Contacts of the helix formed by residues 466 - 476 (chain A) in PDB entry 3JUE
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 GLU 466 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A SER 4.3 0.6 + - - -
465A TRP* 1.3 72.0 - - - +
467A PRO* 1.3 67.9 - - + +
468A GLU* 3.1 35.4 - - - +
469A LEU* 2.8 34.6 + - + +
470A VAL* 3.2 10.0 + - - +
624A GLU* 5.8 1.3 - - - +
661A LYS* 2.7 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL 6.2 1.3 - - - +
465A TRP 3.6 5.6 - - - +
466A GLU* 1.3 93.0 - - + +
468A GLU* 1.3 71.4 + - - +
469A LEU 3.2 0.2 + - - -
470A VAL* 3.3 10.6 + - + +
471A LYS* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A GLU* 3.1 33.6 - - - +
467A PRO* 1.3 86.2 - - + +
469A LEU* 1.3 56.7 + - - +
471A LYS* 3.4 7.9 + - - +
472A LEU* 2.8 28.9 + - - +
620A LEU* 3.5 44.8 - - + +
621A LEU* 4.2 8.2 - - + +
624A GLU* 4.4 25.0 - - + +
658A LEU* 4.5 9.9 - - - +
661A LYS* 4.8 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ILE* 4.0 26.9 - - + -
458A ARG* 6.0 0.9 - - + -
464A SER 5.9 0.9 - - - +
465A TRP* 3.8 26.5 - - + -
466A GLU* 2.8 24.3 + - + +
468A GLU* 1.3 76.5 + - - +
470A VAL* 1.3 65.9 + - - +
472A LEU* 3.3 14.2 + - + +
473A MET* 2.9 46.6 + - + +
624A GLU* 3.5 21.5 - - - +
628A GLN* 4.0 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL 5.3 2.7 - - - +
405A GLY 5.9 0.4 - - - +
407A VAL* 4.2 17.9 - - + -
410A GLN* 3.8 40.4 - - + +
411A VAL* 4.4 9.6 - - + -
465A TRP* 3.7 35.2 - - + +
466A GLU 3.2 7.5 + - - +
467A PRO* 3.7 10.1 - - + +
469A LEU* 1.3 75.9 - - - +
471A LYS* 1.3 67.7 + - - +
473A MET* 3.1 10.9 + - - +
474A CYS* 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLN* 3.7 27.6 + - - +
467A PRO* 3.0 28.0 + - + +
468A GLU* 3.7 7.4 - - - +
470A VAL* 1.3 81.6 - - - +
472A LEU* 1.3 64.1 + - - +
474A CYS* 3.0 18.1 + - + +
475A GLU* 3.1 20.7 + - + +
621A LEU* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ILE 4.5 4.9 - - - +
468A GLU 2.8 18.4 + - - +
469A LEU* 3.5 17.5 - - + +
470A VAL 3.2 0.2 - - - -
471A LYS* 1.3 76.7 - - - +
473A MET* 1.3 71.6 + - + +
475A GLU* 3.1 11.9 + - - -
476A LEU* 3.3 17.5 + - + +
585A LEU* 4.0 19.7 - - + -
621A LEU* 3.7 25.9 - - + +
624A GLU* 3.7 15.3 - - + +
625A PHE* 3.7 49.8 - - + +
628A GLN* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A VAL* 4.2 24.9 - - + -
414A VAL* 4.5 1.6 - - - +
417A ASN* 4.4 7.0 + - - +
431A ALA* 5.0 4.5 - - - -
432A SER 4.1 2.9 - - - +
433A ILE* 3.4 37.0 - - - +
436A GLY* 3.8 28.7 - - - +
437A VAL 4.7 1.1 - - - -
465A TRP* 3.6 28.3 - - + -
469A LEU* 2.9 32.7 + - + +
470A VAL* 3.4 8.1 - - - +
472A LEU* 1.3 83.7 - - + +
474A CYS* 1.3 61.4 + - - +
476A LEU* 3.3 12.1 + - + +
477A GLY* 3.6 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLN* 4.0 35.2 - - - -
411A VAL* 4.9 3.1 - - - -
414A VAL* 3.6 38.1 - - + +
470A VAL* 3.0 19.5 + - - -
471A LYS* 3.0 13.9 + - + +
473A MET* 1.3 76.8 - - - +
475A GLU* 1.3 65.1 + - - +
476A LEU 3.4 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A LYS* 3.1 14.0 + - - +
472A LEU 3.1 6.0 + - - +
474A CYS* 1.3 80.9 - - - +
476A LEU* 1.3 70.7 + - - +
480A ILE* 4.6 3.5 - - - +
585A LEU* 3.5 23.4 - - + +
586A PRO* 4.5 14.5 - - + +
621A LEU* 3.6 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A VAL* 4.3 9.4 - - - +
415A ASP* 5.4 1.0 - - - +
435A LEU 4.0 11.2 - - - +
436A GLY* 3.8 16.4 - - - +
472A LEU* 3.3 22.1 + - + +
473A MET* 3.3 5.2 + - + +
474A CYS 4.5 0.3 - - - +
475A GLU* 1.3 90.6 - - - +
477A GLY* 1.3 66.5 + - - +
480A ILE* 3.8 24.4 - - + +
481A ILE* 4.2 18.8 - - + -
585A LEU* 3.8 33.9 - - + +
586A PRO 4.2 0.2 - - - -
589A ALA* 4.3 2.5 - - + -
625A PHE* 3.5 37.0 - - + -
----------------------------------------------------------
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