Contacts of the helix formed by residues 461 - 469 (chain A) in PDB entry 1N54
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 TYR 461 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A MET* 3.6 6.5 - - - -
460A SER* 1.3 92.4 + - - +
462A HIS* 1.3 56.4 + - - +
463A GLN* 2.8 37.8 + - + -
464A ARG* 3.0 45.1 + - + +
465A ILE* 3.8 4.4 + - - +
55B GLN* 4.5 7.2 - - - +
107B ASP* 4.4 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A MET* 3.4 29.1 - - - +
461A TYR* 1.3 69.3 - - - +
463A GLN* 1.3 66.3 + - - +
464A ARG 3.5 0.2 - - - -
465A ILE* 3.7 14.6 + - - +
466A LEU* 3.7 35.9 - - + +
478A PRO* 2.6 25.6 + - + +
479A ALA 3.0 30.2 + - - -
480A ASN* 3.2 30.7 + - + +
481A PRO* 4.2 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A TYR* 2.8 25.7 + - + -
462A HIS* 1.3 80.1 + - - +
464A ARG* 1.3 57.7 + - - +
466A LEU* 2.9 57.0 + - - +
467A ASP* 3.5 19.1 + - - +
480A ASN* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLN* 5.2 11.5 + - - +
426A PHE* 4.2 22.3 - - - -
460A SER* 4.3 8.7 - - - +
461A TYR* 3.0 46.3 + - + +
463A GLN* 1.3 77.8 - - - +
465A ILE* 1.3 60.6 + - - +
467A ASP* 3.4 21.3 + - - +
468A ILE* 3.1 45.9 + - - +
108B ASP* 3.2 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PHE* 4.6 10.3 - - + -
453A LEU* 3.8 32.5 - - + +
456A CYS* 3.9 21.8 - - + +
457A MET* 3.9 22.7 - - + +
460A SER* 3.5 22.2 - - - +
461A TYR 3.9 8.1 - - - +
462A HIS 3.8 8.5 - - - +
463A GLN 3.1 0.4 - - - -
464A ARG* 1.3 77.5 - - + +
466A LEU* 1.3 65.2 + - + +
467A ASP 3.1 0.4 - - - -
468A ILE* 2.9 25.9 - - + +
469A VAL* 3.2 14.0 - - + +
477A CYS* 4.6 2.9 - - - -
478A PRO* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A HIS* 3.7 34.5 - - + +
463A GLN* 2.9 34.8 + - - +
465A ILE* 1.3 76.6 - - - +
467A ASP* 1.3 65.5 + - - +
469A VAL* 3.7 19.7 - - + +
474A SER* 4.6 11.4 - - - +
477A CYS* 3.7 31.9 - - + -
478A PRO* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A GLN* 3.5 26.0 + - - +
464A ARG* 3.4 16.7 + - - +
465A ILE 3.1 0.8 - - - -
466A LEU* 1.3 83.1 - - - +
468A ILE* 1.3 62.4 + - + +
469A VAL 3.5 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLN 5.4 1.6 - - - +
426A PHE* 4.0 45.6 - - + +
430A TRP* 3.6 32.3 + - + -
453A LEU* 4.4 7.0 - - + -
456A CYS* 6.0 0.4 - - + -
464A ARG* 3.1 39.7 - - - +
465A ILE* 2.9 32.5 - - + +
467A ASP* 1.3 78.5 - - - +
469A VAL* 1.3 72.2 + - + +
470A PRO* 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TRP* 4.5 8.5 - - + -
453A LEU* 3.6 34.8 - - + -
465A ILE* 3.2 19.1 - - + +
466A LEU* 3.7 17.5 - - + +
467A ASP 4.3 3.6 - - - +
468A ILE* 1.3 87.8 - - + +
470A PRO* 1.3 79.4 - - + +
471A PRO* 4.0 1.2 - - - +
473A PHE* 4.4 9.0 - - + -
474A SER* 4.9 3.4 - - - +
477A CYS* 3.6 24.2 - - - -
----------------------------------------------------------
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