Contacts of the helix formed by residues 583 - 592 (chain B) in PDB entry 1JPW
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 ASP 583 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B HIS* 4.0 24.2 + - + +
525B ALA* 4.4 2.4 + - - +
528B ARG* 3.3 24.4 + - - -
580B LEU 3.2 11.4 + - - +
582B ARG* 1.3 79.9 - - - +
584B VAL* 1.3 80.8 + - - +
585B HIS* 3.3 18.9 + - - -
586B ASN* 3.5 14.2 - - - +
587B ARG* 3.1 24.6 + - - +
289C THR* 5.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ARG 4.0 0.6 + - - -
583B ASP* 1.3 80.4 + - - +
585B HIS* 1.3 87.6 + - + +
587B ARG* 3.3 33.2 + - - +
588B ILE* 3.3 32.4 + - + +
591B ARG* 5.0 1.1 + - - +
624B ASP* 5.8 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ARG* 3.5 30.7 - - - +
583B ASP* 3.2 13.3 + - - +
584B VAL* 1.3 89.4 - - + +
586B ASN* 1.3 66.6 + - - +
588B ILE* 3.5 23.9 + - + +
589B VAL* 3.5 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B HIS* 3.8 11.2 + - - +
528B ARG* 3.2 33.9 + - - +
533B ILE* 3.9 16.4 - - + +
580B LEU* 2.8 58.5 + - + +
581B ALA* 4.5 0.2 - - - -
583B ASP* 3.1 18.2 + - - +
585B HIS* 1.3 77.2 - - - +
587B ARG* 1.3 64.1 + - - +
589B VAL* 3.1 5.2 + - - +
590B ILE* 3.0 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B ALA* 2.8 48.1 + - - +
582B ARG* 3.3 23.4 + - - +
583B ASP 3.1 8.4 + - - +
584B VAL* 3.3 38.4 - - + +
585B HIS 3.3 0.2 - - - -
586B ASN* 1.3 77.4 - - - +
588B ILE* 1.3 61.6 + - - +
590B ILE* 3.4 2.8 + - - -
591B ARG* 3.0 35.9 + - - +
620B GLU* 3.2 29.5 + - - -
621B LEU* 3.7 28.7 + - + +
623B GLN* 3.1 26.3 + - - +
624B ASP* 5.4 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B VAL* 3.3 25.3 + - + +
585B HIS* 3.7 21.3 - - + +
586B ASN 3.3 0.6 - - - -
587B ARG* 1.3 75.8 - - - +
589B VAL* 1.3 58.7 + - + +
591B ARG* 3.4 30.3 - - - +
592B GLY* 2.8 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ARG* 4.4 19.1 - - + -
533B ILE* 3.7 28.9 - - + -
534B PRO* 4.9 7.4 - - + -
585B HIS 3.5 14.1 + - - +
586B ASN 3.1 7.7 + - - +
588B ILE* 1.3 76.7 - - + +
590B ILE* 1.3 67.3 + - - +
591B ARG 3.1 1.6 - - - -
592B GLY* 2.8 13.4 + - - -
593B LEU* 3.2 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ILE* 3.8 24.7 - - + -
537B VAL* 5.2 0.4 - - + -
577B LEU* 4.1 27.8 - - + +
580B LEU* 4.9 3.1 - - + -
581B ALA* 3.9 32.1 - - + +
586B ASN* 3.0 17.1 + - + +
587B ARG* 3.8 6.1 - - - +
589B VAL* 1.3 74.5 - - - +
591B ARG* 1.3 64.1 + - - +
593B LEU* 3.1 12.2 + - - +
595B THR* 3.1 47.3 + - + +
599B PHE* 3.9 16.8 - - + -
617B VAL* 4.9 1.8 - - + -
621B LEU* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 591 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B VAL* 5.0 1.8 + - - +
587B ARG* 3.0 23.3 + - - +
588B ILE* 3.4 41.1 - - - +
590B ILE* 1.3 78.4 - - - +
592B GLY* 1.3 57.2 + - - +
593B LEU 2.9 6.4 + - - -
594B ASN* 3.0 15.8 + - - -
595B THR* 4.8 3.8 - - - +
596B ILE* 4.3 23.5 - - + +
621B LEU* 4.9 12.1 + - + +
624B ASP* 2.8 35.1 + - - +
626B GLU* 5.4 8.0 + - - +
627B ALA* 4.0 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B ILE 2.8 17.1 + - - -
589B VAL* 2.8 9.3 + - - -
591B ARG* 1.3 75.1 - - - +
593B LEU* 1.3 67.2 + - - +
594B ASN 3.5 1.5 + - - -
----------------------------------------------------------
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