Contacts of the strand formed by residues 473 - 476 (chain A) in PDB entry 5NOI
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 LEU 473 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ALA 3.6 0.3 - - - +
436A LEU* 3.4 4.2 - - - -
437A LEU* 3.1 32.9 + - + +
451A TRP* 3.7 36.3 - - + +
458A PHE* 4.0 24.5 - - + -
459A PRO* 4.2 17.5 - - + -
465A ALA* 4.4 1.8 - - + -
466A THR 4.1 3.1 - - - +
467A ILE* 4.3 9.4 - - + +
471A GLY 3.4 4.0 + - - -
472A THR* 1.3 84.6 + - - +
474A GLN* 1.3 72.1 + - - +
475A ILE* 4.3 7.0 - - + +
486A TYR* 3.6 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 4.7 7.0 - - - +
435A ALA 3.5 8.5 - - - +
436A LEU* 4.5 10.1 - - + -
464A ARG 4.0 0.6 - - - +
465A ALA* 3.1 7.6 - - - +
466A THR* 2.9 52.9 + - - +
468A GLN* 2.9 32.7 + - + +
473A LEU* 1.3 75.9 - - - +
475A ILE* 1.3 60.5 + - - +
476A LYS* 5.7 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLY 4.2 0.2 - - - +
434A THR* 3.6 3.6 + - - -
435A ALA* 3.0 58.0 + - + +
437A LEU* 5.7 2.2 - - + -
458A PHE* 4.5 16.8 - - + -
462A ASP* 4.9 1.3 - - - +
464A ARG* 3.6 24.2 - - + +
465A ALA* 4.0 14.4 - - + -
473A LEU* 5.3 8.5 - - + -
474A GLN* 1.3 73.4 - - - +
476A LYS* 1.3 68.8 + - - +
478A LEU* 3.6 21.7 - - + +
482A ASP* 4.0 18.6 - - + +
486A TYR* 5.3 7.0 - - + +
503A LEU* 5.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLY 3.6 5.2 - - - +
434A THR* 4.5 10.1 - - - +
464A ARG* 3.1 34.2 + - - +
474A GLN* 5.7 6.5 - - - +
475A ILE* 1.3 78.2 - - - +
477A ASN* 1.3 74.3 + - + +
478A LEU* 3.5 1.1 - - - -
----------------------------------------------------------
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