Contacts of the helix formed by residues 481 - 488 (chain S) in PDB entry 6CNF
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 PHE 481 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477S LEU* 6.5 0.2 - - + -
478S PRO* 4.9 4.3 - - + +
479S PRO 2.9 3.6 + - - -
480S ASN* 1.3 86.5 + - - +
482S ASP* 1.3 82.2 + - + +
484S TYR* 3.0 24.5 + - - +
485S CYS* 3.3 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 482 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430S LYS* 3.1 42.0 + - - +
434S MET* 3.6 18.1 - - + +
477S LEU* 5.6 2.5 - - + -
479S PRO 3.7 1.2 + - - -
481S PHE* 1.3 88.7 - - + +
483S GLU* 1.3 57.1 + - - +
484S TYR 3.0 5.4 - - - -
485S CYS* 3.0 17.5 + - - +
486S CYS* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 483 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619R ALA* 6.0 0.7 - - - +
622R LEU* 3.5 28.0 - - + +
623R LYS* 4.5 4.7 - - - +
626R ILE* 3.8 15.2 - - + +
434S MET* 3.3 11.9 - - + +
435S TRP* 3.1 46.9 - - + +
441S LEU* 4.0 5.4 - - - +
479S PRO* 3.0 40.0 + - - +
482S ASP* 1.3 74.6 - - - +
484S TYR* 1.3 49.8 + - - +
486S CYS* 4.6 3.1 - - - +
487S GLU* 2.3 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 484 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622R LEU* 5.1 5.4 - - + -
480S ASN 3.2 16.8 + - - +
481S PHE* 3.0 14.6 + - - +
483S GLU* 1.3 78.3 - - - +
485S CYS* 1.3 70.6 + - - +
487S GLU* 3.5 12.5 + - - +
488S ILE* 3.1 52.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 485 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481S PHE* 3.3 31.4 + - - -
482S ASP* 3.0 19.9 + - - +
484S TYR* 1.3 87.2 - - - +
486S CYS* 1.3 59.3 + - - +
488S ILE 2.8 24.1 - - - +
489S LYS* 4.3 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 486 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427S LYS* 3.6 45.3 - - - -
430S LYS* 5.4 0.9 - - - -
444S GLN* 4.9 6.9 - - - +
445S LEU* 3.7 22.5 - - + +
482S ASP* 2.9 31.7 + - - +
483S GLU* 5.0 3.1 - - - -
485S CYS* 1.3 73.3 - - - +
487S GLU* 1.3 66.6 + - - +
488S ILE 3.3 0.7 - - - -
489S LYS* 3.3 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 487 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622R LEU* 3.3 33.7 - - - +
625R ARG* 4.8 7.4 - - - -
626R ILE* 3.4 41.0 - - + +
444S GLN* 6.1 0.7 - - - +
483S GLU* 2.3 39.3 + - + +
484S TYR* 3.5 14.9 - - - +
485S CYS 3.3 0.2 - - - -
486S CYS* 1.3 78.9 - - - +
488S ILE* 1.3 70.2 + - + +
489S LYS* 3.5 4.0 + - - +
490S LYS* 4.9 4.9 + - - +
492S ILE* 4.0 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 488 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484S TYR* 3.1 53.6 + - + +
485S CYS 2.8 20.6 - - - +
487S GLU* 1.3 89.6 - - + +
489S LYS* 1.3 59.0 + - - +
490S LYS 4.5 0.7 - - - +
491S ASN* 3.9 24.2 - - + +
492S ILE* 4.3 21.8 - - + +
----------------------------------------------------------
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