Contacts of the helix formed by residues 490 - 501 (chain A) in PDB entry 1YOJ
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 PRO 490 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU* 3.6 29.6 - - + -
485A CYS* 4.1 0.7 - - - -
488A GLU 3.7 6.5 - - - +
489A CYS* 1.4 92.9 - - - +
491A GLU* 1.3 65.4 + - - +
492A SER* 3.9 0.2 - - - +
493A LEU* 3.0 12.4 + - + -
494A HIS 3.3 7.6 + - - -
521A TYR* 3.3 24.2 - - - +
526A GLU* 3.9 24.7 - - + +
529A TYR* 5.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A CYS* 3.6 23.9 - - - +
489A CYS 3.4 3.2 + - - -
490A PRO* 1.3 71.4 - - - +
492A SER* 1.3 52.0 + - - +
494A HIS* 3.1 23.7 + - - +
495A ASP* 2.7 41.0 + - + +
498A CYS* 5.6 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
490A PRO* 3.9 0.5 - - - +
491A GLU* 1.3 77.4 - - - +
493A LEU* 1.3 58.9 + - - +
495A ASP* 3.4 9.9 + - - +
496A LEU 3.3 14.4 + - - -
517A PHE* 3.8 13.5 - - - -
521A TYR* 3.0 16.0 + - - -
525A THR* 3.4 24.1 - - - +
526A GLU* 2.6 29.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
362A LEU* 3.9 18.8 - - + -
366A VAL* 4.1 11.4 - - + -
454A LEU* 4.6 12.1 - - + -
458A THR* 3.7 28.9 - - + -
489A CYS* 3.8 8.1 - - - -
490A PRO* 3.0 11.3 + - + +
492A SER* 1.3 78.0 + - - +
494A HIS* 1.3 65.9 + - - +
495A ASP 3.1 0.2 - - - -
496A LEU* 3.2 11.9 + - + +
497A MET* 3.1 30.9 + - + +
517A PHE* 4.3 5.2 - - + -
518A LEU* 3.7 30.1 - - + -
521A TYR* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ARG* 6.1 0.2 - - + -
483A MET 2.7 26.5 + - - -
484A PRO* 3.3 9.2 - - + -
485A CYS* 3.6 47.0 + - - -
486A PRO* 4.9 0.7 - - + -
489A CYS* 4.3 1.8 - - - -
490A PRO 3.3 2.8 + - - -
491A GLU* 3.1 29.6 + - - +
493A LEU* 1.3 76.4 - - - +
495A ASP* 1.3 64.3 + - - +
497A MET* 3.3 27.3 - - + +
498A CYS* 3.0 44.9 + - - -
501A TRP* 4.3 1.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLU* 2.7 27.0 + - + +
492A SER* 3.5 12.1 - - - +
493A LEU 3.1 0.2 - - - -
494A HIS* 1.3 71.8 - - - +
496A LEU* 1.3 57.3 + - - +
498A CYS* 3.1 10.1 + - - +
499A GLN* 2.8 54.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU* 4.0 14.8 - - + -
492A SER 3.3 9.6 + - - +
493A LEU* 3.2 10.9 + - + +
495A ASP* 1.3 75.3 + - - +
497A MET* 1.3 67.1 + - - +
499A GLN* 3.1 28.7 + - - +
500A CYS* 3.1 25.5 + - - -
513A TYR* 4.4 4.0 - - + -
514A LEU* 3.6 31.6 - - + -
517A PHE* 3.7 49.6 - - + -
518A LEU* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A GLY* 4.1 18.8 - - - +
454A LEU* 4.0 25.4 - - + +
455A THR* 3.8 19.7 - - - +
458A THR* 3.6 27.4 - - + +
484A PRO 5.6 0.2 - - - +
486A PRO* 4.3 8.1 - - + -
489A CYS* 4.0 21.5 - - - -
493A LEU* 3.3 15.3 - - + +
494A HIS* 3.3 26.9 - - + +
496A LEU* 1.3 74.8 - - - +
498A CYS* 1.3 61.6 + - - +
500A CYS* 3.0 13.8 + - - +
501A TRP* 3.1 36.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ARG* 5.1 9.6 - - + -
491A GLU* 5.6 0.2 - - - -
494A HIS* 3.0 47.0 + - - +
495A ASP* 3.1 13.2 + - - +
497A MET* 1.3 75.4 - - - +
499A GLN* 1.3 62.1 + - - +
501A TRP* 3.4 18.3 + - - +
502A ARG* 3.4 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ASP* 2.8 38.2 + - - +
496A LEU* 3.1 22.5 + - - +
498A CYS* 1.3 75.0 - - + +
500A CYS* 1.3 62.2 + - - +
502A ARG* 3.3 51.8 + - - +
508A ARG* 3.6 3.8 - - - -
509A PRO* 3.4 25.3 - - + +
513A TYR* 3.9 29.7 + - - -
517A PHE* 5.8 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A VAL* 3.3 38.8 - - - +
448A TRP* 3.3 12.6 - - - -
450A PHE* 4.4 3.6 - - - -
451A GLY* 3.7 21.1 - - - -
454A LEU* 4.8 1.8 - - - -
496A LEU 3.1 18.9 + - - -
497A MET* 3.0 9.0 + - - +
499A GLN* 1.3 75.8 - - - +
501A TRP* 1.3 58.7 + - + +
502A ARG 3.4 0.9 - - - -
508A ARG* 3.1 21.9 + - - -
509A PRO* 4.2 2.0 - - - -
514A LEU* 3.9 29.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A TRP* 3.3 36.6 + + + -
451A GLY* 3.4 25.0 - - - -
452A ILE* 3.3 35.0 - - + +
455A THR* 3.7 19.7 - - + -
465A TYR* 5.4 1.3 - - - -
482A ARG* 2.9 57.6 + - + +
483A MET* 3.8 36.3 - - + -
494A HIS* 4.3 5.2 - - - -
497A MET* 3.1 39.6 + - + +
498A CYS* 3.4 12.8 + - - +
499A GLN 3.1 0.2 - - - -
500A CYS* 1.3 83.5 - - + +
502A ARG* 1.3 60.5 - - - +
----------------------------------------------------------
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