Contacts of the helix formed by residues 603 - 614 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A ARG* 2.9 53.2 + - - +
653A PRO 4.7 1.4 - - - +
654A LYS* 4.2 24.1 - - + +
478B LEU* 3.8 31.8 - - + +
601B TRP 4.2 5.3 - - - +
602B LEU* 1.3 78.7 - - - +
604B LYS* 1.3 65.9 + - - +
605B GLU* 3.3 13.5 - - + +
606B ALA* 3.1 11.5 + - + +
607B LYS* 3.1 19.2 + - - +
633B LEU* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B LEU 3.6 2.7 + - - -
603B GLU* 1.3 72.3 - - - +
605B GLU* 1.3 70.1 + - + +
607B LYS* 3.6 8.2 + - - +
608B ASP* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A LYS* 5.0 9.5 + - - -
603B GLU* 3.9 11.3 - - + +
604B LYS* 1.3 89.8 + - + +
606B ALA* 1.3 58.6 + - - +
608B ASP* 3.5 4.1 + - - +
609B LEU* 3.1 10.7 + - - +
631B HIS* 3.0 27.6 - - - -
632B PRO* 4.1 15.9 - - + +
633B LEU* 4.0 26.0 - - + +
635B ARG* 3.2 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LEU* 4.4 12.1 - - + -
569B LEU* 5.1 0.3 - - - +
573B LEU* 3.9 23.2 - - + +
602B LEU* 3.9 11.9 - - + -
603B GLU* 3.1 10.5 + - + +
605B GLU* 1.3 78.4 + - - +
607B LYS* 1.3 62.8 + - - +
609B LEU* 3.6 2.4 + - - +
610B LEU* 3.2 30.0 + - - +
633B LEU* 4.0 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B TYR* 3.9 43.9 - - + +
602B LEU* 3.9 19.8 - - + +
603B GLU 3.1 15.5 + - - +
604B LYS* 3.9 7.9 - - - +
606B ALA* 1.3 74.7 - - - +
608B ASP* 1.3 58.9 + - - +
610B LEU* 3.3 5.2 + - - +
611B VAL* 2.9 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B LYS* 3.0 23.7 + - + +
605B GLU* 3.7 6.7 - - - +
606B ALA 3.3 0.2 - - - -
607B LYS* 1.3 74.4 - - - +
609B LEU* 1.3 64.0 + - - +
611B VAL* 3.3 11.4 + - - +
612B LYS* 3.0 49.2 + - - +
631B HIS* 2.8 22.8 + - + +
632B PRO* 5.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 5.0 2.5 - - + -
569B LEU* 3.6 15.0 - - + -
605B GLU 3.1 11.0 + - - +
606B ALA 3.9 5.2 - - - +
608B ASP* 1.3 74.7 - - - +
610B LEU* 1.3 62.1 + - - +
612B LYS* 3.2 4.4 + - - +
613B LEU* 3.0 44.1 + - + +
622B LEU* 3.5 30.1 - - + -
628B ILE* 4.1 9.4 - - + -
631B HIS* 3.3 25.6 + - + +
633B LEU* 3.6 29.2 - - + -
634B PHE* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B GLY* 3.4 30.3 - - - +
569B LEU* 3.8 19.7 - - + -
570B TYR* 3.6 27.4 - - + +
573B LEU* 4.0 17.9 - - + -
574B ILE* 4.5 1.1 - - + -
598B TYR* 3.9 27.8 - - + +
602B LEU* 4.2 11.9 - - + -
606B ALA 3.2 15.7 + - - +
607B LYS 3.3 6.9 + - - +
609B LEU* 1.3 78.6 - - - +
611B VAL* 1.3 57.3 + - - +
613B LEU* 3.2 3.6 + - + +
614B PHE* 2.9 41.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B TYR* 3.7 27.8 - - + +
607B LYS* 2.9 34.7 + - + +
608B ASP* 3.3 11.9 + - - +
610B LEU* 1.3 74.5 - - - +
612B LYS* 1.3 66.5 + - + +
613B LEU 3.5 0.2 + - - -
614B PHE* 3.5 11.2 + - - +
615B VAL* 3.6 14.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B ASP* 3.0 45.7 + - - +
609B LEU 3.2 7.4 + - - +
611B VAL* 1.3 80.6 - - + +
613B LEU* 1.3 60.0 + - - +
615B VAL* 3.6 20.2 - - - +
620B LYS 4.6 0.3 - - - +
621B ARG* 3.9 0.5 - - - -
622B LEU* 3.3 42.3 + - + -
625B ARG* 4.7 10.7 + - - +
631B HIS* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B TRP* 3.8 18.2 - - + +
563B TRP* 3.7 8.7 - - - -
565B PHE* 3.7 26.2 - - + -
566B GLY* 3.8 23.6 - - - -
569B LEU* 4.5 5.2 - - + -
609B LEU* 3.0 41.6 + - + +
610B LEU* 3.2 5.6 + - - +
612B LYS* 1.3 73.5 - - - +
614B PHE* 1.3 58.3 + - - +
615B VAL 3.1 5.4 - - - -
621B ARG* 2.7 29.7 - - + -
622B LEU* 3.3 27.1 - - + +
628B ILE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B TRP* 3.4 26.0 - + + -
566B GLY* 3.3 26.7 - - - -
567B VAL* 3.6 22.0 - - + -
570B TYR* 4.2 8.5 - + + -
578B PRO* 4.2 5.2 - - + -
579B PHE* 3.7 28.9 - + + -
596B PRO* 3.7 20.4 - - + -
598B TYR* 3.5 18.6 - - - +
610B LEU* 2.9 36.2 + - + +
611B VAL* 3.5 7.1 + - - +
612B LYS 3.5 0.4 - - - -
613B LEU* 1.3 79.0 - - - +
615B VAL* 1.3 63.4 + - - +
616B ARG* 3.2 25.5 + - - +
----------------------------------------------------------
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