Contacts of the helix formed by residues 248 - 251 (chain B) in PDB entry 2JIB
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 GLY 248 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B MET* 1.3 78.6 - - - +
249B MET* 1.3 61.9 + - - +
251B LYS* 3.6 7.7 - - - +
286B LEU* 6.3 0.2 - - - +
408B ARG* 3.9 27.8 - - - +
419B ARG* 3.1 24.8 + - - -
421B ASP* 3.9 11.7 - - - -
1569B COA 5.6 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.0 14.8 - - + -
68B TYR* 3.2 56.1 + - + +
99B PHE* 4.1 12.3 - - + -
222B LYS* 3.9 31.9 - - + +
225B ALA* 4.1 2.9 - - - +
247B MET* 3.3 1.4 - - - +
248B GLY* 1.3 73.2 - - - +
250B ALA* 1.3 57.7 + - - +
251B LYS 3.3 10.7 + - - +
417B ARG* 5.1 4.3 + - - -
419B ARG* 3.4 26.6 + - - +
420B LEU* 4.1 1.6 - - - -
421B ASP* 3.3 45.3 - - - +
423B GLY* 5.1 3.6 - - - -
434B TYR* 5.6 0.2 - - - -
1568B ADP 5.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 3.2 34.1 - - + +
221B GLY 3.6 21.3 - - - +
222B LYS* 4.6 1.4 - - - +
225B ALA* 4.5 9.2 - - - -
246B PRO* 3.6 11.3 - - + +
247B MET 2.9 10.4 + - - +
249B MET* 1.3 75.2 - - - +
251B LYS* 1.3 64.7 + - - +
252B GLY 3.4 0.2 + - - -
253B LEU* 3.2 22.9 + - + +
254B LEU 4.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PRO* 4.0 15.7 - - + +
247B MET 3.3 8.1 + - - +
248B GLY* 3.6 20.2 - - - +
249B MET 3.3 7.0 - - - +
250B ALA* 1.3 77.6 - - - +
252B GLY* 1.3 58.8 + - - +
253B LEU 3.3 1.8 + - - -
256B ASP* 2.8 32.2 + - - +
263B ALA* 6.3 0.8 - - - +
408B ARG* 2.7 47.0 + - + +
409B MET 4.8 1.8 + - - -
411B VAL 3.3 22.3 + - - -
412B ASP* 4.4 4.2 + - - +
413B MET* 3.8 17.2 - - + +
415B LYS 4.1 3.6 - - - +
416B PRO* 4.8 2.3 - - - +
417B ARG 4.9 2.1 + - - -
419B ARG* 3.8 18.1 + - + +
1569B COA 6.1 0.4 + - - -
----------------------------------------------------------
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