Contacts of the helix formed by residues 195 - 207 (chain B) in PDB entry 1DBQ
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 195 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ALA* 4.9 3.8 - - - -
163B PHE* 3.7 19.6 - - - -
194B ALA* 1.3 75.4 - - - +
196B ARG* 1.4 54.4 - - - +
198B ALA* 2.8 9.2 + - - +
199B GLY* 2.6 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 4.3 22.4 - - - -
162B ALA* 3.5 25.0 + - + +
166B GLY* 3.4 9.2 - - - -
194B ALA 3.7 9.4 - - - +
195B GLY* 1.4 71.7 - - - +
197B LEU* 1.3 56.7 + - - +
199B GLY* 2.7 24.1 + - - -
200B PHE* 3.0 10.4 + - - +
221B PHE* 4.8 9.7 - - - -
244B PHE* 5.0 7.6 - - + -
246B GLY* 2.9 35.8 + - - -
247B GLY* 4.3 2.0 - - - +
274B TYR* 3.3 51.1 - - + +
275B ASP* 3.6 14.6 + - - -
292B GLN* 3.1 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL* 3.6 29.2 - - + -
185B PRO* 4.3 20.9 - - + -
194B ALA* 3.8 21.0 - - - +
195B GLY 3.2 0.2 - - - -
196B ARG* 1.3 82.2 - - + +
198B ALA* 1.3 63.6 + - - +
200B PHE* 3.0 7.3 + - + -
201B MET* 2.9 54.0 + - + +
216B ILE* 5.1 7.6 - - + -
218B GLN* 5.8 3.1 - - - +
244B PHE* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PHE* 3.7 20.5 - - + -
194B ALA 2.9 21.4 + - - +
195B GLY* 2.8 12.6 + - - +
197B LEU* 1.3 75.3 - - - +
199B GLY* 1.3 61.4 + - - +
201B MET* 3.4 5.1 + - - +
202B LYS* 3.2 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PHE* 3.3 37.2 - - - -
167B TYR* 3.5 23.0 - - - -
195B GLY 2.6 13.9 + - - -
196B ARG 2.7 8.3 + - - -
198B ALA* 1.3 72.0 - - - +
200B PHE* 1.3 60.1 + - - -
202B LYS* 3.3 10.7 + - - +
203B ALA 3.5 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY 3.6 13.5 - - - +
167B TYR* 4.7 0.4 - - - +
170B GLY* 3.4 31.0 - - - -
173B LEU* 4.2 2.7 - - + -
181B ILE* 3.6 29.6 - - + -
183B VAL* 3.1 27.6 - - + -
196B ARG 3.0 8.6 + - - +
197B LEU* 3.0 8.9 + - + +
199B GLY* 1.3 72.2 - - - +
201B MET* 1.3 93.7 + - + +
203B ALA* 3.5 3.2 + - - +
204B MET* 3.2 49.0 + - + +
211B VAL* 4.7 2.9 - - + -
244B PHE* 3.7 36.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL* 4.9 0.2 - - + -
197B LEU* 2.9 45.8 + - + +
198B ALA* 4.1 4.9 - - - +
199B GLY 3.3 0.2 - - - -
200B PHE* 1.3 116.8 - - + +
202B LYS* 1.3 53.7 + - - +
204B MET* 3.3 5.4 - - + +
205B GLU* 2.5 39.6 + - + +
211B VAL* 4.2 18.4 - - + -
216B ILE* 4.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PHE* 4.1 22.4 - - + -
167B TYR* 4.3 12.1 - - + -
198B ALA 3.2 13.3 + - - +
199B GLY 3.3 8.5 + - - +
200B PHE 3.3 0.2 - - - -
201B MET* 1.3 77.8 - - - +
203B ALA* 1.3 57.0 + - - +
205B GLU* 3.6 27.0 + - - +
206B GLU* 2.7 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 3.6 34.5 - - + +
170B GLY* 4.3 2.0 - - - -
171B ARG* 3.6 25.3 + - + +
174B ILE* 3.4 10.2 - - + +
199B GLY 3.5 4.3 + - - +
200B PHE 3.5 6.5 + - - +
201B MET 3.2 0.8 - - - -
202B LYS* 1.3 75.3 - - - +
204B MET* 1.3 61.2 + - - +
206B GLU* 3.6 6.1 - - - +
207B ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLY 4.6 2.7 - - - +
174B ILE* 4.3 12.6 - - - -
181B ILE* 3.4 36.8 - - + -
200B PHE* 3.2 47.7 + - + +
201B MET* 3.3 13.5 - - + +
203B ALA* 1.3 75.9 - - - +
205B GLU* 1.3 65.7 + - - +
207B ALA 3.0 1.9 + - - -
208B MET 3.0 18.4 + - - -
209B ILE* 3.1 56.2 + - + +
211B VAL* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B MET 2.5 27.2 + - - +
202B LYS* 3.6 26.5 + - - +
204B MET* 1.3 72.9 - - - +
206B GLU* 1.3 66.7 + - - +
207B ALA 2.9 1.6 + - - -
208B MET* 3.0 18.1 + - - +
209B ILE 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 2.3 36.3 + - - -
171B ARG* 4.5 12.9 + - - +
202B LYS* 2.7 47.7 + - - +
203B ALA* 3.9 5.3 - - - +
204B MET 3.4 0.2 - - - -
205B GLU* 1.3 76.0 - - - +
207B ALA* 1.4 57.3 + - - +
208B MET* 5.0 3.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
171B ARG* 5.1 5.2 - - - +
174B ILE* 3.8 26.5 - - + -
179B ARG* 2.5 30.0 + - - -
203B ALA 2.9 16.7 + - - +
204B MET 3.0 0.6 + - - +
205B GLU 3.0 0.8 - - - -
206B GLU* 1.4 75.7 - - - +
208B MET* 1.3 61.3 + - - +
209B ILE* 3.3 12.3 - - + -
339B TYR* 5.6 2.9 - - - +
----------------------------------------------------------
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