Contacts of the helix formed by residues 585 - 595 (chain A) in PDB entry 4JGV
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 PRO 585 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN* 5.8 2.9 - - - +
407A TYR* 3.6 30.3 - - + -
408A ASP* 6.0 0.7 - - - +
411A SER* 3.4 25.6 - - - +
583A PRO 3.6 1.5 - - - +
584A PRO* 1.3 87.1 - - + +
586A PRO* 1.3 76.5 - - + +
587A ILE* 4.6 5.4 - - + +
588A ILE* 3.1 15.8 + - + -
589A ASP* 2.9 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A PRO 4.1 2.7 - - - +
585A PRO* 1.3 86.7 - - + +
587A ILE* 1.3 62.5 + - + +
589A ASP* 3.4 7.4 + - + +
590A LYS* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 3.6 20.2 - - + -
415A GLU* 5.8 3.4 - - - +
418A ARG* 3.6 30.1 - - - +
440A GLU* 5.5 2.2 - - + +
585A PRO* 3.2 4.2 - - + -
586A PRO* 1.3 82.3 - - + +
588A ILE* 1.3 62.5 + - + +
590A LYS* 3.4 11.1 + - + +
591A ILE* 3.3 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A TYR* 4.6 8.5 - - + +
410A LEU* 4.0 34.8 - - + +
411A SER* 4.0 16.8 - - - +
414A LEU* 4.4 13.5 - - + -
443A PHE* 4.0 28.0 - - + -
573A ILE* 4.5 15.4 - - + +
584A PRO* 4.8 1.6 - - + -
585A PRO* 3.1 34.4 + - + +
587A ILE* 1.3 76.1 - - + +
589A ASP* 1.3 61.0 + - - +
591A ILE* 3.2 9.7 + - + +
592A PHE* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ILE* 6.2 0.2 - - - -
577A LYS* 2.7 34.6 + - - +
584A PRO* 3.8 26.4 - - + +
585A PRO 2.9 16.9 + - - +
586A PRO* 3.5 9.1 - - + +
588A ILE* 1.3 78.4 - - - +
590A LYS* 1.3 61.6 + - - +
592A PHE* 3.3 6.2 + - - +
593A MET* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLU* 3.3 17.7 + - - +
586A PRO 2.8 21.3 + - - +
587A ILE* 3.5 13.0 - - + +
588A ILE 3.2 0.4 - - - -
589A ASP* 1.3 72.9 - - - +
591A ILE* 1.3 57.9 + - - +
593A MET* 3.4 4.7 + - - +
594A ASP* 2.7 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 4.0 29.2 - - + -
440A GLU* 3.5 53.2 - - + +
443A PHE* 4.2 29.4 - - + -
444A LEU* 5.7 7.4 - - + +
570A LEU* 6.1 0.9 - - + -
587A ILE* 3.3 19.0 + - + +
588A ILE* 3.2 11.4 + - + +
590A LYS* 1.3 73.9 - - - +
592A PHE* 1.3 61.2 + - - +
595A THR* 2.4 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A LEU* 3.3 41.3 - - + -
573A ILE* 3.7 24.0 - - + -
574A PHE* 3.8 28.9 - + + -
577A LYS* 3.8 27.8 - - + -
588A ILE 2.9 12.8 + - - +
589A ASP* 3.5 10.8 - - - +
591A ILE* 1.3 80.5 - - - +
593A MET* 1.3 77.0 + - + +
595A THR* 3.2 10.9 + - - -
596A LEU* 3.3 34.6 - - + +
574B PHE* 4.1 20.2 - + - -
598B PHE* 4.9 7.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LYS* 4.1 14.4 - - - -
589A ASP* 3.1 24.3 + - - +
590A LYS* 3.8 5.2 - - - +
592A PHE* 1.3 91.4 - - + +
594A ASP* 1.3 69.0 + - - +
596A LEU* 3.1 35.7 + - + +
598A PHE 5.4 0.7 - - - +
598B PHE* 4.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLU* 2.7 29.3 - - - +
590A LYS* 2.7 57.1 + - - +
591A ILE 4.1 1.1 - - - +
593A MET* 1.3 76.3 - - - +
595A THR* 1.3 61.9 + - + +
596A LEU 3.2 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLU* 3.6 30.1 - - + +
441A SER* 4.2 10.5 - - - +
570A LEU* 4.0 20.1 - - - +
591A ILE* 2.4 35.7 + - + +
592A PHE* 3.2 8.5 + - - -
594A ASP* 1.3 79.3 - - + +
596A LEU* 1.3 63.1 + - - +
597A PRO* 3.4 8.7 - - - +
----------------------------------------------------------
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