Contacts of the helix formed by residues 482 - 498 (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 SER 482 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ARG* 5.7 0.2 - - - -
388A ARG* 3.0 24.8 + - - -
391A THR* 3.9 0.7 - - - +
450A HIS* 6.4 0.2 - - - -
479A SER* 5.6 0.2 + - - -
481A GLY* 1.3 72.6 - - - +
483A SER* 1.3 64.1 - - - +
484A SER 4.0 2.5 - - - +
485A MET* 3.1 32.4 + - - +
486A ALA* 3.5 5.4 + - - +
510A ALA* 3.6 26.5 - - - +
532A ASP* 5.8 0.7 - - - -
533A ILE* 5.6 1.1 - - - -
544A ASP* 5.1 5.5 + - - -
546A LYS* 3.9 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A THR* 4.0 14.6 - - - -
393A VAL* 4.0 1.6 - - - +
427A TYR* 2.5 28.2 + - - -
450A HIS* 4.1 8.1 - - - -
476A VAL* 3.7 24.5 - - - -
479A SER* 4.0 13.6 + - - -
481A GLY 3.5 2.0 - - - -
482A SER* 1.3 75.9 - - - +
484A SER* 1.3 57.8 + - - +
486A ALA* 3.2 2.7 + - - +
487A SER* 2.8 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A TYR* 4.6 2.9 - - - -
450A HIS* 3.1 44.1 + - - -
453A LEU* 3.6 29.8 - - - +
454A ALA* 3.7 8.3 + - - +
482A SER* 3.2 1.4 - - - +
483A SER* 1.3 81.2 + - - +
485A MET* 1.3 64.9 + - - +
487A SER* 3.5 8.8 + - - -
488A ALA* 3.5 13.5 + - - +
546A LYS* 5.1 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 3.9 6.3 - - - +
453A LEU* 3.6 44.6 - - + +
457A ALA* 5.3 0.4 - - + -
482A SER* 3.1 23.2 + - - +
483A SER 3.3 0.2 - - - -
484A SER* 1.3 81.2 - - - +
486A ALA* 1.3 65.7 + - - +
488A ALA* 3.2 15.8 + - + +
489A CYS* 3.4 17.5 + - - -
508A GLY* 3.6 22.7 - - - +
509A VAL* 3.6 16.6 - - - +
546A LYS* 4.0 10.3 - - + -
547A ILE 3.6 30.5 - - - +
548A ALA* 3.8 12.6 - - + -
556A ALA* 6.1 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PHE* 3.8 19.9 - - + -
388A ARG* 3.8 11.5 - - + +
391A THR* 4.0 15.0 - - + +
393A VAL* 3.5 27.5 - - + +
482A SER 3.5 11.7 + - - +
483A SER 3.2 8.2 + - - +
485A MET* 1.3 75.7 - - - +
487A SER* 1.3 59.8 + - - +
489A CYS* 3.1 3.3 + - - +
490A GLY 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A VAL* 3.9 6.5 - - - +
395A CYS* 3.8 4.1 - - - -
425A LEU* 4.4 7.0 - - - +
427A TYR* 3.7 17.8 - - - -
454A ALA* 4.0 13.9 - - - -
474A SER* 2.9 34.6 + - - -
483A SER 2.8 17.5 + - - -
484A SER* 3.6 9.0 - - - -
485A MET 3.2 0.2 - - - -
486A ALA* 1.3 76.5 - - - +
488A ALA* 1.3 57.5 + - - +
491A GLY* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ALA* 4.2 7.1 - - + +
457A ALA* 4.1 25.4 - - + -
458A LEU* 3.6 19.0 - - + +
484A SER 3.5 8.4 + - - +
485A MET* 3.2 14.0 + - + +
486A ALA 3.2 0.6 - - - -
487A SER* 1.3 75.7 - - - +
489A CYS* 1.3 60.9 + - - +
491A GLY 3.2 0.7 + - - -
492A SER* 2.9 25.1 + - - -
506A VAL* 3.9 13.0 - - + +
508A GLY 4.9 2.7 - - - +
548A ALA* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PHE* 3.8 28.0 - - + -
388A ARG* 4.3 1.3 - - - -
485A MET 3.4 9.9 - - - -
486A ALA 3.1 5.9 + - - +
488A ALA* 1.3 75.0 - - - +
490A GLY* 1.3 57.8 + - - +
492A SER* 3.2 3.8 + - - -
493A LEU* 3.0 33.0 + - - +
506A VAL 3.7 9.0 - - - -
507A ALA* 3.6 11.2 - - - -
508A GLY 3.3 34.8 - - - -
585A ILE* 4.1 4.7 - - - -
589A MET* 3.8 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ALA* 3.6 4.9 - - - +
386A PHE* 4.0 18.2 - - - +
395A CYS* 3.3 29.7 - - - +
486A ALA 2.9 12.9 + - - -
489A CYS* 1.3 76.9 - - - +
491A GLY* 1.3 57.7 + - - +
493A LEU* 4.5 5.4 - - - -
494A ALA* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A CYS* 3.5 6.6 - - - -
458A LEU* 3.9 16.4 - - - -
472A VAL* 4.2 13.7 - - - -
487A SER 2.9 19.1 + - - -
488A ALA 3.2 2.0 + - - -
490A GLY* 1.3 75.4 - - - +
492A SER* 1.3 59.9 + - - +
494A ALA* 3.9 1.2 - - - +
495A LEU* 3.0 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A LEU* 3.7 12.9 - - - +
488A ALA 2.9 8.9 + - - -
489A CYS 3.2 7.8 + - - -
491A GLY* 1.3 76.5 - - - +
493A LEU* 1.3 62.7 + - - +
495A LEU* 3.9 4.1 - - - +
496A MET* 3.1 28.8 + - - +
502A ILE* 4.3 7.6 - - - +
505A ALA* 3.7 10.8 - - - +
506A VAL 3.5 33.1 + - - -
589A MET* 3.4 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A CYS* 3.5 35.0 - - + -
373A GLU 4.5 8.1 - - - +
374A VAL* 3.9 9.7 - - + +
384A ALA* 3.6 14.4 - - + -
385A LEU 4.8 0.4 - - - +
386A PHE* 4.3 16.6 - - + -
489A CYS 3.0 19.6 + - - +
490A GLY* 3.9 2.2 - - - +
492A SER* 1.3 77.5 - - - +
494A ALA* 1.3 57.9 + - - +
496A MET* 3.3 5.4 + - - +
497A ASP* 2.9 28.4 + - - +
589A MET* 3.8 36.6 - - + +
592A THR* 4.9 1.6 - - + -
593A ILE* 3.7 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLY* 4.1 1.6 - - - -
383A SER* 4.0 4.7 - - - -
384A ALA* 3.4 17.6 - - + +
395A CYS* 4.0 21.3 - - + +
396A THR 4.4 0.4 - - - +
397A VAL* 3.6 18.1 - - + +
472A VAL* 5.5 0.4 - - + -
490A GLY 2.9 19.5 + - - +
491A GLY* 4.0 3.1 - - - +
493A LEU* 1.3 76.5 - - - +
495A LEU* 1.3 58.7 + - - +
497A ASP* 3.0 8.2 + - - +
498A SER* 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 3.7 16.4 - - + -
423A PHE* 3.8 15.3 - - + -
458A LEU* 4.6 8.7 - - + -
462A ILE* 3.6 26.0 - - + -
470A ILE* 3.5 28.5 - - + -
472A VAL* 4.0 5.8 - - + -
491A GLY 3.0 24.6 + - - +
492A SER* 3.9 4.5 - - - +
494A ALA* 1.3 76.8 - - - +
496A MET* 1.3 60.6 + - - +
498A SER* 3.0 15.5 + - - -
500A VAL* 3.1 41.8 + - + -
502A ILE* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A SER* 3.1 17.4 + - - +
493A LEU* 3.7 3.6 - - - +
495A LEU* 1.3 76.5 - - - +
497A ASP* 1.3 60.0 + - - +
499A GLY 3.5 1.9 + - - -
500A VAL 4.7 0.2 - - - -
502A ILE* 3.6 37.9 - - + +
503A SER 5.8 0.2 - - - +
504A SER* 4.3 3.1 - - - -
505A ALA* 3.8 30.1 - - + +
590A ASN* 5.3 0.2 - - - +
593A ILE* 3.5 30.9 - - + +
594A SER* 3.8 31.9 - - - +
595A LYS 4.0 2.5 - - - +
596A PRO* 3.9 24.2 - - + -
597A ARG* 3.1 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A VAL* 3.7 9.0 - - + +
375A ASP* 3.3 16.5 + - - +
383A SER 3.0 29.8 + - - +
493A LEU 2.9 14.6 + - - +
494A ALA 3.0 8.9 + - - +
496A MET* 1.3 78.7 - - - +
498A SER* 1.3 58.3 + - - +
499A GLY 3.2 1.1 + - - -
593A ILE* 3.8 2.4 - - - +
597A ARG* 2.5 51.5 + - - +
601A LYS* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A HIS 3.3 23.9 - - - +
382A GLY* 3.7 7.0 - - - -
397A VAL* 3.6 13.9 - - - +
399A PHE* 3.4 27.4 - - - -
494A ALA 2.8 12.3 + - - -
495A LEU* 3.0 15.6 + - - -
497A ASP* 1.3 75.4 - - - +
499A GLY* 1.3 58.6 + - - +
500A VAL* 3.3 18.0 - - - +
597A ARG* 5.1 0.2 - - - -
600A ARG* 3.7 15.2 - - - +
601A LYS* 5.1 0.7 - - - +
----------------------------------------------------------
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