Contacts of the helix formed by residues 685 - 700 (chain B) 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 ASN 685 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B THR 5.2 1.7 + - - +
651B GLY* 3.8 21.0 + - - -
653B THR* 4.3 3.1 + - - -
680B ALA* 2.8 17.2 + - - +
683B THR* 4.0 11.9 - - - +
684B ALA* 1.3 72.2 - - - +
686B ALA* 1.3 61.6 + - - +
687B ASP* 3.2 12.6 + - - +
688B ILE* 3.1 46.3 + - + +
689B VAL* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B ALA 3.7 5.1 + - - -
685B ASN* 1.3 73.0 + - - +
687B ASP* 1.3 59.3 + - - +
689B VAL* 3.5 7.9 + - - +
690B THR* 2.8 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B THR* 4.2 23.6 + - + +
685B ASN* 3.2 9.0 + - - +
686B ALA* 1.3 81.3 - - - +
688B ILE* 1.3 58.2 + - - +
690B THR* 3.5 6.0 + - - -
691B LEU* 3.1 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B THR* 3.9 28.5 - - + +
651B GLY* 4.1 12.8 - - - -
652B HIS 4.2 2.9 - - - +
653B THR* 3.5 40.6 - - + +
656B ALA* 4.4 13.7 - - + -
680B ALA* 3.9 10.1 - - + -
685B ASN* 3.1 30.0 + - - +
687B ASP* 1.3 72.8 - - - +
689B VAL* 1.3 64.8 + - - +
691B LEU* 3.4 6.8 - - + +
692B LEU* 2.9 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B LEU* 4.1 12.6 - - + +
680B ALA* 3.6 26.8 - - + +
681B MET* 3.7 38.1 - - + -
684B ALA* 6.2 0.2 - - - -
685B ASN 3.1 21.0 + - - +
686B ALA* 3.6 7.6 - - - +
688B ILE* 1.3 75.9 - - - +
690B THR* 1.3 58.9 + - - +
692B LEU* 3.2 4.0 + - - +
693B ARG* 2.9 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B ALA* 2.8 23.8 + - - +
687B ASP* 3.7 7.1 - - - -
689B VAL* 1.3 73.9 - - - +
691B LEU* 1.3 57.7 - - - +
693B ARG* 3.1 6.7 + - - +
694B LEU* 2.8 57.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B THR* 3.9 26.7 - - + +
656B ALA* 4.6 6.1 - - + -
657B CYS* 3.2 40.2 - - - +
660B LEU* 4.2 15.5 - - + +
687B ASP 3.1 12.9 + - - +
688B ILE* 3.4 10.5 - - + +
690B THR* 1.3 79.7 - - + +
692B LEU* 1.3 58.7 + - + +
694B LEU* 3.2 10.7 + - + +
695B ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B LEU* 4.1 12.6 - - + -
656B ALA* 6.0 0.2 - - + -
660B LEU* 4.0 16.2 - - + -
666B LEU* 3.5 35.3 - - + +
676B PRO* 3.4 49.4 - - + +
677B LEU* 3.5 18.2 - - + +
680B ALA* 4.0 4.7 - - + -
688B ILE* 2.9 39.7 + - + +
689B VAL 3.6 3.6 - - - +
691B LEU* 1.3 73.7 - - - +
693B ARG* 1.3 58.1 + - - +
695B ALA* 3.4 1.8 + - - -
696B LYS* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B LEU* 4.3 28.6 - - + +
689B VAL* 2.9 24.9 + - + +
690B THR* 3.6 6.5 - - - +
692B LEU* 1.3 76.0 - - - +
694B LEU* 1.3 59.9 + - + +
696B LYS* 3.3 39.3 + - - +
697B MET* 3.1 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B THR* 2.8 36.7 + - + +
691B LEU* 3.7 11.4 - - + +
693B ARG* 1.3 76.0 - - + +
695B ALA* 1.3 60.1 + - - +
697B MET* 3.4 12.2 + - + +
698B ARG* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B LEU* 4.1 25.8 - - + -
666B LEU* 3.6 16.1 - - + +
691B LEU 2.9 16.7 + - - +
692B LEU 3.7 5.2 - - - +
694B LEU* 1.3 75.6 - - - +
696B LYS* 1.3 65.4 + - - +
698B ARG* 3.3 6.0 + - - +
699B GLU* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B LEU* 3.5 18.5 - - + +
667B GLY* 6.3 0.8 - - - -
692B LEU 3.0 18.0 + - - +
693B ARG* 3.6 35.7 - - - +
694B LEU 3.3 0.2 - - - -
695B ALA* 1.3 76.4 - - - +
697B MET* 1.3 68.7 + - + +
699B GLU* 3.5 17.2 + - - +
700B ALA* 3.1 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B ARG* 3.1 59.8 + - + +
694B LEU* 3.7 13.7 - - + +
695B ALA 3.2 0.2 - - - -
696B LYS* 1.3 83.3 - - + +
698B ARG* 1.3 65.4 + - - +
700B ALA* 3.1 21.6 + - + +
701B GLU 3.2 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B LEU 3.0 17.9 + - - +
695B ALA* 3.8 6.3 - - - +
697B MET* 1.3 74.7 - - - +
699B GLU* 1.3 58.7 + - - +
701B GLU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B ASP* 5.7 0.3 - - - +
666B LEU* 3.3 31.1 + - + +
695B ALA 3.0 15.9 + - - +
696B LYS* 3.7 15.3 + - - +
698B ARG* 1.3 72.3 - - - +
700B ALA* 1.3 57.9 + - - +
701B GLU* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B LYS* 3.1 14.2 + - + +
697B MET* 3.1 17.9 + - + +
699B GLU* 1.3 75.5 - - - +
701B GLU* 1.3 70.5 + - - +
----------------------------------------------------------
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