Contacts of the helix formed by residues 189 - 196 (chain B) in PDB entry 4LGD
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 189 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TRP 3.7 0.8 + - - -
188B MET* 1.3 76.0 - - - +
190B PRO* 1.3 76.8 - - + +
191B GLU* 3.4 23.6 - - - +
192B VAL* 3.2 26.5 + - + +
193B ILE* 3.4 8.7 + - - +
202B ALA 4.1 7.9 + - - +
205B TRP* 3.4 25.9 - - + -
206B SER* 5.1 0.4 + - - -
233B ILE* 4.4 1.1 - - - -
266B ARG* 3.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B MET 4.1 0.2 - - - -
189B ALA* 1.3 88.7 - - + +
191B GLU* 1.3 68.4 + - - +
193B ILE* 3.1 15.2 + - - +
194B GLN* 3.2 24.0 + - - +
205B TRP* 3.6 41.7 - - + -
233B ILE* 4.1 17.5 - - + +
234B PRO* 4.0 20.5 - - + +
261B LYS* 4.2 24.9 - - + +
266B ARG* 3.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA* 3.5 14.5 - - - +
190B PRO* 1.3 76.0 - - - +
192B VAL* 1.3 57.7 + - + +
194B GLN* 3.7 9.0 - - - +
195B GLU* 2.7 67.5 + - + +
197B GLY 5.2 0.2 - - - +
199B ASN* 3.3 27.0 - - - +
202B ALA* 3.9 3.6 - - - +
261B LYS 4.0 3.1 - - - +
263B PRO* 4.0 19.2 - - + +
266B ARG* 3.0 42.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A MET* 3.7 4.9 - - - +
171B LEU* 4.0 5.6 - - + -
188B MET* 3.3 26.0 - - + -
189B ALA* 3.4 31.4 - - + +
190B PRO 3.1 0.6 - - - -
191B GLU* 1.3 82.7 - - + +
193B ILE* 1.3 58.0 + - - +
196B ILE* 3.1 24.1 + - - -
197B GLY 3.4 22.2 - - - +
198B TYR* 3.7 26.5 - - + -
202B ALA* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A MET* 4.0 28.3 - - + +
228A ARG* 3.8 8.8 - - - -
231A PHE* 4.4 7.6 - - + +
185B PRO* 5.1 1.1 - - + +
188B MET* 4.4 13.0 - - + -
189B ALA 3.4 6.9 + - - +
190B PRO 3.1 8.6 + - - +
192B VAL* 1.3 79.8 - - - +
194B GLN* 1.3 56.8 + - - +
196B ILE* 3.4 20.1 - - - +
230B ILE* 3.4 54.7 - - + +
233B ILE* 3.9 31.2 - - + -
234B PRO* 3.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ARG* 2.9 41.9 + - - +
231A PHE* 4.0 29.4 - - + -
190B PRO* 3.2 21.7 + - - +
191B GLU* 4.1 6.1 + - - +
193B ILE* 1.3 79.0 - - - +
195B GLU* 1.3 66.6 + - + +
196B ILE 3.3 0.2 - - - -
234B PRO* 3.4 28.6 - - + +
261B LYS* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU* 2.7 50.7 + - + +
194B GLN* 1.3 75.3 - - + +
196B ILE* 1.3 71.1 + - - +
197B GLY* 4.3 12.3 - - - +
198B TYR 5.8 0.5 - - - -
199B ASN* 4.0 13.8 + - - -
263B PRO* 4.8 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A HIS* 3.5 52.5 - - + +
227A MET* 3.3 25.8 - - + -
228A ARG* 3.8 20.0 - - + +
171B LEU* 4.3 18.4 - - + +
172B THR* 4.9 9.1 + - - +
192B VAL 3.1 10.7 + - - -
193B ILE 3.4 15.7 - - - +
194B GLN 3.3 2.4 - - - +
195B GLU* 1.3 81.9 - - - +
197B GLY* 1.3 58.2 + - - +
----------------------------------------------------------
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