Contacts of the helix formed by residues 603 - 614 (chain A) in PDB entry 2JED
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 603 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A LEU* 3.9 40.0 - - + +
601A TRP* 3.4 4.5 + - - -
602A LEU* 1.3 76.4 - - + +
604A LYS* 1.3 70.5 + - - +
605A GLU* 3.1 35.7 + - + +
606A ALA* 3.0 24.9 + - + +
607A LYS* 3.0 11.4 + - - +
633A LEU* 4.7 3.4 - - + -
635A ARG* 5.4 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A LEU 3.4 5.6 + - - +
603A GLU* 1.3 79.9 + - - +
605A GLU* 1.3 72.1 + - + +
607A LYS* 3.4 7.7 + - - +
608A ASP* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A GLU* 3.1 17.7 + - + +
604A LYS* 1.3 91.8 + - + +
606A ALA* 1.3 60.3 + - - +
608A ASP* 3.8 9.6 - - - +
609A LEU* 3.1 23.4 + - - +
631A HIS* 3.1 19.2 + - - -
632A PRO* 3.4 35.2 - - + +
633A LEU* 4.0 24.4 - - + +
635A ARG* 4.6 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A LEU* 4.2 4.3 - - + -
569A LEU* 5.1 0.7 - - - +
573A LEU* 3.8 25.7 - - + +
602A LEU* 4.1 13.0 - - + -
603A GLU* 3.0 20.0 + - + +
605A GLU* 1.3 76.3 - - - +
607A LYS* 1.3 64.7 + - - +
609A LEU* 3.4 3.5 + - - +
610A LEU* 3.1 26.7 + - - +
633A LEU* 3.9 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A TYR* 3.8 42.6 + - + +
602A LEU* 3.8 20.4 - - + +
603A GLU 3.0 10.5 + - - +
604A LYS* 3.6 11.7 - - - +
606A ALA* 1.3 75.7 - - - +
608A ASP* 1.3 53.5 + - - +
610A LEU* 3.2 6.6 + - - +
611A VAL* 2.8 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A LYS 2.9 19.3 + - - +
605A GLU* 3.7 15.3 - - - +
606A ALA 3.3 0.2 - - - -
607A LYS* 1.3 78.6 - - - +
609A LEU* 1.3 61.0 + - - +
611A VAL* 3.5 9.3 + - - +
612A LYS* 2.6 58.8 + - - +
631A HIS* 2.7 17.4 + - + +
632A PRO* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A PHE* 4.8 3.6 - - + -
569A LEU* 3.6 17.5 - - + -
605A GLU 3.1 12.2 + - - +
606A ALA 3.8 4.5 - - - +
608A ASP* 1.3 74.9 - - - +
610A LEU* 1.3 56.9 + - - +
612A LYS* 3.1 5.5 + - - +
613A LEU* 3.0 38.1 + - + +
622A LEU* 3.4 31.9 - - + -
628A ILE* 4.2 13.7 - - + -
631A HIS* 3.4 26.8 + - + -
633A LEU* 3.6 27.6 - - + -
634A PHE* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLY* 3.4 30.3 - - - +
569A LEU* 3.9 18.2 - - + -
570A TYR* 3.7 33.0 - - + +
573A LEU* 4.2 13.7 - - + -
574A ILE* 4.5 1.6 - - + -
598A TYR* 3.7 31.4 - - + +
602A LEU* 4.4 8.3 - - + -
606A ALA 3.1 18.1 + - - +
607A LYS 3.5 6.5 - - - +
609A LEU* 1.3 76.1 - - - +
611A VAL* 1.3 53.6 + - - +
613A LEU* 3.2 3.9 + - + +
614A PHE* 2.8 46.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A TYR* 3.9 28.0 - - + +
607A LYS* 2.8 38.7 + - + +
608A ASP* 3.7 11.4 - - - +
610A LEU* 1.3 73.3 - - - +
612A LYS* 1.3 64.8 + - + +
614A PHE* 3.6 11.2 + - - +
615A VAL* 3.6 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ASP* 2.6 47.6 + - - +
609A LEU 3.1 8.0 + - - +
611A VAL* 1.3 79.3 - - + +
613A LEU* 1.3 61.1 + - - +
615A VAL* 3.5 18.1 - - + +
620A LYS 4.5 0.3 - - - +
621A ARG* 3.8 1.4 - - - -
622A LEU* 3.3 35.2 + - + -
625A ARG* 4.3 26.6 + - - +
631A HIS* 4.0 17.7 + - + -
632A PRO* 5.6 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A TRP* 3.7 23.1 - - + +
563A TRP* 3.8 6.2 - - - -
565A PHE* 3.6 25.8 - - + -
566A GLY* 3.7 22.0 - - - -
569A LEU* 4.6 5.6 - - + -
609A LEU* 3.0 39.1 + - + +
610A LEU* 3.2 4.9 + - - +
612A LYS* 1.3 71.8 - - - +
614A PHE* 1.3 59.9 + - - +
615A VAL 3.0 11.1 + - - -
621A ARG* 3.2 24.4 + - - +
622A LEU* 3.3 26.9 - - + +
628A ILE* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A TRP* 3.6 36.2 - + + -
566A GLY* 3.5 24.7 - - - -
567A VAL* 3.7 27.8 - - + -
570A TYR* 4.1 16.6 - + + -
578A PRO* 3.9 16.2 - - + -
579A PHE* 4.2 5.8 - + + -
596A PRO* 3.7 24.9 - - + -
598A TYR* 3.4 19.7 - - - +
610A LEU* 2.8 32.2 + - + +
611A VAL* 3.9 8.2 - - - +
612A LYS 3.5 0.4 - - - -
613A LEU* 1.3 77.3 - - - +
615A VAL* 1.3 58.5 + - - -
616A ARG* 3.7 9.7 + - - +
----------------------------------------------------------
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