Contacts of the strand formed by residues 585 - 589 (chain B) in PDB entry 4HPF
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 585 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B THR* 3.4 22.9 - - + +
528B GLN* 3.3 29.6 - - - +
529B ARG* 3.4 9.2 - - + +
557B ILE* 3.2 6.8 - - - +
558B GLU* 2.9 36.8 + - + -
567B PHE* 4.1 27.5 - - + -
583B ASN 3.8 2.0 + - - -
584B THR* 1.3 75.6 - - - +
586B GLY* 1.3 59.9 + - - +
587B PHE* 4.3 10.9 - - + -
918B HIS* 3.6 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B THR* 3.6 8.7 + - - -
528B GLN 2.7 36.8 + - - +
530B LEU* 4.1 8.4 - - - +
554B LEU* 4.2 1.1 - - - -
556B ALA 3.5 5.8 - - - -
557B ILE* 3.8 9.0 - - - -
584B THR 3.9 1.8 + - - -
585B LEU* 1.3 73.3 - - - +
587B PHE* 1.3 63.6 + - - -
588B PHE* 3.7 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ILE* 5.0 5.8 - - + -
526B LEU 4.3 0.7 - - - -
527B THR* 3.7 22.7 - - - -
554B LEU* 3.5 3.3 - - - +
555B ILE* 2.7 35.7 + - + +
556B ALA* 2.7 40.7 + - + +
557B ILE* 3.9 6.3 - - - -
558B GLU* 3.8 21.5 - - + -
570B LEU* 3.3 34.3 - - + -
585B LEU* 4.3 8.7 - - + -
586B GLY* 1.3 76.1 - - - -
588B PHE* 1.3 59.6 + - - +
918B HIS* 3.8 35.0 - - + -
919B VAL* 4.8 1.1 - - - -
922B LEU* 4.2 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ILE* 3.6 21.9 - - - +
526B LEU 3.2 18.7 + - - +
528B GLN* 4.1 7.0 - - + -
530B LEU* 3.7 17.3 - - + -
546B CYS* 4.7 3.6 - - + -
552B LEU* 3.8 38.6 - - + -
553B LEU 3.4 7.2 - - - -
554B LEU* 3.5 36.6 - - + -
555B ILE* 4.4 2.1 - - - +
586B GLY* 3.7 25.6 - - - -
587B PHE* 1.3 79.1 - - - +
589B ILE* 1.3 71.3 + - - +
590B ALA 4.3 0.2 - - - -
596B VAL* 3.6 35.0 - - + -
599B ALA* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B PHE* 5.1 1.3 - - + -
499B LEU* 4.1 20.4 - - + -
523B ASN* 3.9 15.6 - - + +
524B LYS 3.4 13.7 - - - +
525B ILE* 4.6 4.3 - - + -
551B HIS 5.6 0.2 - - - +
552B LEU* 5.1 0.3 - - - -
553B LEU* 2.8 38.0 + - + +
555B ILE* 3.9 22.4 - - + -
588B PHE* 1.3 82.1 - - - +
590B ALA* 1.3 65.8 + - - +
998B VAL* 3.4 33.9 - - + +
1019B THR* 5.7 0.2 - - - -
1020B ARG* 3.7 27.3 + - + +
----------------------------------------------------------
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