Contacts of the strand formed by residues 210 - 215 (chain J) in PDB entry 1J0B
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 ARG 210 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J ASP 2.8 18.3 + - - +
184J SER* 3.0 28.2 + - - -
185J ILE 3.1 9.0 + - - -
202J LEU* 4.1 2.8 - - - +
208J ASP 5.5 1.1 - - - +
209J ILE* 1.3 77.5 - - - +
211J PRO* 1.3 66.1 - - + +
212J VAL* 4.4 2.0 - - + -
247J GLU* 2.6 49.8 + - - +
249J TYR* 4.2 6.9 + - - -
298J GLU* 2.3 37.6 + - - +
299J LEU* 3.7 18.0 - - - +
300J GLY 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 211 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J ILE 4.3 2.2 - - - +
195J LEU* 4.6 4.7 - - + -
198J LEU* 4.5 5.4 - - + -
199J SER* 2.8 40.8 - - - +
202J LEU* 3.7 20.4 - - + -
209J ILE 3.9 4.9 - - - +
210J ARG* 1.3 84.7 - - + +
212J VAL* 1.3 60.7 + - - +
244J VAL 5.7 2.0 - - - +
245J ARG 5.5 1.3 - - - +
246J PRO* 2.9 17.1 - - + +
247J GLU* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184J SER* 3.6 28.9 - - - -
185J ILE 3.2 13.8 + - - +
186J VAL* 3.4 18.8 - - + +
187J VAL* 3.0 29.1 + - - +
195J LEU* 4.1 3.9 - - - +
198J LEU* 4.6 0.4 - - - +
210J ARG 3.9 1.1 - - - +
211J PRO* 1.3 73.5 - - - +
213J GLY* 1.3 62.1 + - - +
214J ILE* 4.0 17.9 - - + -
247J GLU* 3.3 23.3 - - - +
249J TYR* 4.2 8.3 - - + -
293J LEU* 4.0 14.6 - - + -
299J LEU* 3.7 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J VAL 3.4 6.5 - - - -
189J ALA* 4.7 1.6 - - - -
195J LEU* 3.9 15.2 - - - +
212J VAL* 1.3 72.1 - - - +
214J ILE* 1.3 65.8 + - - +
215J ALA 3.9 1.1 - - - -
247J GLU 2.5 20.8 + - - -
248J LEU* 4.0 6.3 - - - -
249J TYR* 2.6 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186J VAL* 3.5 32.1 - - + -
187J VAL 3.2 10.2 + - - +
188J ALA* 4.0 0.2 - - - -
189J ALA* 3.2 17.6 + - - +
212J VAL* 4.0 2.2 - - + -
213J GLY* 1.3 84.5 - - - +
215J ALA* 1.3 64.1 + - - +
216J VAL* 3.0 11.0 + - + +
249J TYR* 3.2 7.2 - - + -
251J TYR* 3.5 36.1 - - + -
285J LYS 3.7 1.1 - - - +
286J ALA* 3.6 33.4 - - + +
289J GLY* 4.0 7.2 - - - +
293J LEU* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189J ALA 3.8 9.2 - - - -
214J ILE* 1.3 68.3 - - - +
216J VAL* 1.3 60.4 + - - +
217J GLY 3.3 0.4 - - - +
218J ARG 4.0 8.3 - - - +
219J PHE* 3.5 34.5 - - + -
223J MET* 4.4 6.1 - - - -
248J LEU* 3.6 22.3 - - + +
249J TYR 2.9 6.3 + - - -
250J ASP* 3.9 2.9 - - - +
251J TYR* 2.8 29.8 + - - -
252J SER* 3.0 5.2 + - - -
----------------------------------------------------------
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