Contacts of the helix formed by residues 492 - 509 (chain U) in PDB entry 3FKS
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 492 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490U GLU* 3.6 6.2 + - - -
491U LEU* 1.3 72.6 - - - +
493U LYS* 1.3 59.7 + - - +
494U GLU* 3.6 9.5 + - - +
495U LEU* 3.1 32.0 + - - +
496U LEU* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 493 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492U SER* 1.3 75.3 - - - +
494U GLU* 1.3 60.3 + - - +
496U LEU* 4.4 10.8 - - + +
497U ALA* 3.6 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 494 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492U SER* 3.1 10.1 + - - +
493U LYS* 1.3 82.4 - - - +
495U LEU* 1.3 64.4 + - + +
497U ALA* 4.0 4.3 + - - +
498U SER* 3.3 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 495 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481U LEU* 4.6 14.6 - - + +
484U GLU* 3.3 49.8 - - + +
485U ILE* 5.3 1.8 - - + -
488U LYS* 5.5 4.0 - - + -
490U GLU 3.2 27.1 - - - +
491U LEU* 3.8 20.5 - - + +
492U SER* 3.1 22.9 + - - +
494U GLU* 1.3 81.4 - - + +
496U LEU* 1.3 65.3 + - - +
497U ALA 3.2 0.2 - - - -
498U SER* 3.0 18.2 + - - -
499U LEU* 3.1 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387U GLN* 5.0 13.2 - - + -
388U VAL* 5.7 1.1 - - + -
448U TYR* 4.5 20.6 + - + -
491U LEU* 3.8 43.1 - - + +
492U SER 2.8 27.4 + - - +
493U LYS* 4.4 9.6 - - + +
495U LEU* 1.3 73.8 - - - +
497U ALA* 1.3 61.8 + - - +
499U LEU* 3.2 8.4 + - + +
500U LYS* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 497 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493U LYS 3.6 16.0 + - - +
494U GLU 4.1 5.6 - - - +
495U LEU 3.2 0.6 - - - -
496U LEU* 1.3 77.5 - - - +
498U SER* 1.3 62.1 + - - +
499U LEU 3.5 0.3 + - - -
500U LYS* 3.5 5.6 + - - +
501U SER* 3.5 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 498 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478U HIS* 4.8 4.2 + - - -
481U LEU* 3.8 28.3 - - - +
494U GLU 3.3 13.7 + - - -
495U LEU* 3.0 9.4 + - - +
497U ALA* 1.3 78.7 - - - +
499U LEU* 1.3 59.2 + - - +
501U SER* 3.8 3.9 + - - -
502U ALA* 3.2 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 499 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388U VAL* 4.8 1.8 - - + -
444U VAL* 4.8 6.7 - - + -
445U PRO* 4.7 22.0 - - + +
448U TYR* 3.8 40.1 - - + -
470U PHE* 6.1 1.6 - - + -
474U LEU* 5.7 6.5 - - + -
481U LEU* 5.9 9.4 - - + -
485U ILE* 6.2 1.6 - - + -
491U LEU* 4.3 27.6 - - + -
495U LEU 3.1 11.7 + - - +
496U LEU* 3.2 11.6 + - + +
498U SER* 1.3 77.2 - - - +
500U LYS* 1.3 60.3 + - - +
502U ALA* 4.4 6.7 - - + -
503U THR* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 500 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448U TYR* 3.1 30.7 + - + +
452U ASN* 5.6 0.2 - - - +
454U HIS* 4.3 6.6 + - - +
496U LEU 3.1 12.8 + - - +
497U ALA* 3.9 7.4 - - - +
499U LEU* 1.3 79.7 - - - +
501U SER* 1.3 63.5 + - - +
502U ALA 3.6 0.2 + - - -
503U THR* 3.8 2.6 + - - -
504U GLU* 3.1 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 501 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497U ALA 3.5 15.3 + - - -
498U SER* 4.5 3.1 - - - -
499U LEU 3.4 0.4 - - - -
500U LYS* 1.3 80.4 - - - +
502U ALA* 1.3 62.6 + - - +
504U GLU* 3.4 27.9 + - - +
505U SER* 3.9 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470U PHE* 4.9 2.8 - - + -
473U TYR* 4.6 9.5 - - - -
474U LEU* 5.4 6.0 - - + +
478U HIS* 3.5 39.8 + - + +
481U LEU* 6.1 0.7 - - + -
498U SER 3.2 20.8 + - - +
499U LEU* 4.0 9.4 - - + +
500U LYS 3.3 0.2 - - - -
501U SER* 1.3 77.8 - - - +
503U THR* 1.3 64.5 + - - +
505U SER* 3.4 18.3 + - - -
506U PHE* 3.9 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 503 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445U PRO 5.4 1.1 + - - +
448U TYR* 3.9 9.9 - - - +
449U ALA* 4.1 15.3 - - + +
454U HIS* 3.6 38.1 - - + +
466U PHE* 5.7 1.6 - - + -
470U PHE* 3.7 32.6 - - + -
499U LEU* 2.8 22.9 + - - +
500U LYS 4.2 0.7 - - - -
501U SER 3.5 0.2 - - - -
502U ALA* 1.3 75.0 - - - +
504U GLU* 1.3 65.4 + - - +
505U SER 3.1 1.1 + - - -
506U PHE* 3.3 12.0 + - - +
507U VAL* 3.4 14.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 504 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454U HIS* 4.9 10.1 - - + +
500U LYS* 3.1 40.5 - - + +
501U SER* 3.4 24.7 + - - +
502U ALA 3.3 0.4 - - - -
503U THR* 1.3 79.0 - - - +
505U SER* 1.3 62.5 + - - +
507U VAL* 3.3 17.1 + - - +
508U ALA* 3.5 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 505 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473U TYR* 3.3 24.1 + - - -
478U HIS* 5.8 1.3 - - - -
501U SER 3.9 6.7 + - - -
502U ALA* 3.4 15.1 + - - -
503U THR 3.1 0.8 - - - -
504U GLU* 1.3 80.3 - - - +
506U PHE* 1.3 60.8 + - - +
507U VAL 3.3 0.3 + - - -
508U ALA* 3.7 3.1 + - - +
509U THR* 3.3 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 506 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462U ARG* 6.0 3.1 - - - -
466U PHE* 3.3 43.6 - + + -
469U SER* 3.1 42.0 - - - -
470U PHE* 3.3 42.4 - + + -
473U TYR* 3.4 37.8 - + + -
502U ALA 3.9 2.5 + - - +
503U THR 3.3 3.8 + - - +
505U SER* 1.3 78.8 - - - +
507U VAL* 1.3 63.6 + - - +
509U THR* 3.8 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 507 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454U HIS* 4.4 31.4 - - + +
457U GLY* 6.3 2.9 - - - -
458U ILE* 5.9 6.3 - - + -
466U PHE* 5.4 10.5 - - + -
503U THR* 3.4 19.5 - - + +
504U GLU* 3.5 10.5 - - - +
505U SER 3.2 0.4 - - - -
506U PHE* 1.3 80.5 - - + +
508U ALA* 1.3 67.9 + - - +
509U THR 4.1 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 508 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504U GLU 3.5 10.2 + - - +
505U SER* 4.4 2.7 - - - +
507U VAL* 1.3 81.7 - - - +
509U THR* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 509 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473U TYR* 6.4 1.8 - - - -
505U SER* 3.3 18.3 + - - -
506U PHE* 3.9 15.3 - - - -
507U VAL 3.2 3.9 - - - -
508U ALA* 1.3 83.2 - - - +
----------------------------------------------------------
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