Contacts of the helix formed by residues 494 - 514 (chain A) in PDB entry 6RKU
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 494 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ARG* 3.0 28.7 + - - +
491A ILE 3.1 17.0 - - - +
492A LEU 4.8 1.1 - - - -
493A GLY* 1.3 75.9 - - - +
495A ALA* 1.3 62.9 + - - +
496A ASP* 4.5 4.0 - - - -
497A ARG* 3.7 17.7 + - - +
498A LEU* 3.6 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLY 3.8 4.0 + - - +
494A SER* 1.3 70.0 - - - +
496A ASP* 1.3 63.6 + - - +
497A ARG 3.2 1.6 - - - -
498A LEU* 3.1 14.5 + - + +
499A MET* 2.9 34.3 + - + +
667B ARG* 5.3 11.2 - - - +
669B HIS 5.6 5.8 - - - +
670B GLY* 6.0 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A SER* 3.4 4.1 - - - +
495A ALA* 1.3 80.0 - - - +
497A ARG* 1.3 57.5 + - - +
499A MET* 3.3 10.5 + - - +
500A GLU* 2.9 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLU* 3.7 24.7 + - - +
490A ARG* 5.0 8.7 - - + +
491A ILE* 3.6 29.8 - - + +
494A SER* 3.7 23.0 + - - +
496A ASP* 1.3 79.5 - - - +
498A LEU* 1.3 56.5 + - - +
500A GLU* 3.3 25.7 + - - +
501A VAL* 2.9 47.0 + - - +
504A GLU* 5.1 11.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ARG* 4.2 17.5 - - + +
362A VAL* 4.6 19.7 - - + +
363A THR* 3.8 22.7 - - - +
491A ILE* 4.5 16.3 - - + +
494A SER 3.6 6.9 + - - +
495A ALA* 3.1 16.5 + - + +
497A ARG* 1.3 78.7 - - - +
499A MET* 1.3 75.1 + - - +
501A VAL* 3.2 7.8 + - - +
502A ILE* 3.0 51.9 + - + +
669B HIS* 5.8 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.6 41.5 - - + +
355A VAL* 5.7 1.8 - - + -
359A ARG* 3.7 37.9 - - - +
495A ALA* 2.9 23.4 + - + +
496A ASP* 3.3 12.3 + - - +
498A LEU* 1.3 87.5 - - - +
500A GLU* 1.3 58.2 + - + +
502A ILE* 3.3 10.7 + - + +
503A ARG* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ASP* 2.9 28.0 + - + +
497A ARG* 3.6 32.8 + - - +
499A MET* 1.3 76.0 - - + +
501A VAL* 1.3 56.8 + - - +
503A ARG* 3.3 10.4 + - - +
504A GLU* 2.9 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A VAL* 5.2 13.2 - - + -
365A ARG* 5.3 3.4 - - - +
491A ILE* 3.7 27.1 - - + -
497A ARG* 2.9 37.1 + - - +
498A LEU* 3.2 6.7 + - - +
500A GLU* 1.3 77.1 - - + +
502A ILE* 1.3 62.7 + - + +
504A GLU* 3.3 12.8 + - - +
505A GLU* 2.9 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 4.3 11.7 - - + -
355A VAL* 5.4 4.9 - - + +
358A ARG* 4.4 29.6 - - + +
359A ARG* 4.1 21.1 - - + +
362A VAL* 4.5 12.8 - - + -
498A LEU* 3.0 42.3 + - + +
499A MET* 3.3 12.3 + - + +
501A VAL* 1.3 76.5 - - + +
503A ARG* 1.3 63.3 + - - +
505A GLU* 3.3 9.5 + - - +
506A LEU* 3.0 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 4.1 27.7 + - + +
198A ILE* 3.5 30.6 - - + +
199A ASP* 2.4 39.8 + - - +
499A MET* 2.9 18.8 + - - +
500A GLU* 3.6 10.5 - - - +
502A ILE* 1.3 77.7 - - - +
504A GLU* 1.3 58.3 + - + +
506A LEU* 3.3 6.6 + - - +
507A GLU* 2.9 55.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A ARG* 5.1 10.8 + - - -
500A GLU* 2.9 29.3 + - + +
501A VAL* 3.7 12.1 - - - +
503A ARG* 1.3 76.8 - - + +
505A GLU* 1.3 59.9 + - + +
507A GLU* 3.3 13.8 + - - +
508A LEU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LYS* 5.4 6.2 + - + +
358A ARG* 2.4 40.1 + - - +
362A VAL* 4.7 4.8 - - - +
365A ARG* 3.4 24.4 + - - -
501A VAL* 2.9 35.7 + - + +
502A ILE* 3.7 6.9 - - - +
503A ARG 3.3 0.2 - - - -
504A GLU* 1.3 76.7 - - + +
506A LEU* 1.3 58.5 + - + +
508A LEU* 3.3 9.1 + - + +
509A VAL* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LYS* 4.4 16.8 - - + +
191A ILE* 3.9 26.2 - - + +
194A CYS* 4.6 14.6 - - + -
195A LEU* 4.3 15.5 - - + -
198A ILE* 3.7 29.2 - - + -
354A PHE* 4.8 17.3 - - + -
358A ARG* 6.0 6.1 - - + +
502A ILE* 3.0 28.8 + - + +
503A ARG 3.8 3.6 - - - +
505A GLU* 1.3 77.9 - - + +
507A GLU* 1.3 58.4 + - - +
509A VAL* 3.3 7.5 + - + +
510A ARG* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 5.4 0.9 - - - -
195A LEU* 4.6 13.6 - - + +
503A ARG* 2.9 45.3 + - + +
504A GLU* 3.7 12.6 - - - +
506A LEU* 1.3 74.4 - - - +
508A LEU* 1.3 58.2 + - - +
510A ARG* 3.3 26.5 + - - +
511A GLU* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A GLU 2.9 17.8 + - - +
505A GLU* 3.6 8.5 - - - +
507A GLU* 1.3 76.8 - - - +
509A VAL* 1.3 63.6 + - + +
511A GLU* 3.3 15.0 + - + +
512A GLN* 2.9 56.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 4.6 15.3 - - - +
162A LYS* 4.9 21.5 - - + +
163A ILE* 4.3 24.5 - - + -
187A LEU* 5.1 6.4 - - + +
191A ILE* 5.1 10.1 - - + -
505A GLU* 2.9 23.9 + - + +
506A LEU* 3.3 9.2 + - + +
508A LEU* 1.3 77.6 - - + +
510A ARG* 1.3 62.9 + - - +
512A GLN* 3.2 11.5 + - - +
513A PHE* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 5.6 3.1 - - + -
188A THR* 4.4 24.0 - - + +
191A ILE* 3.8 27.3 - - + +
192A ASN* 2.4 37.3 + - - +
195A LEU* 3.6 20.6 - - - +
506A LEU 2.9 16.7 + - - +
507A GLU* 3.6 23.6 + - - +
509A VAL* 1.3 78.5 - - - +
511A GLU* 1.3 58.6 + - - +
513A PHE 5.2 0.7 - - - -
514A GLY* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A GLU 2.9 18.5 + - - +
508A LEU* 3.8 14.8 - - + +
510A ARG* 1.3 78.3 - - - +
512A GLN* 1.3 63.8 + - + +
514A GLY 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 4.2 11.3 - - - +
508A LEU* 2.9 52.8 + - + +
509A VAL* 3.7 4.9 - - - +
511A GLU* 1.3 81.8 - - + +
513A PHE* 1.3 91.5 + - + +
514A GLY 3.6 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 4.6 9.5 + - + -
129A LYS* 4.5 15.3 - - + -
130A ILE* 4.4 43.3 - - + -
133A GLU* 4.1 20.9 - - + -
163A ILE* 6.3 1.3 - - + -
187A LEU* 3.3 31.7 - - + +
509A VAL* 3.0 23.5 + - + +
510A ARG 3.7 1.8 - - - -
512A GLN* 1.3 109.6 - - + +
514A GLY* 1.3 65.3 + - - +
515A ASP* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 5.2 0.4 - - - -
188A THR* 3.6 19.1 - - - -
510A ARG 2.9 16.6 + - - -
511A GLU 4.5 1.6 + - - -
512A GLN 3.6 3.0 + - - +
513A PHE* 1.3 82.7 - - - +
515A ASP* 1.3 62.6 + - - +
----------------------------------------------------------
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