Contacts of the helix formed by residues 494 - 515 (chain A) in PDB entry 5P9I
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 494 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ARG 3.5 4.0 + - - +
493A PHE* 1.3 75.9 - - - +
495A THR* 1.3 66.2 + - - +
496A GLN* 4.0 15.4 - - + +
497A GLN* 2.8 38.6 + - + +
498A LEU* 3.2 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A PHE 4.1 0.8 + - - +
494A GLN* 1.3 73.0 - - - +
496A GLN* 1.3 58.7 + - - +
498A LEU* 3.1 12.5 + - + +
499A LEU* 2.9 29.2 + - - +
591A TYR* 3.8 8.1 + - - -
621A LEU* 3.4 50.0 - - + +
658A GLU* 4.9 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLN* 3.1 14.8 - - + +
495A THR* 1.3 80.3 + - - +
497A GLN* 1.3 62.2 + - + +
499A LEU* 3.5 8.0 + - - +
500A GLU* 3.0 23.4 + - - +
655A MET* 4.8 2.3 - - - +
658A GLU 5.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A TYR* 5.6 1.6 + - - -
491A HIS 5.0 2.9 + - - +
492A ARG 4.3 1.6 - - - +
493A PHE* 3.4 33.7 - - + -
494A GLN* 2.8 47.3 + - + +
496A GLN* 1.3 76.9 - - + +
498A LEU* 1.3 65.4 + - - +
500A GLU* 3.3 7.7 + - - +
501A MET* 3.1 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LEU* 4.3 2.0 - - + -
493A PHE* 3.9 25.6 - - + +
494A GLN 3.2 9.2 + - - +
495A THR* 3.1 17.1 + - + +
497A GLN* 1.3 75.9 - - - +
499A LEU* 1.3 62.0 + - - +
501A MET* 3.2 21.9 + - + +
502A CYS* 3.1 24.3 + - - -
590A ILE* 3.6 37.0 - - + +
591A TYR* 3.9 25.1 - - + -
593A LEU* 4.1 8.3 - - + -
621A LEU* 4.0 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A THR 2.9 13.6 + - - +
496A GLN* 3.9 8.5 - - - +
498A LEU* 1.3 76.2 - - - +
500A GLU* 1.3 57.9 + - - +
502A CYS* 3.1 13.5 + - + +
503A LYS* 2.8 26.9 + - - +
587A MET* 5.1 4.0 - - + -
591A TYR* 3.1 22.1 + - + +
626A VAL* 4.3 10.5 - - + -
629A ILE* 5.7 1.6 - - + -
651A ILE* 3.9 22.2 - - + +
654A VAL* 3.9 16.4 - - + +
655A MET* 3.4 48.0 - - + +
658A GLU* 4.6 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LYS* 4.9 2.3 + - - -
496A GLN 3.0 18.3 + - - +
497A GLN* 3.5 8.1 - - - +
499A LEU* 1.3 77.0 - - - +
501A MET* 1.3 56.2 + - - +
503A LYS* 3.2 20.5 + - - +
504A ASP* 2.9 48.9 + - - +
655A MET* 3.2 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 4.0 12.6 - - + -
485A TYR* 4.0 11.0 - - + -
486A LEU* 3.9 21.8 - - + -
493A PHE* 3.5 42.8 - - + -
497A GLN* 3.1 19.3 + - + +
498A LEU* 3.4 18.8 - - + +
500A GLU* 1.3 74.1 - - - +
502A CYS* 1.3 63.7 + - - +
504A ASP* 3.3 11.3 + - - +
505A VAL* 3.1 26.7 + - - +
533A GLY 5.3 3.8 - - - +
535A VAL* 3.7 20.1 - - + +
590A ILE* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU 3.1 15.9 + - - -
499A LEU* 3.1 12.8 + - + +
501A MET* 1.3 79.9 - - - +
503A LYS* 1.3 56.5 + - - +
505A VAL* 3.4 3.6 + - - -
506A CYS* 2.9 28.9 + - - +
583A PHE* 3.7 7.8 - - - -
587A MET* 3.8 33.2 - - + -
590A ILE* 3.8 20.9 - - - -
591A TYR* 3.7 24.5 - - - -
651A ILE* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LYS* 4.8 4.2 - - - +
499A LEU 2.8 15.6 + - - +
500A GLU* 3.2 23.3 + - - +
502A CYS* 1.3 73.7 - - - +
504A ASP* 1.3 66.6 + - - +
506A CYS* 3.2 4.2 + - - +
507A GLU* 2.9 58.6 + - - +
648A LEU* 3.7 14.8 - - + -
651A ILE* 3.8 15.0 - - + +
652A LEU* 3.5 32.2 - - + +
655A MET* 3.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LYS* 2.7 51.2 + - + +
500A GLU* 2.9 33.8 + - - +
501A MET* 3.5 8.6 - - - +
503A LYS* 1.3 76.8 + - - +
505A VAL* 1.3 63.7 + - - +
507A GLU 3.3 0.2 + - - -
508A ALA* 3.2 16.8 + - - +
533A GLY 4.5 1.2 - - - +
534A VAL* 3.8 9.0 - - - +
535A VAL* 2.9 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LYS 5.7 0.2 - - - -
482A LEU* 5.2 2.2 - - + -
501A MET 3.1 15.9 + - - +
502A CYS* 3.8 5.4 - - - +
504A ASP* 1.3 75.3 - - - +
506A CYS* 1.3 57.7 + - - +
508A ALA* 3.1 4.0 + - - +
509A MET* 2.9 33.6 + - + +
522A LEU* 4.3 2.5 - - + -
527A CYS* 4.0 14.1 - - - -
535A VAL* 3.7 25.8 - - + +
537A VAL* 3.8 20.9 - - + -
583A PHE* 3.7 17.9 - - + -
586A LEU* 3.7 27.6 - - + -
590A ILE* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A CYS 2.9 18.9 + - - +
503A LYS* 3.2 5.1 + - - +
505A VAL* 1.3 75.4 - - - +
507A GLU* 1.3 57.7 + - - +
509A MET* 3.3 4.9 + - - +
510A GLU* 2.8 31.6 + - - +
583A PHE* 3.8 13.0 - - + -
644A PHE* 3.5 19.7 - - - +
647A LEU* 3.7 14.4 - - - -
648A LEU* 3.5 37.0 - - + -
651A ILE* 3.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A HIS* 3.9 19.3 + - + +
456A LYS* 2.7 35.7 + - + +
503A LYS* 2.9 50.6 + - - +
504A ASP 3.6 3.1 - - - +
505A VAL 3.3 0.2 - - - -
506A CYS* 1.3 75.1 - - - +
508A ALA* 1.3 62.5 + - - +
510A GLU* 3.4 8.9 + - - +
511A TYR* 3.1 23.2 + - - +
648A LEU* 3.9 23.4 - - + +
652A LEU* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A HIS* 4.2 10.8 - - - -
456A LYS* 3.2 31.8 - - - +
457A LEU* 4.4 6.2 - - + +
504A ASP 3.2 5.5 + - - +
505A VAL 3.1 9.3 + - - +
507A GLU* 1.3 77.7 - - - +
509A MET* 1.3 58.6 + - - +
511A TYR* 3.2 6.4 + - - +
512A LEU* 2.9 31.9 + - - +
537A VAL* 3.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A VAL* 2.9 25.8 + - + +
506A CYS 3.7 0.9 - - - +
508A ALA* 1.3 74.8 - - - +
510A GLU* 1.3 58.6 + - - +
512A LEU* 3.3 24.5 + - + +
513A GLU* 2.8 31.0 + - - +
517A PHE 5.4 0.2 - - - +
519A HIS* 3.9 10.8 - - + +
522A LEU* 4.0 30.3 - - + -
537A VAL* 4.3 9.0 - - - -
579A ASP* 3.4 30.5 - - + +
644A PHE* 3.5 49.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A CYS 2.8 20.3 + - - +
507A GLU* 3.7 7.3 - - - +
509A MET* 1.3 70.7 - - - +
511A TYR* 1.3 58.1 + - - +
513A GLU* 3.4 4.0 + - + +
514A SER* 2.9 29.7 + - - -
644A PHE* 3.6 17.8 - - + +
645A LYS* 3.7 42.4 - - + +
648A LEU* 3.3 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ASN 4.1 3.6 + - - -
452A LEU* 3.5 19.7 - - + +
453A SER* 2.9 43.4 + - - -
454A HIS* 3.6 41.3 - + + -
457A LEU* 4.1 17.5 - - + -
507A GLU 3.1 8.0 + - - +
508A ALA 3.4 7.9 - - - +
510A GLU* 1.3 73.7 - - - +
512A LEU* 1.3 68.9 + - + +
514A SER* 2.7 27.9 + - - -
515A LYS* 3.2 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 4.1 14.1 - - + -
457A LEU* 3.9 40.2 - - + -
508A ALA 2.9 16.8 + - - +
509A MET* 3.8 32.1 - - + +
511A TYR* 1.3 78.8 - - + +
513A GLU* 1.3 63.0 + - - +
515A LYS* 3.0 10.4 + - - +
517A PHE* 3.0 60.0 + - + +
519A HIS* 4.7 4.5 - - + -
537A VAL* 4.5 2.2 - - + -
540A PHE* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A MET* 2.8 21.8 + - - +
510A GLU* 3.6 6.4 - - - +
512A LEU* 1.3 71.0 - - - +
514A SER* 1.3 58.6 + - - +
516A GLN* 3.0 23.8 + - - +
517A PHE 4.3 4.0 + - - +
518A LEU* 6.5 0.4 - - - -
576A SER* 3.3 31.0 + - - +
577A LYS* 5.8 0.5 + - - -
580A ILE* 4.6 3.5 - - - +
643A THR* 3.7 14.1 - - - -
644A PHE* 2.9 47.8 + - + +
645A LYS 4.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLU* 2.9 15.4 + - - -
511A TYR* 2.7 28.5 + - - -
513A GLU* 1.3 75.2 - - - +
515A LYS* 1.3 69.0 + - - +
516A GLN* 3.4 4.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ASN 5.9 0.7 - - - -
452A LEU* 4.1 20.6 - - + -
511A TYR* 3.2 51.1 + - + +
512A LEU 3.0 9.0 + - - +
514A SER* 1.3 84.2 - - - +
516A GLN* 1.3 70.7 + - - +
517A PHE* 3.1 7.0 + - + +
----------------------------------------------------------
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