Contacts of the helix formed by residues 568 - 572 (chain B) in PDB entry 1JB0
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 568 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A PRO* 4.1 12.1 - - + -
578A CYS* 3.9 23.8 - - - +
579A ASP* 4.9 3.1 - - - +
580A GLY* 3.8 23.8 - - - +
724A ILE* 4.3 1.6 - - + -
3001A SF4 4.2 3.4 - - - -
567B GLY* 1.3 79.7 - - - +
569B GLY* 1.3 65.4 + - - +
572B GLY* 3.6 12.9 + - - -
50C CYS 4.7 5.2 - - - +
51C LYS* 5.5 0.4 - - + -
55C THR* 4.7 7.2 - - - +
48E TYR* 3.5 32.5 - - + +
49E SER* 2.9 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 569 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ASP 4.7 3.0 + - - +
567B GLY* 3.1 8.6 - - - +
568B PRO* 1.3 81.0 - - - +
570B ARG* 1.3 78.1 + - - +
571B GLY 3.1 0.9 - - - -
572B GLY* 3.0 11.4 + - - -
573B THR* 4.0 4.9 - - - +
55C THR* 3.6 31.1 + - - -
47E GLY 3.9 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 570 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ARG* 4.2 2.6 + - - -
551B LYS 6.1 0.2 - - - -
552B LEU* 2.8 55.1 + - + +
553B MET* 4.1 12.3 - - - +
566B ASP* 2.7 42.4 + - - +
569B GLY* 1.3 74.9 + - - +
571B GLY* 1.3 56.1 - - - +
572B GLY 3.3 2.7 + - - -
573B THR* 4.1 9.1 - - + +
54C GLU* 4.8 3.8 + - - +
55C THR* 5.7 0.8 - - - +
61C PHE* 3.7 24.9 - - - -
62C LEU* 3.8 24.6 - - + +
65C ARG* 4.0 0.4 - - - +
45E TYR* 3.2 42.7 - - + +
46E THR* 4.8 7.6 - - - +
47E GLY 2.9 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 571 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ARG* 3.1 31.1 + - - -
723A SER* 4.7 0.3 - - - -
568B PRO 3.9 0.2 - - - -
569B GLY 3.1 0.4 - - - -
570B ARG* 1.3 72.5 - - - +
572B GLY* 1.3 53.7 + - - -
45E TYR 3.8 2.4 + - - -
47E GLY 2.7 18.3 + - - -
48E TYR 4.4 1.6 - - - -
49E SER* 3.1 29.5 + - - -
50E GLY 4.2 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 572 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A ARG* 2.9 33.5 + - - +
695A GLY 4.1 0.3 + - - -
724A ILE* 3.6 16.8 - - - -
552B LEU* 4.0 5.7 - - - +
567B GLY 3.9 3.4 - - - -
568B PRO 3.6 4.4 + - - -
569B GLY 3.0 10.7 + - - -
570B ARG 3.3 1.0 - - - +
571B GLY* 1.3 77.3 - - - +
573B THR* 1.3 67.7 + - - +
----------------------------------------------------------
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