.0 9.4 + - + +
432A VAL* 1.3 71.4 - - - +
434A SER* 1.3 60.5 + - - +
436A CYS* 3.2 5.6 + - - +
437A LEU* 2.9 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS* 2.9 54.7 + - - +
404A GLU* 4.1 7.8 + - - +
430A TYR* 2.8 33.8 + - - -
431A SER* 3.2 11.4 + - - -
433A ALA* 1.3 72.0 - - - +
435A GLN* 1.3 63.9 + - - +
437A LEU* 3.2 7.0 + - - -
438A HIS* 3.5 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER* 3.0 41.7 + - - +
432A VAL* 3.6 7.8 - - - +
434A SER* 1.3 75.3 - - - +
436A CYS* 1.3 63.7 + - - +
438A HIS* 3.5 20.6 + - - +
443A LYS 5.0 0.3 - - - +
444A ARG* 3.8 1.7 - - - -
445A PRO* 3.3 32.8 - - + +
449A LYS* 5.5 1.4 - - - +
453A LEU* 3.8 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 3.4 31.6 - - - +
371A TYR* 3.4 11.7 + - - -
373A PHE* 4.6 5.6 - - - -
374A GLY* 3.6 15.7 - - - -
377A LEU* 4.8 0.2 - - - -
432A VAL* 2.9 29.1 + - - +
433A ALA* 3.2 8.3 + - - +
435A GLN* 1.3 75.0 - - - +
437A LEU* 1.3 57.0 + - - +
438A HIS 3.2 4.4 + - - -
444A ARG* 3.4 21.5 - - - -
445A PRO* 4.2 1.8 - - - -
450A VAL* 3.6 33.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A TYR* 3.4 44.0 - - + +
374A GLY 4.1 7.0 - - - +
375A VAL* 3.7 20.2 - - + +
378A LEU* 3.5 36.6 - - + -
397A LEU* 4.4 9.4 - - + -
400A LYS* 3.6 30.0 + - + +
433A ALA 2.9 20.9 + - - +
434A SER 3.2 7.3 + - - +
436A CYS* 1.3 74.3 - - - +
438A HIS* 1.3 63.6 + - - +
439A GLU* 3.3 17.8 + - - +
----------------------------------------------------------
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