Contacts of the helix formed by residues 438 - 465 (chain C) in PDB entry 4KYI
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 GLU 438 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS* 5.4 12.1 - - + +
436C LYS 4.3 2.3 - - - +
437C SER* 1.3 90.7 + - - +
439C LYS* 1.3 60.1 + - + +
440C GLU* 4.3 10.1 - - + +
441C ILE* 3.1 21.4 + - + +
442C PHE* 2.6 41.4 + - - +
82D ARG* 5.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C GLU* 1.3 75.0 - - + +
440C GLU* 1.3 64.2 + - - +
442C PHE* 3.3 8.9 + - + +
443C GLU* 3.2 45.8 + - + +
82D ARG* 5.3 7.6 - - - +
85D SER* 5.6 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS* 4.2 16.9 - - + +
28C TYR* 2.1 41.3 + - + -
416C PRO* 4.3 9.9 - - + +
438C GLU* 3.3 8.0 - - + +
439C LYS* 1.3 81.7 - - + +
441C ILE* 1.3 69.9 + - + +
443C GLU* 3.5 12.3 + - - +
444C ALA* 3.4 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 4.2 33.4 - - + +
22C LYS* 5.0 11.7 - - + +
28C TYR* 4.2 20.9 - - + -
416C PRO* 4.1 23.6 - - + -
420C ILE* 5.8 4.9 - - + +
429C LYS* 5.0 4.7 - - - +
431C ALA* 3.6 26.7 - - + -
437C SER* 4.7 1.3 - - - +
438C GLU* 3.1 24.0 + - + +
440C GLU* 1.3 80.9 - - + +
442C PHE* 1.3 58.2 + - - +
444C ALA* 3.2 4.6 + - + +
445C SER* 2.7 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ALA* 4.2 4.7 - - - +
432C LEU* 3.3 38.7 - - + +
438C GLU 2.6 26.5 + - - +
439C LYS* 3.5 9.4 - - + +
441C ILE* 1.3 77.1 - - - +
443C GLU* 1.3 65.0 + - + +
445C SER* 4.5 3.4 - - - -
446C ALA* 3.3 17.0 + - - +
82D ARG* 3.2 56.1 - - - +
83D TYR* 3.4 39.7 - + - -
85D SER* 4.5 4.9 - - - -
86D LEU* 3.5 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LYS* 3.2 41.9 + - + +
440C GLU* 3.7 11.2 - - - +
442C PHE* 1.3 78.2 - - + +
444C ALA* 1.3 59.8 + - - +
446C ALA* 2.8 5.2 + - - +
447C HIS* 2.8 53.0 + - + +
484C ASP 5.3 0.5 - - - +
486C LYS* 4.9 12.6 - - - -
85D SER* 5.4 7.5 + - - +
86D LEU* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C HIS* 5.5 2.2 - - + -
416C PRO* 4.1 26.7 - - + -
417C LEU* 3.6 24.7 - - + +
420C ILE* 4.4 6.7 - - + +
440C GLU 3.4 10.2 + - - +
441C ILE* 3.2 8.1 + - + +
443C GLU* 1.3 78.8 - - - +
445C SER* 1.3 59.5 + - - +
446C ALA 3.1 0.4 - - - -
447C HIS* 3.6 12.7 + - + +
448C ALA* 3.3 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C ILE* 4.7 17.7 - - - +
425C HIS* 3.2 30.6 + - - -
429C LYS 5.1 1.0 + - - -
430C ASP* 4.2 1.6 + - - -
431C ALA* 3.9 25.9 + - - +
432C LEU* 3.5 28.0 - - - +
441C ILE* 2.7 22.9 + - - -
444C ALA* 1.3 72.7 - - - +
446C ALA* 1.3 58.7 + - - +
448C ALA 4.3 1.6 - - - -
449C GLN 4.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C LEU* 3.8 10.1 - - + -
442C PHE 3.3 12.3 + - - +
443C GLU 2.8 8.0 + - - +
445C SER* 1.3 79.8 - - - +
447C HIS* 1.3 64.3 + - - +
448C ALA 3.2 1.3 - - - -
449C GLN* 3.4 23.7 - - + +
450C ALA* 3.5 4.2 + - - +
55D GLY* 5.3 1.6 - - - -
86D LEU* 3.6 32.3 - - + -
89D MET* 3.6 15.3 - - + +
90D TYR* 4.4 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LEU* 3.7 18.6 - - + +
443C GLU* 2.8 47.5 + - + +
444C ALA* 3.5 11.0 + - - +
446C ALA* 1.3 78.9 - - - +
448C ALA* 1.3 56.9 + - - +
450C ALA* 3.3 3.3 + - - +
451C ILE* 3.0 33.8 + - - +
480C ILE* 3.8 11.8 - - + +
484C ASP* 4.0 15.5 + - + +
485C ALA* 3.3 34.6 - - + +
86D LEU* 4.8 3.8 - - + +
89D MET* 3.6 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LEU* 3.9 13.6 - - + +
420C ILE* 3.7 27.4 - - + +
421C LEU* 4.7 6.3 - - + +
425C HIS* 3.7 17.5 - - + +
444C ALA 3.3 14.7 + - - +
445C SER 4.6 0.2 - - - +
446C ALA 3.2 0.6 - - - -
447C HIS* 1.3 77.1 - - - +
449C GLN* 1.3 55.1 + - - +
451C ILE* 3.3 5.6 + - - +
452C LEU* 2.8 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 449 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C HIS* 3.4 30.7 + - + +
432C LEU* 4.5 8.6 - - + +
445C SER 4.7 0.2 - - - +
446C ALA* 3.4 19.0 - - - +
448C ALA* 1.3 78.9 - - - +
450C ALA* 1.3 58.6 + - - +
452C LEU* 4.0 3.5 - - - +
453C HIS* 2.8 46.4 + - + +
54D ILE* 3.5 11.9 + - - +
55D GLY* 3.1 8.6 - - - -
56D ALA* 2.4 52.3 + - + +
90D TYR* 4.2 2.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 450 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C ALA 3.5 10.1 + - - +
447C HIS 3.3 10.0 + - - +
448C ALA 3.1 0.4 - - - -
449C GLN* 1.3 81.5 - - + +
451C ILE* 1.3 64.4 + - - +
453C HIS* 3.2 5.6 + - - +
454C LEU* 3.2 24.8 + - - +
480C ILE* 3.8 19.3 - - + -
75D TRP* 4.0 22.9 - - + -
89D MET* 4.1 14.6 - - + -
90D TYR* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 451 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LEU* 4.4 7.0 - - + -
421C LEU* 4.3 18.4 - - + -
447C HIS 3.0 17.5 + - - +
448C ALA* 3.8 3.4 - - - +
450C ALA* 1.3 74.8 - - - +
452C LEU* 1.3 53.1 + - - +
454C LEU* 3.1 8.9 + - - +
455C GLN* 2.8 45.8 + - - +
477C ILE* 3.9 20.4 - - + -
480C ILE* 3.7 26.2 - - + -
481C LEU* 3.7 32.5 - - + -
499C CYS* 3.7 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C TYR* 5.1 8.5 - - - +
421C LEU* 5.9 0.8 - - + +
425C HIS* 4.1 30.7 - - + -
426C ASP* 5.4 5.2 - - + +
448C ALA 2.8 22.2 + - - +
449C GLN* 4.2 4.5 - - - +
451C ILE* 1.3 73.5 - - - +
453C HIS* 1.3 62.1 + - + +
455C GLN* 3.5 22.2 + - + +
456C GLU* 3.1 58.5 + - + +
506C LEU* 5.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C GLN* 2.8 38.7 + - + +
450C ALA* 3.3 9.6 - - - +
451C ILE 3.2 0.2 - - - -
452C LEU* 1.3 77.6 - - - +
454C LEU* 1.3 60.7 + - - +
456C GLU* 3.7 14.4 + - - +
457C GLN* 3.3 26.0 + - - +
56D ALA* 3.2 27.7 + - - +
57D ALA* 4.1 2.1 - - - -
58D PHE* 3.6 49.7 + + + +
75D TRP* 4.4 5.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C ALA 3.5 13.5 - - - +
451C ILE* 3.1 7.4 + - - +
453C HIS* 1.3 76.0 - - - +
455C GLN* 1.3 60.2 + - - +
457C GLN* 2.9 4.8 + - - +
458C ILE* 2.9 35.6 + - - +
473C TYR* 4.1 21.7 - - + +
476C GLN* 3.9 34.3 - - + +
477C ILE* 3.7 31.2 - - + +
480C ILE* 4.7 9.6 - - + -
58D PHE* 4.0 14.1 - - + -
75D TRP* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C TYR* 4.8 1.2 + - - -
421C LEU* 5.3 3.0 - - - +
451C ILE* 2.8 32.6 + - + +
452C LEU* 3.5 30.5 + - + +
454C LEU* 1.3 73.6 - - - +
456C GLU* 1.3 61.0 + - - +
458C ILE* 3.4 5.0 + - - +
459C VAL* 3.2 29.1 + - - +
477C ILE* 4.2 6.0 - - + +
499C CYS* 3.3 39.2 + - - +
502C GLN* 3.1 30.7 + - - +
503C VAL* 3.6 22.0 - - + +
506C LEU* 4.8 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C LEU* 3.1 47.1 + - + +
453C HIS* 4.0 17.5 - - - +
455C GLN* 1.3 75.1 - - + +
457C GLN* 1.3 57.2 + - - +
459C VAL* 3.7 7.5 + - - +
460C LYS* 3.0 27.0 + - - +
506C LEU* 5.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 457 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C HIS 3.3 11.6 + - - +
454C LEU* 2.9 10.2 + - - +
456C GLU* 1.3 77.2 - - + +
458C ILE* 1.3 64.8 + - - +
460C LYS* 3.3 25.7 + - + +
461C GLU* 3.1 47.0 + - - +
473C TYR* 3.9 14.2 + - + -
58D PHE* 3.4 30.8 + - + +
59D LEU* 5.0 3.6 - - - +
60D THR* 3.7 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 458 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C LEU 2.9 19.8 + - - +
455C GLN* 3.7 7.2 - - - +
457C GLN* 1.3 74.6 - - - +
459C VAL* 1.3 62.1 + - - +
461C GLU* 3.6 2.7 + - - +
462C MET* 3.2 47.2 + - + +
470C VAL* 4.1 26.0 - - + +
473C TYR* 3.6 36.3 - - + -
474C LEU* 3.9 27.8 - - + -
477C ILE* 4.5 6.5 - - + -
503C VAL* 3.9 24.5 - - + -
511C LEU* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C GLN 3.2 18.4 + - - +
456C GLU* 3.8 7.6 - - - +
457C GLN 3.2 0.2 - - - -
458C ILE* 1.3 74.7 - - - +
460C LYS* 1.3 65.7 + - - +
462C MET* 3.4 8.3 + - - +
463C ASN* 2.9 43.4 + - - +
503C VAL* 3.7 19.7 - - + +
506C LEU* 3.4 44.9 - - + +
507C SER* 3.8 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 460 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ASN 5.5 2.0 + - - -
464A ASP* 3.5 40.1 + - - +
456C GLU 3.0 20.1 + - - +
457C GLN* 3.3 31.0 + - + +
459C VAL* 1.3 78.3 - - - +
461C GLU* 1.3 64.9 + - + +
463C ASN* 3.3 10.0 + - - +
464C ASP* 3.1 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C GLN* 3.1 23.5 + - - +
458C ILE* 4.2 3.5 - - - +
460C LYS* 1.3 76.7 - - + +
462C MET* 1.3 54.9 + - + +
464C ASP* 2.9 8.9 + - - +
465C GLY 2.7 30.5 + - - -
466C ASP* 2.8 37.0 + - + +
469C SER* 2.3 25.3 + - - -
470C VAL* 5.0 1.1 + - + +
473C TYR* 2.9 22.3 + - - -
60D THR* 5.4 0.2 - - - +
71D LYS* 2.3 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C ILE* 3.2 35.3 + - + +
459C VAL* 3.8 3.1 - - - +
461C GLU* 1.3 77.5 - - - +
463C ASN* 1.3 62.9 - - - +
465C GLY* 3.3 10.4 + - - +
466C ASP 4.2 1.8 - - - +
467C TYR* 3.5 57.0 + - + +
470C VAL* 3.8 20.6 - - + -
503C VAL* 4.3 2.7 - - + -
507C SER* 3.7 30.7 - - - +
510C LYS* 4.1 9.8 + - + +
511C LEU* 4.0 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 463 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LYS* 5.6 2.1 - - - +
459C VAL* 2.9 36.0 + - - +
460C LYS* 3.5 8.6 - - - +
461C GLU 3.2 0.2 - - - -
462C MET* 1.3 77.1 - - - +
464C ASP* 1.3 58.5 + - - +
465C GLY 3.4 0.2 - - - -
506C LEU 5.3 1.4 + - - -
507C SER* 4.7 3.4 - - - +
510C LYS* 3.1 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 464 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LYS* 3.2 35.2 + - - +
464A ASP* 3.2 30.8 - - - +
460C LYS* 3.1 11.8 + - + +
461C GLU* 2.9 13.5 + - - +
463C ASN* 1.3 78.3 - - - +
465C GLY* 1.3 58.8 + - - +
466C ASP* 3.5 4.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C GLU 2.7 5.4 + - - -
462C MET 3.3 11.8 + - - -
463C ASN 3.4 0.4 - - - -
464C ASP* 1.3 78.6 - - - +
466C ASP* 1.3 56.6 + - - -
467C TYR* 3.1 24.7 + - - -
----------------------------------------------------------
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