Contacts of the helix formed by residues 199 - 212 (chain B) in PDB entry 2JI8
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 ALA 199 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE 4.1 0.2 + - - -
198B PRO* 1.3 77.7 - - - +
200B GLU* 1.3 67.5 + - - +
201B ASP* 3.2 21.8 - - - +
202B ALA* 3.1 17.1 + - + +
203B ILE* 3.3 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO 3.9 0.8 + - - -
199B ALA* 1.3 72.1 - - - +
201B ASP* 1.3 53.2 + - - +
203B ILE* 3.2 9.8 + - - +
204B ALA* 2.8 34.8 + - - +
332B LEU* 5.9 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA* 4.1 15.8 - - - +
200B GLU* 1.3 76.7 + - - +
202B ALA* 1.3 69.6 + - - +
204B ALA* 3.8 8.7 - - + +
205B ARG* 3.2 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO* 4.4 11.0 - - + -
199B ALA* 3.1 20.0 + - + +
201B ASP* 1.3 85.3 + - - +
203B ILE* 1.3 61.6 + - - +
205B ARG* 3.7 15.7 + - - +
206B ALA* 3.2 21.1 + - - +
320B ALA* 5.1 1.6 - - - +
321B PRO 4.0 17.6 - - - +
322B VAL* 3.7 11.2 - - - +
323B VAL 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO* 3.9 8.7 - - + -
199B ALA 3.7 11.2 - - - +
200B GLU* 3.2 9.3 + - - +
202B ALA* 1.3 75.8 - - - +
204B ALA* 1.3 55.0 + - - +
206B ALA* 3.1 6.5 + - - +
207B ALA* 2.8 32.1 + - - +
305B ILE* 6.5 0.4 - - + -
322B VAL* 3.9 24.5 - - + -
329B ALA 3.7 23.1 - - - +
332B LEU* 3.9 25.1 - - + +
333B LEU* 3.8 19.0 - - + +
336B ALA* 3.8 26.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
200B GLU 2.8 20.5 + - - +
201B ASP* 4.2 8.7 - - - -
202B ALA 3.4 0.2 - - - -
203B ILE* 1.3 73.7 - - - +
205B ARG* 1.3 61.6 + - - +
207B ALA* 4.2 6.5 - - - -
208B ASP* 3.1 37.8 + - - +
336B ALA* 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ASP* 3.2 33.6 + - - +
202B ALA* 3.7 20.5 - - - +
204B ALA* 1.3 74.4 - - - +
206B ALA* 1.3 63.3 + - - +
208B ASP* 3.5 5.3 + - - +
209B LEU* 3.1 24.6 + - + +
319B ALA 3.4 25.6 - - - +
320B ALA* 4.3 6.0 - - + +
321B PRO* 4.1 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ALA 3.2 11.2 + - - +
203B ILE* 3.1 8.9 + - + +
205B ARG* 1.3 78.8 - - - +
207B ALA* 1.3 63.5 + - - +
209B LEU* 3.3 4.3 + - - +
210B ILE* 3.1 27.1 + - - +
303B VAL* 3.6 27.3 - - + +
320B ALA* 3.8 11.8 - - + +
322B VAL* 3.8 11.4 - - + -
333B LEU* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE 2.8 18.9 + - - +
204B ALA* 3.8 7.6 - - - +
205B ARG 3.3 0.2 - - - -
206B ALA* 1.3 73.9 - - - +
208B ASP* 1.3 62.9 + - - +
210B ILE* 3.5 0.6 + - - -
211B LYS* 2.9 37.5 + - - +
333B LEU* 4.1 6.5 - - + +
336B ALA* 4.1 24.0 - - + +
337B LEU* 3.6 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA* 3.1 22.0 + - - +
205B ARG* 4.0 5.4 - - - +
207B ALA* 1.3 79.4 - - - +
209B LEU* 1.3 65.0 + - - +
211B LYS* 4.1 19.5 + - - +
212B ASN* 3.0 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ARG* 3.1 14.2 + - + +
206B ALA 3.3 9.4 + - - +
208B ASP* 1.3 77.3 - - - +
210B ILE* 1.3 60.9 + - - +
212B ASN* 3.9 1.8 - - - +
213B ALA* 3.2 20.8 + - - +
275B VAL* 3.6 13.7 - - + +
301B LYS* 3.2 46.2 - - + +
302B TYR 3.8 4.9 - - - +
303B VAL* 3.7 24.0 - - + -
319B ALA* 3.6 27.4 - - + -
320B ALA* 3.8 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA 3.1 17.8 + - - +
207B ALA 3.8 3.8 - - - +
209B LEU* 1.3 78.2 - - - +
211B LYS* 1.3 65.4 + - - +
213B ALA* 3.1 22.6 + - - +
216B PRO* 5.0 3.5 - - + +
218B ILE* 6.4 0.4 - - + -
236B LEU* 6.1 0.7 - - + -
240B THR* 5.0 2.2 - - + -
242B ILE* 3.5 28.0 - - + -
275B VAL* 4.7 3.8 - - + -
277B VAL* 3.9 30.7 - - + -
303B VAL* 4.3 8.3 - - + -
333B LEU* 4.1 19.7 - - + -
337B LEU* 4.0 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ALA* 2.9 29.1 + - - +
208B ASP* 3.9 20.7 + - - +
209B LEU 3.4 0.2 - - - -
210B ILE* 1.3 75.1 - - - +
212B ASN* 1.3 67.5 + - - +
213B ALA 3.5 4.7 + - - +
336B ALA 4.0 20.5 + - - -
337B LEU* 3.9 13.7 - - + -
340B ALA* 4.2 26.0 - - + -
341B PRO* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASP* 3.0 33.0 + - - +
209B LEU* 3.9 2.9 - - - +
211B LYS* 1.3 80.5 - - - +
213B ALA* 1.3 64.6 + - - +
214B LYS* 3.7 16.5 + - - +
274B ASP* 4.8 0.7 - - - +
----------------------------------------------------------
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