Contacts of the helix formed by residues 200 - 211 (chain B) in PDB entry 4J1O
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 200 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER 3.6 8.0 - - - +
199B LEU* 1.3 88.0 - - + +
201B SER* 1.3 67.2 + - - +
202B ARG* 4.2 29.4 - - + +
203B ASP* 2.9 29.3 + - - +
204B ALA 3.2 7.1 + - - -
222B CYS* 4.4 0.2 - - - -
227B GLU* 4.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU 3.7 1.2 + - - -
200B PRO* 1.3 71.7 - - - +
202B ARG* 1.3 65.0 + - - +
203B ASP 3.1 0.3 + - - -
204B ALA* 3.2 1.9 + - - +
205B LEU* 2.9 36.2 + - - +
222B CYS* 4.1 15.6 - - - -
227B GLU* 4.6 10.7 + - - -
231B ILE* 3.4 28.0 - - - -
234B ARG* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PRO* 4.2 20.4 - - + +
201B SER* 1.3 79.2 + - - +
203B ASP* 1.3 90.1 + - - +
205B LEU* 3.8 10.8 - - - +
206B ARG* 3.3 24.5 + - + +
209B ARG* 5.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG 5.6 1.0 - - - +
170B VAL* 3.7 41.7 + - + +
199B LEU* 4.4 10.5 - - + +
200B PRO* 2.9 26.3 + - + +
202B ARG* 1.3 115.0 + - - +
204B ALA* 1.3 61.2 + - - +
205B LEU 3.3 0.4 - - - -
206B ARG* 3.3 8.3 + - - +
207B LEU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 4.1 12.4 - - + +
200B PRO 3.2 10.1 + - - +
201B SER 3.8 5.8 - - - +
203B ASP* 1.3 74.7 - - - +
205B LEU* 1.3 65.5 + - - +
207B LEU* 3.4 3.2 + - - +
208B SER* 3.2 23.4 + - - -
218B LEU* 4.2 10.2 - - + +
221B PRO* 4.0 21.3 - - + -
222B CYS* 4.1 5.8 - - - -
231B ILE* 3.9 24.7 - - + -
235B VAL* 4.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B SER* 2.9 30.9 + - - +
202B ARG* 3.8 8.7 - - - +
204B ALA* 1.3 77.8 - - - +
206B ARG* 1.3 56.5 + - - +
208B SER* 3.5 1.4 + - - -
209B ARG* 2.9 43.0 + - - +
231B ILE* 4.4 10.8 - - + -
234B ARG* 3.7 66.1 - - + +
235B VAL* 4.1 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 3.5 28.4 - - - +
171B GLU* 3.8 31.7 + - - +
174B ILE* 3.7 11.0 - - + +
202B ARG* 3.3 15.8 + - - +
203B ASP* 3.7 9.5 + - - +
204B ALA 3.3 0.4 - - - -
205B LEU* 1.3 77.7 - - - +
207B LEU* 1.3 66.0 + - - +
209B ARG* 3.6 25.1 - - - +
210B GLU* 2.9 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ILE* 3.8 25.4 - - + -
170B VAL* 4.8 4.5 - - + -
173B ASP 5.4 0.2 - - - -
174B ILE* 3.9 31.8 - - + +
177B VAL* 4.4 15.9 - - + -
193B VAL* 4.1 7.0 - - + -
199B LEU* 4.5 5.2 - - + -
203B ASP 2.9 16.5 + - - +
204B ALA 3.8 3.4 - - - +
205B LEU 3.4 0.2 - - - -
206B ARG* 1.3 77.9 - - - +
208B SER* 1.3 64.8 + - - +
211B CYS* 3.5 26.6 + - - +
216B PHE* 3.9 21.9 - - + -
218B LEU* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA 3.2 13.5 + - - -
205B LEU 4.0 2.7 - - - -
207B LEU* 1.3 77.9 - - - +
209B ARG* 1.3 65.0 + - - +
211B CYS 3.2 11.4 + - - -
212B PRO* 3.7 3.1 - - - +
216B PHE* 4.3 2.9 - - - -
218B LEU* 4.9 4.9 - - - -
234B ARG 5.7 0.7 - - - -
235B VAL* 3.5 30.2 - - - +
236B GLN* 3.6 10.7 + - - +
237B HIS* 2.7 42.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG 5.1 1.0 + - - -
205B LEU* 2.9 27.7 + - - +
206B ARG* 3.3 47.7 + - - +
208B SER* 1.3 77.0 - - - +
210B GLU* 1.3 69.4 + - - +
212B PRO* 3.5 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 3.5 23.8 - - + +
178B ARG* 2.7 28.8 + - - +
206B ARG* 2.9 56.7 + - + +
207B LEU 4.3 0.2 - - - +
209B ARG* 1.3 87.7 + - - +
211B CYS* 1.3 61.5 + - - +
212B PRO* 3.4 6.8 - - - +
213B GLU* 4.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 4.1 19.1 - - - -
177B VAL* 5.0 2.5 - - - -
178B ARG* 3.8 23.8 - - - +
207B LEU* 3.5 24.2 + - - +
208B SER 3.2 3.2 + - - -
210B GLU* 1.3 85.6 - - - +
212B PRO* 1.3 65.3 - - - +
213B GLU* 3.1 8.3 - - - -
214B ILE* 3.1 24.3 + - + +
216B PHE* 3.8 15.5 - - + -
237B HIS* 3.0 19.0 + - - -
----------------------------------------------------------
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