Contacts of the helix formed by residues 514 - 534 (chain A) in PDB entry 4PK7
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 514 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ALA 4.3 0.8 - - - -
513A LEU* 1.3 75.3 - - - +
515A ASP* 1.3 60.1 + - - +
516A ARG* 3.8 8.4 + - - +
517A GLN* 3.0 49.0 + - - +
518A GLU* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A LEU 3.8 2.0 + - - +
514A THR* 1.3 70.6 - - - +
516A ARG* 1.3 65.5 + - - +
518A GLU* 2.6 30.6 - - - +
519A SER* 2.9 22.3 + - - -
578A TYR* 4.8 1.6 - - - -
584A LYS* 3.4 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 3.2 50.2 + - + +
472A GLU* 4.4 15.2 + - - -
514A THR* 3.2 9.8 + - - +
515A ASP* 1.3 77.7 - - - +
517A GLN* 1.3 58.5 + - + +
519A SER* 2.7 22.3 + - - +
520A ALA* 3.1 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LYS* 5.0 0.3 + - - -
465A VAL* 3.8 8.0 - - + +
466A PHE* 3.2 34.7 - - + -
469A LEU* 3.7 24.8 - - + +
512A ALA 4.3 2.8 - - - +
513A LEU* 3.5 26.0 - - + +
514A THR* 3.0 45.7 + - - +
516A ARG* 1.3 76.7 - - + +
518A GLU* 1.3 65.9 + - - +
521A LEU* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LEU 4.7 3.6 - - - +
502A LEU* 3.4 10.8 - - + +
513A LEU* 3.6 36.6 - - + +
514A THR 2.9 16.3 + - - +
515A ASP* 2.6 32.1 + - - +
517A GLN* 1.3 76.5 - - - +
519A SER* 1.3 56.1 + - - +
521A LEU 3.6 0.2 + - - -
522A ILE* 2.9 33.6 + - - +
577A LYS* 4.4 11.3 + - - -
578A TYR* 3.0 42.2 + - + +
584A LYS* 4.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ASP 2.9 10.0 + - - -
516A ARG* 2.7 25.8 + - - +
518A GLU* 1.3 73.7 - - - +
520A ALA* 1.3 57.4 + - - -
522A ILE* 2.9 6.3 + - - +
523A GLU* 2.8 29.5 + - - +
583A GLU* 4.7 16.3 + - - -
584A LYS* 3.5 32.9 - - - +
587A ASN* 5.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A VAL* 3.9 19.7 - - + -
468A PHE* 3.9 22.9 - - + -
469A LEU* 4.1 14.6 - - + -
516A ARG 3.1 16.9 + - - +
519A SER* 1.3 75.7 + - - +
521A LEU* 1.3 58.0 + - - +
523A GLU* 3.3 8.5 + - - +
524A ILE* 2.8 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A VAL* 3.8 25.6 - - + -
465A VAL* 3.9 18.0 - - + +
498A MET* 3.8 33.4 - - + +
501A LEU* 3.9 23.1 - - + -
502A LEU* 3.8 29.6 - - + -
513A LEU* 4.4 9.9 - - + -
517A GLN 3.0 18.6 + - - +
518A GLU 3.9 2.7 - - - +
520A ALA* 1.3 75.0 - - - +
522A ILE* 1.3 63.2 + - - +
524A ILE* 4.4 4.3 - - + -
525A MET* 2.9 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LEU* 3.6 21.5 - - + -
518A GLU 2.9 19.7 + - - +
519A SER* 2.9 10.7 + - - +
521A LEU* 1.3 76.3 - - - +
523A GLU* 1.3 63.1 + - - +
525A MET* 3.4 7.6 - - + +
526A LEU* 3.1 22.1 + - + +
578A TYR* 4.0 23.1 - - + -
584A LYS* 3.6 45.8 - - + +
587A ASN* 3.7 26.2 - - + +
588A LEU* 4.1 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PHE* 4.1 10.8 - - + -
475A GLU 5.0 2.2 - - - +
476A HIS* 3.5 18.1 + - - +
477A ALA* 3.1 35.0 + - + +
519A SER 2.8 11.5 + - - +
520A ALA* 3.4 11.9 - - - +
522A ILE* 1.3 74.4 - - - +
524A ILE* 1.3 66.9 + - - +
526A LEU* 3.1 17.3 + - - +
527A CYS* 3.1 31.7 + - - -
530A ARG* 5.3 0.5 + - - -
587A ASN* 3.2 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A VAL* 6.3 1.6 - - + -
464A LEU* 3.8 42.8 - - + +
465A VAL* 3.9 29.8 - - + -
468A PHE* 4.2 14.1 - - + -
477A ALA* 3.8 24.7 - - + -
480A LEU* 5.0 1.3 - - + -
481A VAL* 4.1 5.8 - - + +
492A LEU* 5.4 0.4 - - + -
498A MET* 4.6 9.2 - - - -
520A ALA 2.8 20.9 + - - +
521A LEU* 4.0 7.4 - - + +
523A GLU* 1.3 72.0 - - - +
525A MET* 1.3 64.5 + - - +
527A CYS* 3.1 13.4 + - - +
528A THR* 3.1 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TRP 5.0 0.2 - - - +
498A MET* 4.0 37.2 - - + -
499A ASN* 4.4 6.3 - - - -
502A LEU* 3.8 30.1 - - + -
521A LEU* 2.9 20.6 + - + +
522A ILE* 3.4 9.9 - - - +
523A GLU 3.1 0.2 - - - -
524A ILE* 1.3 77.5 - - - +
526A LEU* 1.3 60.3 + - - +
528A THR* 2.2 26.9 + - - -
529A ILE* 3.2 24.6 + - + +
567A PHE* 3.7 31.6 - - + -
574A LEU* 4.1 12.8 - - + -
588A LEU* 4.4 12.6 - - + -
591A LEU* 4.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ILE 3.1 9.0 + - - +
523A GLU* 3.1 16.2 + - - +
525A MET* 1.3 77.7 - - - +
527A CYS* 1.3 66.5 + - - +
529A ILE* 3.2 10.3 + - - +
530A ARG* 3.0 39.8 + - - +
587A ASN* 3.0 38.8 - - + +
590A GLN* 3.8 36.1 - - + +
591A LEU* 4.8 9.2 - - + +
594A TYR* 4.0 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ALA* 3.7 4.5 - - - -
478A ALA* 3.4 28.7 - - - -
481A VAL* 3.5 22.7 - - + -
523A GLU* 3.1 36.9 + - - -
524A ILE 3.1 8.1 + - - +
526A LEU* 1.3 78.2 - - - +
528A THR* 1.3 65.8 + - - +
529A ILE 3.2 0.2 + - - -
530A ARG* 3.7 22.5 + - - +
531A GLN* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A VAL* 4.1 8.3 - - + +
485A TRP* 3.4 15.1 - - - -
492A LEU* 3.3 53.2 - - + +
495A TRP* 3.4 11.1 + - - -
498A MET* 3.8 5.1 - - + +
524A ILE* 3.1 21.8 + - + +
525A MET* 2.2 37.1 + - - -
527A CYS* 1.3 72.3 - - - +
529A ILE* 1.3 54.9 + - - -
532A ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TRP* 3.5 20.2 - - + +
525A MET* 3.2 31.2 + - + +
526A LEU* 3.5 7.0 - - - +
527A CYS 3.2 0.6 - - - -
528A THR* 1.3 77.7 + - - +
530A ARG* 1.3 55.9 + - - +
532A ALA* 3.0 3.3 + - - +
533A ALA* 2.7 37.4 + - - +
563A ILE* 3.7 26.8 - - + +
567A PHE* 3.8 18.8 - - + -
591A LEU* 3.4 31.2 - - + -
594A TYR* 4.0 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A HIS* 5.7 0.6 + - - -
478A ALA* 3.9 17.2 - - - +
523A GLU* 5.3 0.6 + - - -
526A LEU* 3.0 31.8 + - + +
527A CYS* 3.7 33.0 + - - +
529A ILE* 1.3 75.5 - - - +
531A GLN* 1.3 59.1 + - - +
534A GLU* 2.8 61.5 + - - +
590A GLN* 4.8 6.5 + - - -
594A TYR* 3.2 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ARG* 5.1 0.4 - - - +
478A ALA 4.4 2.4 - - - +
481A VAL* 3.7 10.4 - - - +
482A ASP* 3.0 46.0 + - - +
485A TRP* 3.6 40.3 + - + +
527A CYS 3.0 16.1 + - - +
528A THR 4.0 2.7 - - - +
530A ARG* 1.3 75.4 - - + +
532A ALA* 1.3 55.3 + - - +
534A GLU 2.6 23.4 - - - +
535A CYS* 4.1 7.6 - - - -
536A HIS 4.1 14.5 + - - +
537A PRO* 3.7 16.6 - - - +
538A PRO* 4.3 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A TRP* 3.5 13.2 - - + -
493A LYS* 4.8 0.2 - - - -
495A TRP* 3.6 25.8 - - + -
528A THR 2.9 19.0 + - - +
529A ILE 3.0 4.9 + - - +
531A GLN* 1.3 77.7 - - - +
533A ALA* 1.3 63.9 + - - +
534A GLU 3.8 1.0 - - - +
535A CYS* 4.1 13.0 - - - -
556A GLN* 4.1 6.2 - - - +
559A ASP* 3.6 30.3 - - + +
563A ILE* 4.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ILE 2.7 20.3 + - - +
530A ARG 3.7 2.2 - - - +
532A ALA* 1.3 74.7 - - - +
534A GLU* 1.3 62.5 + - - +
556A GLN* 3.2 26.9 + - - +
559A ASP* 5.7 0.2 - - - -
560A ARG* 3.6 23.0 + - + +
563A ILE* 4.9 7.2 - - + -
594A TYR* 3.8 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ARG* 2.8 36.5 + - + +
531A GLN* 2.6 32.4 - - - +
532A ALA 3.6 0.2 - - - -
533A ALA* 1.3 73.0 + - - +
535A CYS* 1.3 54.8 + - - +
536A HIS* 2.9 41.4 + - + +
556A GLN* 5.0 1.6 - - - +
560A ARG* 5.6 0.2 - - - +
594A TYR* 3.6 23.2 + - + -
----------------------------------------------------------
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