Contacts of the strand formed by residues 455 - 459 (chain B) in PDB entry 4H1S
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 ILE 455 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B MET* 3.9 27.4 - - + -
387B CYS 3.7 24.5 - - - +
388B ILE* 3.9 16.6 - - + -
431B LEU* 5.3 1.1 - - + -
435B PHE* 3.9 18.2 - - + -
452B VAL* 3.6 20.4 - - + +
453B GLY 3.1 5.5 - - - +
454B GLY* 1.3 86.4 - - - +
456B HIS* 1.3 79.3 + - - +
457B VAL* 4.4 2.9 - - + +
472B LEU* 3.8 24.9 - - + -
473B ASP 3.4 9.9 - - - +
474B VAL* 4.0 4.0 - - + -
484B TYR* 3.7 1.8 + - - -
495B VAL* 5.6 0.2 - - + -
545B ARG* 3.5 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A GLU* 3.6 24.6 - - - +
455B ILE* 1.3 85.2 - - - +
457B VAL* 1.3 61.5 + - - +
458B VAL* 5.5 2.5 - - + -
471B LYS* 3.9 2.3 - - - +
472B LEU* 3.5 2.9 + - - -
473B ASP* 2.8 47.9 + - + +
484B TYR* 3.4 43.0 + + - +
544B GLY 4.4 8.4 + - - +
545B ARG* 3.4 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B PHE* 4.1 17.3 - - + -
450B LEU 5.8 0.2 - - - +
452B VAL* 5.0 3.1 - - + -
455B ILE* 4.5 1.6 - - + -
456B HIS* 1.3 75.7 - - - +
458B VAL* 1.3 70.4 + - - +
459B TYR* 3.9 33.7 - - + +
469B VAL* 4.3 6.3 - - + -
471B LYS 3.4 9.9 - - - +
472B LEU* 3.8 19.3 - - + -
544B GLY 5.3 0.3 - - - +
545B ARG 2.9 16.0 + - - +
546B ILE* 3.4 27.0 - - + -
547B LYS* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B HIS* 5.5 2.7 - - + -
457B VAL* 1.3 81.0 - - - +
459B TYR* 1.3 65.0 + - - +
469B VAL* 3.8 4.0 - - - -
470B VAL* 3.0 32.8 + - + -
471B LYS* 2.8 44.4 + - + +
547B LYS* 3.2 29.6 - - + +
548B PHE 4.6 0.7 - - - -
549B SER* 3.6 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B PHE* 3.3 40.2 - - - -
438B SER* 3.1 18.9 + - - -
439B VAL* 3.5 34.5 - - + -
449B PHE* 4.1 7.9 - + - -
450B LEU 4.9 4.0 + - - -
457B VAL* 3.9 15.8 - - + +
458B VAL* 1.3 76.1 - - - +
460B ASP* 1.3 55.4 + - - +
461B LEU* 3.9 9.4 + - + -
468B ARG 3.3 7.6 - - - +
469B VAL* 3.9 19.3 - - + -
470B VAL* 4.3 0.9 - - - -
546B ILE* 3.8 26.5 - - + -
547B LYS 2.8 7.6 + - - -
548B PHE* 3.3 30.7 - + + +
549B SER* 2.7 35.0 + - - -
----------------------------------------------------------
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