Contacts of the helix formed by residues 568 - 593 (chain A) in PDB entry 5ZF6
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 ILE 568 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A SER* 3.8 21.7 + - - +
226A ILE* 4.3 10.3 - - + +
245A ILE* 4.6 9.2 - - + -
246A LYS* 4.2 28.9 - - + +
249A VAL* 3.7 33.7 - - + -
566A ILE 3.7 1.2 + - - -
567A PRO* 1.3 70.9 - - - +
569A LYS* 1.3 64.7 + - - +
571A VAL* 2.9 13.3 + - - +
572A MET* 2.9 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A TYR* 3.5 27.6 + - - +
567A PRO* 3.1 12.2 - - + +
568A ILE* 1.3 78.6 - - - +
570A ILE* 1.3 63.7 + - - +
572A MET* 3.4 7.9 + - - +
573A GLU* 3.0 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A LEU* 4.0 16.2 - - + -
515A THR* 4.7 0.2 - - + -
524A ILE* 4.3 13.2 - - + -
527A TYR* 3.6 49.1 - - + +
529A LEU* 3.9 24.7 - - + +
543A MET* 5.1 1.6 - - - -
566A ILE* 4.1 17.7 - - + -
567A PRO* 3.1 34.3 + - + +
569A LYS* 1.3 77.9 - - - +
571A VAL* 1.3 59.1 + - - +
573A GLU* 3.3 5.9 + - - +
574A ALA* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 3.7 25.6 - - + -
229A LEU* 3.7 28.7 - - + -
245A ILE* 4.1 4.7 - - + -
543A MET* 6.1 0.2 - - - -
545A PHE* 3.9 17.3 - - + -
561A ILE* 5.2 0.9 - - + -
566A ILE* 3.7 27.6 - - + -
567A PRO 3.5 2.9 + - - +
568A ILE 2.9 7.9 + - - +
570A ILE* 1.3 78.3 - - - +
572A MET* 1.3 73.2 + - + +
574A ALA* 3.3 7.0 + - - +
575A ILE* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A CYS* 3.7 38.8 - - - +
245A ILE* 3.6 46.4 - - + -
246A LYS* 3.8 24.9 - - - +
568A ILE* 2.9 26.4 + - + +
569A LYS* 3.8 6.7 - - - +
571A VAL* 1.3 82.5 - - + +
573A GLU* 1.3 63.8 + - + +
575A ILE* 3.5 6.7 + - + +
576A GLN* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A TYR* 2.8 40.4 + - - -
529A LEU* 3.6 14.9 - - + +
569A LYS* 3.0 31.7 + - + +
570A ILE 3.8 0.7 - - - +
571A VAL 3.3 0.2 - - - -
572A MET* 1.3 76.8 - - + +
574A ALA* 1.3 60.5 + - - +
576A GLN* 3.4 5.3 + - - +
577A GLN* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ILE* 3.8 28.4 - - + +
529A LEU* 3.5 14.7 - - + +
543A MET* 4.5 3.8 - - + -
545A PHE* 4.1 21.5 - - + -
570A ILE 2.9 17.9 + - - +
571A VAL* 3.6 7.4 - - - +
573A GLU* 1.3 78.1 - - - +
575A ILE* 1.3 59.6 + - - +
577A GLN* 3.6 1.4 + - - -
578A ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN* 3.9 28.0 - - + +
241A PHE* 3.9 15.5 - - + -
242A CYS* 4.2 7.9 - - - -
245A ILE* 3.6 30.5 - - + -
545A PHE* 3.7 20.2 - - + -
547A ILE* 4.1 9.5 - - + +
554A ILE* 4.1 14.4 - - + -
571A VAL* 3.0 22.8 + - + +
572A MET* 3.8 14.4 - - + +
573A GLU 3.3 0.2 - - - -
574A ALA* 1.3 77.2 - - - +
576A GLN* 1.3 63.7 + - - +
578A ALA* 3.2 7.5 + - - +
579A SER* 3.0 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN* 3.1 28.8 + - - +
572A MET 3.2 16.3 + - - +
573A GLU* 3.9 4.9 - - - +
575A ILE* 1.3 74.9 - - - +
577A GLN* 1.3 66.9 + - - +
579A SER* 3.2 15.2 + - - +
580A VAL* 3.3 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU 3.1 8.3 + - - -
365A THR* 3.5 21.3 - - + +
511A ILE* 4.2 5.8 - - + -
529A LEU* 3.1 44.8 + - - +
530A LEU 4.0 0.8 - - - -
531A THR* 2.5 32.8 + - - +
573A GLU 2.8 22.5 + - - +
574A ALA* 3.9 5.4 - - - +
576A GLN* 1.3 74.0 - - - +
578A ALA* 1.3 62.2 + - - +
580A VAL* 3.3 12.4 + - - +
581A ALA* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A VAL* 3.8 18.3 - - + +
511A ILE* 3.9 10.5 - - + +
547A ILE* 3.5 31.2 - - + -
574A ALA 3.0 18.6 + - - +
575A ILE 3.5 4.3 - - - +
576A GLN 3.2 0.2 - - - -
577A GLN* 1.3 76.0 - - - +
579A SER* 1.3 54.6 + - - +
581A ALA* 3.0 4.2 + - - +
582A LYS* 2.6 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN* 2.5 30.2 + - - -
554A ILE* 5.5 1.2 - - - +
575A ILE* 3.0 10.3 + - - +
576A GLN* 3.2 15.2 + - - -
578A ALA* 1.3 76.2 - - - +
580A VAL* 1.3 61.6 + - - +
582A LYS* 3.9 25.0 + - - +
583A LYS* 3.1 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 6.1 4.5 - - - +
576A GLN* 3.3 32.8 - - - +
577A GLN* 3.5 11.2 - - + +
578A ALA 3.2 0.6 - - - -
579A SER* 1.3 78.0 - - - +
581A ALA* 1.3 61.0 + - - +
583A LYS* 3.6 5.5 + - - +
584A GLU* 3.3 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR 5.6 0.4 - - - +
367A LEU* 3.8 14.5 - - + +
509A VAL* 4.0 14.8 - - + -
531A THR* 3.8 29.4 - - + -
577A GLN 3.3 6.9 + - - +
578A ALA* 3.0 8.7 + - - +
580A VAL* 1.3 77.8 - - - +
582A LYS* 1.3 63.5 + - - +
584A GLU* 3.2 12.3 + - - +
585A ILE* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN* 5.3 0.2 + - - -
507A ALA* 3.9 20.2 - - + +
508A GLY* 5.8 0.4 - - - -
509A VAL* 4.8 5.1 - - + +
548A ALA* 4.8 2.0 - - - -
549A GLY* 3.6 23.8 - - - +
550A THR 2.8 27.5 + - - +
551A ASN* 5.0 2.8 - - - +
553A GLY* 3.1 22.0 + - - +
554A ILE* 4.6 6.7 - - - +
578A ALA* 2.6 18.5 + - + +
579A SER* 3.9 29.3 + - - +
580A VAL 3.4 0.2 - - - -
581A ALA* 1.3 73.0 - - - +
583A LYS* 1.3 60.4 + - - +
585A ILE* 3.3 11.0 + - - +
586A LEU* 2.9 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ASN* 4.3 27.8 - - + +
579A SER* 3.1 25.7 + - - +
580A VAL* 4.1 5.6 - - - +
581A ALA 3.3 0.2 - - - -
582A LYS* 1.3 80.8 - - + +
584A GLU* 1.3 59.2 + - + +
586A LEU* 3.4 6.6 + - - +
587A GLN* 3.0 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR 4.7 10.2 - - - +
367A LEU* 3.7 26.4 + - + +
580A VAL* 3.3 32.8 + - + +
581A ALA* 3.2 9.8 + - - +
583A LYS* 1.3 79.4 - - + +
585A ILE* 1.3 61.1 + - - +
587A GLN* 3.5 10.2 + - - +
588A ILE* 3.3 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 3.6 19.1 - - + -
370A VAL* 4.7 10.1 - - + -
386A PHE* 4.0 20.6 - - + -
388A ARG* 4.4 9.9 - - - +
489A CYS* 4.1 2.0 - - - -
507A ALA* 3.9 8.7 - - + -
508A GLY 3.6 24.0 - - - +
509A VAL* 4.1 20.2 - - + -
581A ALA 3.0 20.5 + - - +
582A LYS* 3.3 8.0 + - - +
584A GLU* 1.3 73.5 - - - +
586A LEU* 1.3 58.9 + - - +
588A ILE* 3.2 9.1 + - - +
589A MET* 2.8 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A SER* 6.0 0.4 - - - +
505A ALA* 3.8 30.1 - - + +
506A VAL 4.1 0.2 - - - -
507A ALA* 3.6 25.1 - - + +
550A THR* 3.8 8.1 - - - -
551A ASN* 3.5 41.5 - - + +
582A LYS* 2.9 28.0 + - + +
583A LYS* 3.8 6.5 - - - +
585A ILE* 1.3 76.0 - - - +
587A GLN* 1.3 54.7 + - + +
589A MET* 3.1 12.5 + - + +
590A ASN* 2.7 49.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A LYS* 3.0 27.2 + - + +
584A GLU* 3.8 9.8 - - - +
585A ILE 3.3 0.2 - - - -
586A LEU* 1.3 75.0 - - + +
588A ILE* 1.3 63.6 + - + +
590A ASN* 4.1 7.0 - - - +
591A LYS* 3.4 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 5.5 4.3 - - + -
370A VAL* 3.3 56.5 - - + +
371A SER* 4.7 2.0 - - - -
372A CYS* 4.2 12.2 - - - +
584A GLU* 3.3 16.8 + - + +
585A ILE* 3.2 7.0 + - - +
587A GLN* 1.3 75.7 - - + +
589A MET* 1.3 66.0 + - - +
591A LYS* 3.3 31.3 + - - +
592A THR* 3.7 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A VAL* 5.7 0.2 - - + -
372A CYS* 4.2 10.8 - - - -
386A PHE* 4.2 13.9 - - + -
489A CYS* 3.8 25.6 - - - +
492A SER* 3.4 25.6 - - - +
493A LEU* 3.8 18.6 - - + +
505A ALA* 4.3 4.0 - - + -
506A VAL 3.5 14.4 - - - +
507A ALA* 4.1 1.1 - - - -
585A ILE* 2.8 40.5 + - + +
586A LEU* 3.5 23.8 - - + +
588A ILE* 1.3 76.7 - - + +
590A ASN* 1.3 61.1 + - - +
592A THR* 3.2 6.8 + - - -
593A ILE 2.9 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A MET* 5.3 0.2 - - - +
505A ALA* 4.1 18.9 - - - +
586A LEU* 2.7 42.8 + - - +
587A GLN* 4.2 6.2 - - - +
588A ILE 3.3 0.2 - - - -
589A MET* 1.3 71.8 - - - +
591A LYS* 1.3 63.8 + - - +
593A ILE 3.2 16.5 + - - +
594A SER* 3.4 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A GLN* 3.4 19.8 + - - +
588A ILE* 3.3 26.8 + - - +
589A MET 3.2 1.0 - - - -
590A ASN* 1.3 77.2 - - - +
592A THR* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A CYS* 3.1 31.7 + - - +
373A GLU* 4.1 7.4 - - - +
374A VAL* 3.6 45.7 - - + +
493A LEU* 4.9 2.0 - - + -
588A ILE 3.7 3.3 + - - -
589A MET 3.2 8.7 + - - +
590A ASN 4.3 0.2 - - - -
591A LYS* 1.3 81.4 - - - +
593A ILE* 1.3 62.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A VAL* 3.8 21.8 - - + -
493A LEU* 3.7 30.1 - - + +
496A MET* 3.5 38.1 - - + +
497A ASP* 3.8 8.7 - - + +
589A MET 2.9 15.5 + - - +
590A ASN* 3.2 10.4 - - - +
592A THR* 1.3 81.3 - - + +
594A SER* 1.3 63.6 + - - +
595A LYS* 3.4 29.4 - - - +
597A ARG* 4.5 14.6 - - + +
----------------------------------------------------------
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