Contacts of the helix formed by residues 518 - 539 (chain A) in PDB entry 5QSY
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 SER 518 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ALA 3.8 1.4 + - - -
517A MET* 1.3 73.6 - - - +
519A ASP* 1.3 59.4 + - - +
520A ARG* 4.1 7.1 + - - +
521A GLN* 3.0 36.4 + - - +
522A GLU* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A SER* 1.3 71.9 - - - +
520A ARG* 1.3 63.0 + - - +
522A GLU* 3.5 12.3 + - - +
523A SER* 3.0 28.4 + - - -
585A ASP* 3.9 5.4 - - - +
588A LYS* 3.3 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PHE* 5.5 4.6 - - - -
473A LEU* 3.3 35.9 - - + +
518A SER* 3.2 7.4 + - - +
519A ASP* 1.3 79.9 - - - +
521A GLN* 1.3 60.5 + - + +
523A SER* 3.5 18.5 + - - -
524A ALA* 3.2 18.6 + - - +
527A GLU* 5.9 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ARG* 4.7 12.0 + - - -
469A VAL* 3.6 11.6 - - + +
470A LEU* 3.4 31.9 - - - +
473A LEU* 3.5 24.0 - - + +
474A GLU* 5.2 2.6 + - - -
516A ALA 5.1 0.7 - - - +
517A MET* 3.6 23.6 - - + +
518A SER* 3.0 33.9 + - - +
520A ARG* 1.3 75.2 - - + +
522A GLU* 1.3 61.6 + - - +
524A ALA 3.2 0.3 + - - -
525A LEU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU 5.5 1.2 - - - +
506A LEU* 3.8 10.7 - - + +
517A MET* 3.8 34.0 - - + +
518A SER 2.8 18.5 + - - +
519A ASP* 3.7 16.2 + - - +
521A GLN* 1.3 74.9 - - - +
523A SER* 1.3 64.9 - - - +
524A ALA 3.1 0.3 + - - -
525A LEU* 3.2 3.1 + - - +
526A ILE* 2.9 25.3 + - - +
581A LYS* 3.8 10.7 + - - -
582A TYR* 3.2 36.9 + - - +
588A LYS* 3.9 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ASP 3.0 13.1 + - - -
520A ARG* 3.6 19.2 - - - -
521A GLN 3.3 0.2 - - - -
522A GLU* 1.3 74.8 - - - +
524A ALA* 1.3 58.0 + - - +
526A ILE* 3.4 4.8 + - - +
527A GLU* 2.9 27.1 + - - +
585A ASP* 4.5 0.9 + - - -
587A GLU* 5.7 4.4 - - - +
588A LYS* 3.1 37.8 + - - +
591A ASN* 4.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A VAL* 3.8 14.6 - - + -
472A PHE* 4.1 15.6 - - + -
473A LEU* 3.9 22.0 - - + -
520A ARG* 3.2 18.2 + - - +
521A GLN 3.7 4.0 - - - +
522A GLU 3.2 0.6 - - - -
523A SER* 1.3 76.7 - - - +
525A LEU* 1.3 61.6 + - - +
527A GLU* 3.3 7.7 + - - +
528A LEU* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ILE* 3.6 25.6 - - + -
469A VAL* 3.9 14.5 - - + +
502A MET* 4.2 19.7 - - + +
505A LEU* 3.9 23.6 - - + -
506A LEU* 3.5 30.3 - - + -
517A MET* 3.6 24.5 - - + -
521A GLN 2.9 17.2 + - - +
522A GLU 3.6 4.0 - - - +
524A ALA* 1.3 74.5 - - - +
526A ILE* 1.3 65.4 + - - +
528A LEU* 3.2 3.5 + - + -
529A MET* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU* 3.7 30.7 - - + -
522A GLU 2.9 13.1 + - - +
523A SER* 3.7 7.2 - - - +
525A LEU* 1.3 75.0 - - - +
527A GLU* 1.3 63.6 + - - +
529A MET* 3.5 7.6 + - + +
530A VAL* 3.1 25.4 + - + +
578A LEU* 5.9 0.2 - - + -
582A TYR* 4.3 9.2 - - + -
588A LYS* 3.8 39.0 - - + +
591A ASN* 3.6 27.4 - - + +
592A LEU* 4.0 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PHE* 4.8 9.8 - - + -
480A HIS* 5.8 0.2 - - - -
481A ALA* 3.5 28.3 + - + +
520A ARG* 5.9 2.3 + - - -
523A SER 2.9 16.0 + - - +
524A ALA* 3.8 8.2 - - - +
525A LEU 3.2 0.4 - - - -
526A ILE* 1.3 79.0 - - - +
528A LEU* 1.3 59.8 + - - +
530A VAL* 3.6 3.7 + - - +
531A CYS* 3.2 25.1 + - - -
591A ASN* 3.6 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 4.6 11.0 - - + +
469A VAL* 3.8 37.0 - - + +
472A PHE* 4.3 16.4 - - + -
481A ALA* 3.9 20.6 - - + +
484A LEU* 4.1 17.9 - - + -
485A VAL* 3.8 22.9 - - + +
496A LEU* 6.5 0.9 - - + -
502A MET* 5.5 0.9 - - + -
524A ALA 2.9 22.7 + - - +
525A LEU* 3.8 5.8 - - + +
527A GLU* 1.3 72.8 - - - +
529A MET* 1.3 67.0 + - - +
531A CYS* 3.2 7.1 + - - +
532A THR* 3.0 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A TRP* 4.4 1.1 - - + -
502A MET* 3.8 40.7 - - + -
503A THR* 4.2 4.7 - - - -
506A LEU* 3.8 23.6 - - + -
525A LEU 2.9 17.7 + - - +
526A ILE* 3.5 8.1 - - + +
528A LEU* 1.3 76.4 - - - +
530A VAL* 1.3 57.3 + - - +
532A THR* 2.4 28.0 + - - -
533A ILE* 2.9 17.2 + - + +
571A PHE* 3.7 39.5 - - + -
578A LEU* 4.0 13.7 - - + -
592A LEU* 4.1 15.0 - - + -
595A ILE* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ILE* 3.1 20.8 + - + +
527A GLU* 3.9 6.1 - - - +
529A MET* 1.3 78.6 - - + +
531A CYS* 1.3 57.5 + - - +
533A ILE* 3.2 7.9 + - - +
534A ARG* 2.9 27.9 + - + +
591A ASN* 3.6 29.6 - - + +
594A GLN* 4.1 26.2 - - + +
595A ILE* 3.8 25.8 - - + -
598A TYR* 5.0 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ALA* 3.8 11.0 - - - -
482A ALA* 3.7 36.8 - - + -
485A VAL* 4.0 19.4 - - + +
527A GLU* 3.2 24.7 - - - -
528A LEU 3.2 7.4 + - - +
530A VAL* 1.3 78.9 - - - +
532A THR* 1.3 57.4 + - - +
534A ARG* 3.4 11.3 + - - +
535A GLN* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A VAL* 4.0 14.4 - - + -
489A TRP* 3.5 12.5 - - - -
496A LEU* 3.1 48.1 + - + +
499A TRP* 3.0 16.9 + - - -
502A MET* 4.1 6.5 - - + +
528A LEU* 3.0 17.4 + - + +
529A MET* 2.4 29.6 + - - -
531A CYS* 1.3 76.6 - - - +
533A ILE* 1.3 54.9 + - - +
536A ALA* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A TRP* 3.8 21.1 - - + +
529A MET* 2.9 24.9 + - + +
530A VAL* 3.2 7.4 + - + +
532A THR* 1.3 74.5 + - - +
534A ARG* 1.3 65.3 + - - +
536A ALA* 3.7 1.7 - - - +
537A ALA* 3.0 21.5 + - - +
567A LEU* 3.8 26.9 - - + +
571A PHE* 3.4 37.0 - - + -
595A ILE* 3.8 32.1 - - + -
598A TYR* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ALA* 5.8 2.8 - - - +
530A VAL* 2.9 14.2 + - + +
531A CYS* 3.6 11.6 + - - +
533A ILE* 1.3 75.4 - - - +
535A GLN* 1.3 96.2 + - - +
537A ALA* 3.1 1.9 + - - -
538A GLU* 2.7 75.3 + - - +
540A HIS* 3.0 34.2 + - - -
542A PRO* 3.4 31.0 - - - +
543A VAL* 6.3 2.5 - - - -
598A TYR* 3.4 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ALA 4.6 1.2 - - - +
485A VAL* 4.1 4.3 - - + +
486A ASP* 3.1 43.9 + - - +
489A TRP* 3.3 54.5 + - + +
531A CYS 2.9 20.4 + - - +
534A ARG* 1.3 102.5 + - - +
536A ALA* 1.3 57.0 + - - +
539A ALA* 2.8 29.9 + - - -
540A HIS 3.9 13.1 + - - +
541A PRO* 4.1 2.6 - - - +
542A PRO* 4.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A TRP* 3.7 8.0 - - + -
493A GLN* 5.9 0.2 - - - +
497A LYS* 3.9 15.3 - - + -
499A TRP* 3.7 28.7 - - + -
532A THR 2.9 18.8 + - - +
533A ILE 3.7 2.5 - - - +
535A GLN* 1.3 80.3 - - - +
537A ALA* 1.3 62.1 + - - +
539A ALA* 3.6 7.7 + - - +
560A GLN* 4.1 11.6 - - - +
563A ASP* 4.1 19.5 - - + +
567A LEU* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A ILE 3.0 17.4 + - - +
534A ARG 3.8 2.5 - - - +
536A ALA* 1.3 76.3 - - - +
538A GLU* 1.3 53.8 + - + +
560A GLN* 2.6 28.4 + - - -
564A ARG* 3.0 38.3 + - + +
567A LEU* 4.4 5.8 - - + +
598A TYR* 3.8 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A ARG* 2.7 59.0 + - + +
537A ALA* 1.3 76.2 - - + +
539A ALA* 1.3 72.2 + - - +
540A HIS* 3.1 37.7 + - + +
552A LEU* 5.7 0.2 - - - +
560A GLN* 3.7 7.0 + - - +
564A ARG* 4.8 2.7 - - - +
598A TYR* 3.7 21.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A TRP* 6.1 2.2 - - - +
535A GLN* 2.8 16.5 + - - -
536A ALA 3.6 3.5 + - - +
537A ALA 3.5 0.8 - - - -
538A GLU* 1.3 79.7 - - - +
540A HIS* 1.3 59.6 + - - +
552A LEU* 3.9 28.8 - - + +
556A GLU* 5.3 2.2 - - + +
560A GLN* 3.8 31.4 - - + +
----------------------------------------------------------
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