Contacts of the helix formed by residues 406 - 429 (chain A) in PDB entry 2KR6
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 406 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A GLY 3.8 2.4 + - - -
403A ASP* 3.2 31.4 + - - +
404A TRP* 5.2 0.9 - - - -
405A ASN* 1.3 83.2 + - - +
407A THR* 1.3 69.0 + - - +
410A CYS* 3.6 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LYS* 4.6 19.3 - - + -
399A THR* 4.7 19.3 - - + +
401A SER 4.1 9.0 + - - -
402A GLY* 3.4 15.4 + - - -
403A ASP* 5.4 0.2 - - - +
406A THR* 1.3 78.8 - - - +
408A ILE* 1.3 68.5 + - - +
409A ALA 3.0 1.6 - - - -
410A CYS* 3.0 18.0 + - + +
411A PHE* 3.0 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PHE* 4.9 5.4 - - + -
391A VAL* 4.7 3.4 - - - +
392A LEU* 3.3 59.9 - - + +
395A LYS* 5.7 1.3 - - + +
396A ALA* 5.5 0.2 - - + -
402A GLY* 3.4 29.4 - - - +
403A ASP 4.2 2.0 - - - +
404A TRP 3.4 26.7 - - - +
405A ASN* 3.6 14.8 - - + -
407A THR* 1.3 75.3 - - - +
409A ALA* 1.3 79.3 + - + +
411A PHE* 3.6 6.0 + - - +
412A VAL* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ASN* 2.8 39.7 + - + +
407A THR 3.0 0.8 - - - -
408A ILE* 1.3 85.5 - - + +
410A CYS* 1.3 65.6 + - - +
412A VAL* 2.9 18.6 + - - +
413A ALA* 3.2 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A THR 3.6 15.8 + - - +
407A THR* 3.0 12.5 + - + +
409A ALA* 1.3 78.5 - - - +
411A PHE* 1.3 62.1 + - + +
413A ALA* 3.6 4.6 + - - +
414A ILE* 3.1 37.9 + - + +
460A LEU* 4.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A VAL* 3.5 39.9 - - + +
395A LYS* 3.4 48.2 - - + -
407A THR* 3.0 23.6 + - + +
408A ILE 3.8 5.6 - - - +
410A CYS* 1.3 77.1 - - + +
412A VAL* 1.3 56.0 + - - +
414A ILE* 3.2 11.9 + - + +
415A LEU* 2.7 38.0 + - - +
442A GLY* 4.3 8.1 - - - -
443A LEU* 5.6 0.9 - - - -
446A TYR* 3.6 37.0 + + - -
460A LEU* 5.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PHE* 3.4 39.3 - - + -
391A VAL* 4.7 4.9 - - + +
408A ILE* 2.9 26.8 + - + +
409A ALA* 2.9 12.0 + - - +
411A PHE* 1.3 77.0 - - - +
413A ALA* 1.3 64.7 + - - +
415A LEU* 3.2 7.3 + - - +
416A ILE* 3.2 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ALA 3.2 7.1 + - - +
410A CYS* 4.0 7.9 - - - +
412A VAL* 1.3 80.5 - - - +
414A ILE* 1.3 65.6 + - + +
416A ILE* 3.1 19.3 + - - +
417A GLY* 3.2 10.2 + - - -
456A PHE* 5.8 1.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A CYS 3.1 23.4 + - - +
411A PHE* 3.7 11.2 - - + +
413A ALA* 1.3 78.4 - - + +
415A LEU* 1.3 60.5 + - - +
417A GLY* 3.7 0.7 + - - -
418A LEU* 3.1 26.8 + - + +
446A TYR* 4.5 20.0 - - + +
456A PHE* 3.2 51.1 - - + +
457A MET* 5.0 1.6 - - - +
460A LEU* 3.4 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU 4.2 3.1 - - - +
387A ILE* 3.5 52.0 - - + +
391A VAL* 4.0 16.6 - - + -
411A PHE 2.7 18.2 + - - +
412A VAL* 3.3 9.2 - - - +
413A ALA 3.0 0.2 - - - -
414A ILE* 1.3 75.2 - - - +
416A ILE* 1.3 62.3 + - + +
418A LEU* 4.7 2.0 - - + -
419A CYS* 2.7 53.2 + - + +
442A GLY* 6.3 0.2 - - - -
446A TYR* 3.3 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 6.5 0.2 - - + -
412A VAL* 3.3 21.8 - - + +
413A ALA* 3.1 9.6 + - - +
415A LEU* 1.3 82.1 - - + +
417A GLY* 1.3 62.9 + - - +
419A CYS* 3.7 5.4 - - + +
420A LEU* 3.1 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ALA 3.2 9.5 + - - -
414A ILE* 4.2 2.0 - - - -
416A ILE* 1.3 80.6 - - - +
418A LEU* 1.3 62.7 + - - +
420A LEU* 3.2 19.7 + - - +
421A THR* 3.2 12.1 + - - -
456A PHE* 6.0 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ILE* 3.1 21.7 + - + +
415A LEU* 4.0 3.4 - - + +
417A GLY* 1.3 71.6 - - - +
419A CYS* 1.3 59.0 + - - +
420A LEU 3.1 0.3 + - - -
421A THR* 3.3 10.1 + - - +
422A LEU* 2.7 55.5 + - + +
445A PHE* 5.7 3.1 - - + -
446A TYR* 4.3 17.7 - - + +
449A THR* 6.1 2.9 - - + -
453A VAL* 6.0 5.6 - - + -
455A PRO* 3.2 40.2 - - + -
456A PHE* 3.5 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 3.9 37.7 - - - -
384A GLY* 6.3 0.2 - - - -
415A LEU* 2.7 35.4 + - + +
416A ILE* 3.7 8.1 - - + +
418A LEU* 1.3 73.4 - - - +
420A LEU* 1.3 54.6 + - - +
422A LEU* 4.3 4.9 - - - -
423A LEU* 2.7 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 3.1 16.1 + - + +
417A GLY* 3.3 13.2 - - - +
418A LEU 3.1 0.2 - - - -
419A CYS* 1.3 79.3 - - - +
421A THR* 1.3 67.6 + - + +
423A LEU* 3.3 6.8 - - - +
424A LEU* 3.2 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLY 3.2 13.9 + - - -
418A LEU* 3.4 12.4 + - - +
420A LEU* 1.3 77.4 - - + +
422A LEU* 1.3 65.9 + - - +
424A LEU* 3.0 25.1 + - + +
425A LEU* 3.2 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 2.7 39.1 + - + +
419A CYS* 4.0 5.4 - - - +
421A THR* 1.3 72.5 - - - +
423A LEU* 1.3 50.4 + - - +
425A LEU* 3.5 8.9 + - + +
426A ALA* 2.7 44.1 + - + +
431A ALA* 3.3 29.6 - - + -
432A LEU* 4.1 12.3 - - + -
437A ILE* 5.3 7.2 - - + -
438A SER 5.7 2.0 - - - +
439A ILE* 6.5 0.9 - - + -
445A PHE* 4.2 28.5 - - + -
449A THR* 5.9 3.1 - - + -
453A VAL* 6.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 4.8 18.4 - - + -
419A CYS* 2.7 29.0 + - - +
420A LEU* 3.3 6.3 - - - +
421A THR 3.0 0.2 - - - -
422A LEU* 1.3 72.0 - - - +
424A LEU* 1.3 84.3 + - + +
426A ALA* 2.9 18.2 + - + +
427A ILE* 2.9 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LEU* 3.2 23.7 + - + +
421A THR* 3.0 15.8 + - + +
423A LEU* 1.3 91.0 - - + +
425A LEU* 1.3 63.0 + - + +
427A ILE* 3.0 25.8 - - - +
428A PHE* 3.2 20.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A THR* 3.2 27.7 + - + +
422A LEU* 4.0 4.7 - - + +
424A LEU* 1.3 77.1 - - + +
426A ALA* 1.3 63.7 - - - +
427A ILE 3.3 0.2 - - - -
428A PHE* 3.6 13.8 - - + +
429A LYS 3.3 6.4 + - - -
430A LYS 3.1 27.4 + - - +
431A ALA* 3.6 34.1 - - + +
453A VAL* 5.5 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU* 2.7 26.3 + - + +
423A LEU* 2.9 12.3 + - - +
425A LEU* 1.3 78.8 - - - +
427A ILE* 1.3 58.1 + - - +
429A LYS* 4.0 1.9 + - - -
431A ALA 4.5 2.5 - - - +
437A ILE* 3.2 53.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 2.9 20.4 + - + +
424A LEU* 3.0 25.6 - - + +
426A ALA* 1.3 76.3 - - - +
428A PHE* 1.3 71.9 + - + +
429A LYS 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 3.2 26.1 + - + +
425A LEU* 3.6 16.4 - - + +
426A ALA 3.3 0.2 - - - -
427A ILE* 1.3 91.0 - - + +
429A LYS* 1.3 73.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU 3.3 1.2 + - - -
426A ALA 4.6 1.3 - - - -
427A ILE 3.4 2.0 - - - -
428A PHE* 1.3 91.6 - - + +
430A LYS* 1.3 126.4 + - + +
437A ILE* 3.2 13.9 - - - +
----------------------------------------------------------
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