Contacts of the helix formed by residues 512 - 533 (chain A) in PDB entry 2QR8
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 512 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A PHE 4.4 0.4 - - - -
511A PHE* 1.3 73.3 - - - +
513A GLU* 1.3 64.1 + - - +
514A ARG* 3.7 3.6 + - - +
515A GLU* 3.0 33.0 + - - +
516A ALA* 3.0 20.4 + - - +
686A PRO 3.6 6.2 + - - -
687A GLN* 3.5 23.1 + - - -
688A TYR 3.2 23.1 - - - -
690A LEU* 4.0 7.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
512A SER* 1.3 71.9 - - - +
514A ARG* 1.3 64.1 + - - +
516A ALA* 3.7 8.8 - - - +
517A SER* 2.9 25.3 + - - -
612A LEU* 4.1 7.9 - - + -
647A SER 4.3 1.7 - - - +
648A VAL* 3.4 16.3 - - - -
649A SER* 2.5 50.9 + - - -
678A TRP* 3.2 19.1 + - - +
685A LEU* 4.0 11.6 - - + +
686A PRO* 4.0 24.9 + - + +
688A TYR 4.7 1.2 + - - -
690A LEU* 3.6 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A SER* 3.2 4.2 - - - +
513A GLU* 1.3 77.6 - - - +
515A GLU* 1.3 62.4 + - + +
517A SER* 3.5 2.8 + - - -
518A ALA* 3.2 21.8 + - - +
682A TRP* 3.6 42.5 + - + +
683A ASP* 2.9 35.2 + - - +
685A LEU* 3.4 27.8 + - + +
686A PRO 3.2 16.9 + - - +
687A GLN* 3.4 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLN* 4.2 7.8 - - - +
510A PHE 3.6 5.4 - - - +
511A PHE* 3.1 38.4 - - + -
512A SER* 3.0 35.5 + - - +
514A ARG* 1.3 76.8 - - + +
516A ALA* 1.3 62.7 + - - +
518A ALA* 3.4 7.6 + - - +
519A VAL* 3.1 27.2 + - + +
554A PRO* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A PHE* 3.6 24.4 - - + -
512A SER 3.0 9.8 + - - +
513A GLU 3.1 6.7 + - - +
515A GLU* 1.3 76.9 - - - +
517A SER* 1.3 57.4 + - - +
519A VAL* 3.4 4.4 + - - +
520A LEU* 2.9 28.9 + - - +
611A MET* 3.9 16.8 - - + +
612A LEU* 4.2 15.9 - - + -
678A TRP* 3.5 15.8 - - + -
690A LEU* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU 2.9 8.3 + - - -
514A ARG 3.7 3.4 - - - -
516A ALA* 1.3 73.7 - - - +
518A ALA* 1.3 60.3 + - - +
520A LEU 3.3 0.7 + - - -
521A PHE* 2.9 30.4 + - - +
678A TRP* 2.9 38.5 + - - -
679A ILE* 3.6 13.5 + - - +
682A TRP* 4.1 9.5 - - - +
685A LEU* 3.5 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ARG 3.2 13.0 + - - +
515A GLU* 3.7 10.5 - - - +
517A SER* 1.3 77.6 + - - +
519A VAL* 1.3 61.5 + - - +
521A PHE* 3.5 8.0 + - - +
522A THR* 3.0 29.1 + - - -
554A PRO* 4.2 18.6 - - + +
682A TRP* 5.6 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LEU* 4.0 15.5 - - + -
505A ILE* 4.2 15.5 - - + -
511A PHE* 4.5 5.8 - - + -
515A GLU 3.1 20.1 + - - +
516A ALA* 3.7 6.1 - - - +
517A SER 3.2 0.2 - - - -
518A ALA* 1.3 77.1 - - - +
520A LEU* 1.3 62.5 + - - +
522A THR* 3.3 4.0 + - - -
523A ILE* 3.2 41.2 + - + +
547A TYR* 4.2 9.9 - - - +
552A GLY 6.2 0.2 - - - +
554A PRO* 4.7 12.3 - - + -
557A ILE* 4.1 12.1 - - + +
611A MET* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ALA 2.9 17.3 + - - +
517A SER 4.0 2.5 - - - +
519A VAL* 1.3 74.9 - - - +
521A PHE* 1.3 60.0 + - - +
523A ILE* 3.3 3.7 + - + +
524A THR* 2.7 50.1 + - - +
604A LEU* 4.0 32.3 - - + +
607A LEU* 4.6 14.6 - - + -
608A LEU* 4.0 16.8 - - + -
611A MET* 4.6 9.4 - - + -
655A LEU* 4.0 11.2 - - + -
659A MET* 3.9 27.1 - - + -
673A VAL* 4.2 7.2 - - + -
678A TRP* 4.3 4.9 - - + -
679A ILE* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A SER 2.9 19.5 + - - +
518A ALA* 3.6 7.9 - - - +
519A VAL 3.3 0.2 - - - -
520A LEU* 1.3 74.2 - - - +
522A THR* 1.3 67.7 + - - +
525A LYS* 2.9 67.9 + - + +
674A LEU* 3.7 17.0 - - + -
679A ILE* 3.6 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ASN* 3.3 32.2 - - + +
518A ALA 3.0 16.5 + - - -
519A VAL 3.8 3.8 - - - -
520A LEU 3.3 0.2 - - - -
521A PHE* 1.3 88.6 - - - +
523A ILE* 1.3 60.5 + - - +
525A LYS* 3.8 4.4 - - - +
526A THR* 2.7 26.5 + - - -
554A PRO* 3.4 34.3 - - - +
555A GLU* 5.3 0.7 - - - -
557A ILE* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LEU* 4.3 4.3 - - + -
519A VAL* 3.2 32.6 + - + +
520A LEU* 3.9 5.2 - - + +
522A THR* 1.3 75.7 - - - +
524A THR* 1.3 63.8 + - - +
526A THR* 3.2 7.3 + - - -
527A VAL* 3.2 20.4 + - + +
545A ILE* 3.9 23.3 - - + -
557A ILE* 4.0 22.2 - - + -
559A ILE* 4.1 19.3 - - + -
604A LEU* 3.6 28.7 - - + -
607A LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A LEU* 2.7 42.9 + - - +
523A ILE* 1.3 69.1 - - - +
525A LYS* 1.3 60.1 + - - +
527A VAL* 3.2 1.5 + - - +
528A GLU* 2.8 29.5 + - - +
604A LEU* 3.6 22.8 - - + +
670A ALA* 3.8 36.3 - - + +
673A VAL* 4.0 15.8 - - + +
674A LEU* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A HIS* 4.5 5.3 + - + +
521A PHE* 2.9 53.5 + - + +
522A THR* 3.8 7.4 - - - +
524A THR* 1.3 74.7 - - - +
526A THR* 1.3 60.9 + - - +
528A GLU* 3.4 25.9 + - - +
529A TYR* 3.3 21.3 + - - +
674A LEU* 3.9 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A HIS* 3.4 29.7 - - + +
475A ASN* 3.4 15.3 + - - +
476A ILE* 3.5 32.8 - - + -
522A THR 2.7 20.5 + - - -
523A ILE* 3.2 9.0 + - - -
524A THR 3.2 0.6 - - - -
525A LYS* 1.3 74.3 - - - +
527A VAL* 1.3 65.2 + - - +
529A TYR* 3.4 4.0 + - - +
530A LEU* 3.1 24.4 + - + +
559A ILE* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ILE* 3.2 14.1 + - + +
524A THR* 3.2 9.5 + - - +
526A THR* 1.3 73.2 - - - +
528A GLU* 1.3 60.8 + - - +
530A LEU* 4.3 9.2 - - + -
531A HIS* 2.8 61.8 + - + +
537A HIS* 6.2 0.9 - - + -
540A LEU* 3.7 26.2 - - + -
559A ILE* 3.8 14.1 - - + -
600A ASP* 4.5 7.0 - - + +
601A ILE* 4.1 16.2 - - + -
604A LEU* 4.3 8.5 - - + -
670A ALA* 4.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A THR 2.8 17.6 + - - +
525A LYS* 3.4 26.3 + - - +
527A VAL* 1.3 76.3 - - - +
529A TYR* 1.3 56.3 + - - +
531A HIS* 3.3 3.4 + - - +
532A ALA* 2.9 34.3 + - + +
670A ALA* 3.7 11.6 - - + +
671A ALA* 3.4 37.5 - - + +
674A LEU* 3.3 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG 4.9 3.1 + - - -
470A TYR* 3.8 37.6 - + + -
473A HIS* 3.6 34.8 - + + +
525A LYS 3.3 10.7 + - - +
526A THR 3.6 8.7 - - - +
527A VAL 3.2 0.2 - - - -
528A GLU* 1.3 79.0 + - - +
530A LEU* 1.3 70.0 + - + +
532A ALA* 3.3 6.8 + - + +
533A GLN* 3.1 55.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ILE* 5.3 0.2 - - + -
470A TYR* 4.1 21.5 - - + -
476A ILE* 3.7 29.6 - - + -
526A THR* 3.1 26.5 + - + +
527A VAL* 3.3 10.3 + - + +
529A TYR* 1.3 79.6 - - + +
531A HIS* 1.3 65.9 + - + +
533A GLN* 3.0 10.8 + - - +
535A VAL* 2.9 50.9 + - + +
537A HIS* 5.5 7.2 - - + +
559A ILE* 5.1 6.3 - - + -
562A PHE* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A VAL* 2.8 44.3 + - + +
528A GLU* 3.8 4.0 - - - +
530A LEU* 1.3 72.4 - - + +
532A ALA* 1.3 57.4 + - - +
534A GLY* 2.9 20.6 + - - -
535A VAL 3.2 20.2 - - - -
536A VAL* 4.1 8.5 - - + -
578A PRO* 3.6 11.0 - - - +
597A ALA* 3.4 38.8 - - + +
600A ASP* 2.8 27.5 + - + -
601A ILE* 4.2 6.9 - - + +
670A ALA* 4.6 9.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
528A GLU* 2.9 24.4 + - + +
529A TYR* 3.3 7.8 + - + +
531A HIS* 1.3 72.2 - - - +
533A GLN* 1.3 68.7 + - - +
534A GLY 3.3 0.4 - - - -
577A THR* 3.7 5.9 - - - +
578A PRO* 3.2 24.1 - - - +
579A CYS* 4.9 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 4.8 9.4 + - - -
470A TYR* 3.6 43.2 + - + +
529A TYR* 3.1 46.3 + - + +
530A LEU* 3.0 7.5 + - - +
532A ALA* 1.3 86.1 + - - +
534A GLY* 1.3 60.3 + - - +
535A VAL* 3.4 0.8 + - + +
567A GLN* 4.2 3.8 + - - -
576A MET 3.8 3.8 - - - +
577A THR* 3.8 25.0 - - - +
----------------------------------------------------------
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