Contacts of the helix formed by residues 469 - 492 (chain A) in PDB entry 5Z66
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 469 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU* 5.9 0.2 - - + -
419A ALA 4.8 3.4 - - - +
420A ASP* 2.8 38.6 + - - +
423A ALA* 3.6 27.9 - - + +
464A LEU* 2.9 28.6 + - + +
467A TYR* 3.9 12.0 + - + +
468A GLY* 1.3 75.2 - - - +
470A GLU* 1.3 57.2 + - - +
471A LYS 3.3 3.1 + - - -
472A VAL* 3.5 13.2 + - + +
473A SER* 3.0 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLN* 3.3 39.4 - - - +
468A GLY* 3.0 10.8 + - - +
469A GLN* 1.3 76.1 - - - +
471A LYS* 1.3 57.6 + - - +
473A SER* 3.6 7.1 + - - -
474A MET* 2.9 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A GLN 3.3 1.0 - - - -
470A GLU* 1.3 75.1 - - - +
472A VAL* 1.3 65.4 + - + +
474A MET* 3.3 4.4 + - - +
475A ASP* 2.9 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ALA* 4.5 13.7 - - + +
426A THR* 4.1 17.9 - - + -
427A SER* 4.3 23.3 - - - +
431A LEU* 4.9 6.3 - - + -
464A LEU* 3.6 24.2 - - + -
469A GLN* 3.5 20.0 + - + +
471A LYS* 1.3 79.5 - - + +
473A SER* 1.3 63.7 + - - +
475A ASP* 3.1 10.7 + - - +
476A VAL* 3.0 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ALA* 2.8 33.5 + - - +
464A LEU* 3.8 15.4 - - - +
465A GLN* 3.8 14.0 + - - +
469A GLN 3.0 20.1 + - - -
470A GLU* 3.6 14.4 + - - -
472A VAL* 1.3 78.0 - - - +
474A MET* 1.3 62.2 + - - +
476A VAL* 3.4 3.5 + - - +
477A THR* 3.1 26.4 + - - -
531A ARG* 4.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLN* 5.0 0.7 - - - +
470A GLU* 2.9 46.0 + - + +
471A LYS* 3.9 4.3 - - - +
473A SER* 1.3 74.1 - - - +
475A ASP* 1.3 63.0 + - - +
477A THR* 4.2 9.0 - - - -
478A TRP* 2.8 54.7 + - + +
531A ARG* 3.5 45.8 - - + +
532A VAL* 5.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER* 5.8 0.2 + - - -
431A LEU* 3.7 27.3 - - + +
471A LYS* 2.9 32.7 + - - +
472A VAL* 3.1 13.0 + - - +
474A MET* 1.3 77.7 - - - +
476A VAL* 1.3 61.9 + - - +
478A TRP* 4.7 3.0 - - - -
479A ARG* 3.0 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A THR* 4.8 4.3 - - + -
431A LEU* 3.9 21.1 - - + -
435A GLY* 4.6 0.5 - - - -
436A ILE* 4.2 19.7 - - + +
457A GLN* 3.7 42.3 - - + +
460A ALA* 4.3 5.6 - - + -
461A ALA* 4.5 5.6 - - + +
464A LEU* 4.2 17.0 - - + -
472A VAL* 3.0 20.5 + - + +
473A SER 3.6 6.7 - - - +
475A ASP* 1.3 74.9 - - - +
477A THR* 1.3 65.3 + - - +
479A ARG* 3.9 1.1 - - - +
480A PHE* 3.0 23.9 + - - +
528A MET* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ALA* 3.5 17.5 - - - +
473A SER* 3.1 18.5 + - - -
474A MET* 3.6 14.4 - - - -
476A VAL* 1.3 76.8 - - - +
478A TRP* 1.3 58.0 + - - +
480A PHE* 3.9 1.2 - - - +
481A LEU* 2.9 39.1 + - + +
528A MET* 3.7 41.7 - - + +
531A ARG* 4.9 12.0 + - + -
532A VAL* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A MET* 2.8 44.4 + - + +
475A ASP* 4.1 4.3 - - - +
477A THR* 1.3 74.1 - - - +
479A ARG* 1.3 60.4 + - + +
481A LEU* 3.4 4.3 + - + +
482A LYS* 2.9 44.4 + - + +
532A VAL* 3.5 38.1 - - + +
542A VAL* 3.8 17.3 - - + -
543A PRO* 3.8 38.1 - - + -
545A ASN 3.2 22.2 - - - -
546A GLN* 3.2 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 3.7 38.4 + - - +
432A LYS* 3.1 32.1 + - - +
433A PRO* 3.4 22.9 - - - +
434A GLY* 3.6 10.9 - - - +
435A GLY* 3.7 9.4 - - - +
475A ASP* 3.0 29.5 + - - +
476A VAL* 4.1 2.2 - - - +
478A TRP* 1.3 76.6 - - + +
480A PHE* 1.3 63.7 + - - +
482A LYS* 3.4 7.3 + - - +
483A ASN* 3.0 18.2 + - - +
503A THR* 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLY 3.6 14.8 + - - -
435A GLY* 4.0 0.6 - - - -
452A GLY 4.6 3.6 - - - -
454A ALA* 3.8 31.4 - - + -
457A GLN* 3.5 43.1 - - + +
476A VAL 3.0 17.6 + - - +
477A THR 4.0 1.8 - - - +
479A ARG* 1.3 78.0 - - - +
481A LEU* 1.3 59.2 + - + +
483A ASN* 3.1 5.4 + - + +
484A VAL* 2.9 47.1 + - + +
498A TYR* 3.7 35.0 - + + -
500A VAL* 5.7 0.2 - - + -
521A SER* 5.2 1.8 - - - -
524A VAL* 4.4 8.7 - - + -
525A THR* 4.5 6.3 - - - -
528A MET* 4.0 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A THR* 2.9 21.2 + - + +
478A TRP* 3.8 5.4 - - + +
480A PHE* 1.3 75.2 - - + +
482A LYS* 1.3 57.6 + - - +
484A VAL* 3.2 6.1 + - + +
485A GLN* 2.8 31.9 + - - +
525A THR* 3.9 31.2 - - + +
528A MET* 3.6 47.6 - - + +
529A LEU* 3.9 4.9 - - + +
532A VAL* 3.7 29.2 - - + -
542A VAL* 3.6 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A TRP* 2.9 32.3 + - + +
479A ARG* 3.7 7.4 - - - +
480A PHE 3.2 0.2 - - - -
481A LEU* 1.3 75.9 - - - +
483A ASN* 1.3 58.7 + - - +
485A GLN* 4.6 3.9 - - + +
486A HIS* 2.9 64.4 + - + +
503A THR* 4.2 10.1 - - + -
542A VAL* 4.1 13.8 + - + -
543A PRO 2.8 27.8 + - - -
544A GLU* 3.0 26.2 + - - +
545A ASN 5.7 0.4 - - - -
546A GLN 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLY* 3.0 31.7 + - - +
479A ARG 3.0 7.5 + - - +
480A PHE* 3.1 9.8 + - + +
482A LYS* 1.3 76.1 - - - +
484A VAL* 1.3 62.4 + - - +
487A THR* 2.8 35.2 + - - -
498A TYR* 3.6 24.4 - - + +
499A ASP 3.0 24.5 + - - +
500A VAL* 4.4 0.2 - - - +
502A THR 3.6 0.2 + - - -
503A THR* 3.4 16.6 - - + +
504A GLY 2.9 22.2 + - - -
505A THR 3.8 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 4.1 10.1 - - + -
480A PHE* 2.9 53.0 + - + +
481A LEU* 3.7 6.7 - - + +
483A ASN* 1.3 74.9 - - - +
485A GLN* 1.3 58.3 + - - +
487A THR* 3.8 1.6 - - - -
488A TYR* 2.9 28.2 + - - +
493A LYS 5.0 0.3 - - - +
494A LEU* 3.7 21.8 - - + -
498A TYR* 3.9 21.4 + - + +
521A SER* 5.9 0.4 - - - -
525A THR* 3.6 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.4 18.0 - - - +
481A LEU 2.8 21.2 + - - +
482A LYS* 4.1 5.6 - - + +
484A VAL* 1.3 75.4 - - - +
486A HIS* 1.3 63.1 + - + +
488A TYR* 3.2 16.5 + - - +
489A ASP* 2.8 66.6 + - - +
541A SER* 3.3 20.1 + - - -
542A VAL* 2.7 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LYS* 2.9 49.2 + - + +
485A GLN* 1.3 82.9 - - + +
487A THR* 1.3 62.6 + - - +
489A ASP* 3.3 13.3 + - + +
490A ARG* 3.0 48.4 + - - +
503A THR* 3.0 24.3 + - + -
504A GLY* 3.8 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASN* 2.8 25.1 + - - -
484A VAL 3.8 1.1 - - - -
486A HIS* 1.3 76.4 - - - +
488A TYR* 1.3 53.2 + - - +
490A ARG* 4.8 0.2 - - - -
491A GLU* 2.7 46.5 + - + +
493A LYS 4.1 10.9 - - - +
495A VAL* 4.6 13.5 - - + -
498A TYR* 3.5 26.9 - - + -
504A GLY* 3.0 32.9 - - - +
505A THR 3.3 2.1 + - - -
506A GLY 4.6 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLN* 2.6 33.2 + - - +
114A SER* 4.5 0.7 - - - -
115A LEU* 3.7 39.0 - - + -
118A HIS* 3.3 46.0 + + + +
484A VAL* 2.9 19.6 + - + +
485A GLN* 3.6 6.5 - - - +
487A THR* 1.3 74.5 - - - +
489A ASP* 1.3 72.4 + - - +
492A LYS* 2.8 44.9 + - + +
493A LYS* 3.5 28.0 + - - +
494A LEU* 4.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLN* 2.8 54.6 + - - +
486A HIS* 3.7 15.0 - - + +
487A THR 3.3 0.2 - - - -
488A TYR* 1.3 78.1 - - - +
490A ARG* 1.3 64.0 + - + +
492A LYS* 4.6 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A HIS* 3.0 35.1 + - - +
487A THR* 4.1 1.8 - - - +
489A ASP* 1.3 84.4 - - + +
491A GLU* 1.3 77.0 + - + +
492A LYS* 3.7 6.0 - - - +
503A THR* 3.5 25.8 + - - -
504A GLY* 4.0 16.6 - - - -
505A THR* 5.1 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A THR* 2.7 35.4 + - + +
490A ARG* 1.3 89.6 - - + +
492A LYS* 1.3 71.8 + - - +
493A LYS* 3.3 33.8 + - + +
495A VAL* 6.4 0.2 - - + -
504A GLY 4.5 7.2 - - - +
505A THR* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 3.8 10.4 + - - -
488A TYR* 2.8 39.1 + - + +
489A ASP 4.7 7.0 - - - +
490A ARG 4.8 4.9 - - - +
491A GLU* 1.3 82.3 - - - +
493A LYS* 1.3 59.2 + - - +
----------------------------------------------------------
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