Contacts of the strand formed by residues 496 - 503 (chain A) in PDB entry 1O0C
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 496 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU* 5.8 2.7 - - - +
289A ARG* 3.7 30.1 - - - +
470A ARG* 3.9 28.3 - - + +
471A LEU 3.6 7.4 - - - +
472A TYR* 3.8 24.7 - - + -
493A PRO 4.3 7.4 + - - +
494A GLU* 4.2 6.0 - - - -
495A SER* 1.3 80.5 + - - +
497A VAL* 1.3 71.1 + - - +
498A ILE* 3.8 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A LEU* 2.9 57.3 + - + +
472A TYR 5.9 0.2 - - - -
473A ASP* 6.2 0.7 - - + -
494A GLU* 4.5 21.3 - - + +
496A LEU* 1.3 75.3 - - - +
498A ILE* 1.3 63.3 + - - +
499A LYS* 3.8 30.5 - - + +
540A ARG* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A GLU* 3.5 37.2 - - + +
469A ILE 3.4 5.6 - - - +
470A ARG* 4.1 28.9 - - + +
496A LEU* 3.8 26.7 - - + -
497A VAL* 1.3 74.2 - - - +
499A LYS* 1.3 70.0 - - - +
500A GLN* 4.1 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 3.5 37.2 - - + +
347A ASP* 4.3 19.1 + - - +
468A GLU* 3.5 0.9 - - - +
469A ILE* 2.7 36.6 + - + +
471A LEU* 3.7 18.2 - - + -
497A VAL* 3.8 22.0 - - - +
498A ILE* 1.3 79.2 - - - +
500A GLN* 1.3 76.3 + - - +
501A GLY 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE 3.3 10.8 - - - +
348A PRO* 3.7 11.1 - - - +
467A VAL 3.7 3.3 - - - +
468A GLU* 3.3 25.3 + - - +
498A ILE* 4.1 7.8 + - - +
499A LYS* 1.3 88.4 + - - +
501A GLY* 1.3 59.4 + - - +
502A PHE* 5.5 1.7 - - - -
535A LYS* 2.7 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A VAL 3.1 15.9 - - - -
346A ILE* 4.0 4.7 + - - -
348A PRO* 4.3 5.8 - - - -
466A PRO* 3.8 1.4 - - - +
467A VAL* 2.9 32.0 + - - +
469A ILE* 4.9 5.9 - - - +
499A LYS 4.1 1.0 - - - -
500A GLN* 1.3 74.7 - - - +
502A PHE* 1.3 74.7 + - - -
535A LYS* 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ALA* 3.3 2.5 - - - -
345A VAL* 2.8 36.3 + - + +
348A PRO* 3.6 28.9 - - + -
386A TRP* 3.5 51.8 - + + -
459A VAL* 3.4 24.3 - - + +
464A ALA* 4.0 12.8 - - + -
465A LEU 3.4 8.7 - - - -
466A PRO* 4.3 18.6 - - + -
467A VAL* 5.1 1.6 - - - -
469A ILE* 5.6 0.6 - - - +
500A GLN 5.5 1.1 - - - -
501A GLY* 1.3 82.2 - - - -
503A ALA* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A MET 3.4 11.2 - - - +
344A ALA* 4.1 10.8 - - + -
459A VAL* 4.0 4.3 - - - -
464A ALA* 3.7 4.0 - - - -
465A LEU* 2.9 33.0 + - + +
467A VAL* 3.8 25.1 - - + +
502A PHE* 1.3 73.1 - - - +
504A GLU* 1.3 70.4 + - - +
505A PRO 3.4 0.3 - - - -
507A LEU* 4.2 16.2 - - + -
518A PHE* 5.3 2.5 - - + -
----------------------------------------------------------
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