Contacts of the strand formed by residues 469 - 475 (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 VAL 469 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LYS* 3.9 30.2 + - + -
435B PHE* 3.7 33.9 - - + +
436B GLU* 2.8 28.2 + - + +
457B VAL* 4.3 4.5 - - + -
458B VAL 3.8 4.9 - - - +
459B TYR* 3.9 11.7 - - + -
467B ASP* 4.9 4.3 - - - +
468B ARG* 1.3 76.9 + - + +
470B VAL* 1.3 61.1 + - - +
471B LYS 3.8 19.1 - - - +
472B LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B VAL* 3.0 35.9 + - + +
460B ASP* 3.7 13.7 - - + +
463B ARG* 3.6 38.6 - - - +
468B ARG 3.9 1.1 - - - +
469B VAL* 1.3 78.2 - - - +
471B LYS* 1.3 65.9 + - + +
549B SER* 3.8 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B HIS 4.2 2.0 - - - +
457B VAL* 3.4 4.9 - - - +
458B VAL* 2.8 55.9 + - + +
469B VAL* 3.6 2.8 - - - +
470B VAL* 1.3 80.8 - - + +
472B LEU* 1.3 66.3 + - - +
473B ASP* 2.9 34.5 + - - +
486B PRO* 6.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LYS* 4.0 27.8 - - + -
435B PHE* 4.0 21.3 - - + -
455B ILE* 3.8 28.3 - - + -
456B HIS 3.5 2.0 - - - -
457B VAL* 3.8 20.6 - - + -
469B VAL* 4.0 17.0 - - + -
471B LYS* 1.3 76.2 - - - +
473B ASP* 1.3 56.0 + - - +
474B VAL* 4.9 1.8 - - + -
486B PRO* 3.8 1.0 - - - +
487B LEU* 2.8 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ILE* 3.4 2.1 - - - +
456B HIS* 2.8 45.7 + - + +
471B LYS* 2.9 35.7 + - - +
472B LEU* 1.3 74.7 + - - +
474B VAL* 1.3 67.5 + - - +
484B TYR* 3.9 19.2 - - + +
485B ASP 3.2 12.1 - - - +
486B PRO* 3.1 29.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B MET* 3.6 30.3 - - + -
431B LEU* 5.3 0.2 - - + -
435B PHE* 6.4 0.2 - - + -
454B GLY 3.5 5.2 - - - +
455B ILE* 4.0 12.3 - - + -
472B LEU* 4.9 2.9 - - + +
473B ASP* 1.3 82.6 - - - +
475B LEU* 1.3 66.6 + - - +
476B CYS* 3.4 1.4 + - - -
484B TYR* 3.8 5.8 - - - -
485B ASP* 2.9 35.5 + - + +
486B PRO 5.3 0.4 - - - +
487B LEU* 4.2 22.9 - - + -
493B TYR* 3.5 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ALA* 4.0 22.2 - - + -
385B SER* 3.4 39.1 + - - +
386B MET* 4.4 8.6 - - + +
454B GLY* 3.1 27.2 + - - +
474B VAL* 1.3 78.1 - - - +
476B CYS* 1.3 67.7 + - - +
477B THR* 3.7 5.4 + - - +
482B PRO* 4.0 6.7 - - + -
483B SER* 3.3 20.4 - - - +
484B TYR* 3.5 40.8 - - + +
----------------------------------------------------------
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