Contacts of the helix formed by residues 188 - 197 (chain B) in PDB entry 3LRB
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 188 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 6.0 0.4 - - - +
186B GLY 2.8 11.1 + - - -
187B LEU* 1.3 79.0 - - - +
189B THR* 1.3 70.9 + - - +
190B PHE* 3.0 8.2 + - - +
192B ALA* 2.9 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.6 32.3 - - + +
188B GLY* 1.3 70.8 - - - +
190B PHE* 1.3 67.2 + - - -
191B GLY 2.8 17.5 + - - -
192B ALA* 3.0 9.2 + - - -
193B ILE* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU 3.7 8.0 - - - +
188B GLY 3.0 9.4 + - - +
189B THR* 1.3 88.4 + - - +
191B GLY* 1.3 58.4 + - - +
192B ALA 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU 5.0 1.1 - - - -
189B THR 2.8 4.0 + - - -
190B PHE* 1.3 71.2 - - - +
192B ALA* 1.3 59.9 + - - +
193B ILE* 3.3 4.7 - - - +
194B GLN* 3.5 24.9 + - - +
195B SER* 4.1 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 4.3 9.1 - - + +
186B GLY* 3.4 34.5 - - - +
187B LEU 3.6 3.6 + - - +
188B GLY 2.9 25.5 + - - +
189B THR* 3.0 3.2 + - - +
190B PHE 3.5 0.2 + - - -
191B GLY* 1.3 74.5 - - - +
193B ILE* 1.3 63.2 + - + +
194B GLN 3.1 1.3 - - - -
195B SER* 2.6 30.6 + - - +
196B THR* 4.0 1.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
42B ALA* 5.5 6.1 - - + -
44B TYR* 3.1 52.0 - - + +
45B GLY* 3.8 7.4 - - - +
48B VAL* 4.8 9.4 - - + -
189B THR* 3.3 23.8 + - - +
191B GLY* 5.1 1.8 - - - +
192B ALA* 1.3 80.4 - - + +
194B GLN* 1.3 62.2 + - + +
196B THR* 2.6 25.4 + - - -
197B LEU* 2.9 38.4 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
191B GLY* 3.5 19.7 + - - +
192B ALA 3.1 1.2 - - - -
193B ILE* 1.3 80.2 - - + +
195B SER* 1.3 58.4 + - - +
197B LEU* 4.2 9.7 - - + +
198B ASN* 3.1 37.4 + - - +
400B TRP* 3.2 47.9 + - + +
403B VAL* 5.4 1.0 - - - +
404B GLY* 4.3 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASN 5.4 0.2 - - - +
35B LEU* 5.8 0.8 - - - +
38B THR* 3.9 31.0 - - - +
39B GLY* 2.9 23.1 + - - -
186B GLY* 5.7 1.1 - - - -
191B GLY 4.1 1.2 + - - -
192B ALA* 2.6 27.1 + - - -
193B ILE 3.0 0.2 - - - -
194B GLN* 1.3 78.4 - - - +
196B THR* 1.3 69.5 + - - +
198B ASN* 3.3 11.6 + - - +
199B VAL* 3.3 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.0 27.4 - - + -
39B GLY 4.1 7.2 - - - +
41B ILE 4.9 1.6 - - - +
42B ALA* 3.1 34.0 + - + +
45B GLY* 2.9 26.5 + - - -
46B TRP* 5.0 2.9 - - + -
192B ALA 4.1 1.2 + - - -
193B ILE* 2.6 21.9 + - - -
195B SER* 1.3 76.9 + - - +
197B LEU* 1.3 50.9 + - - -
198B ASN 3.0 4.3 - - - -
199B VAL* 2.9 4.1 + - - -
200B THR* 2.6 44.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
45B GLY* 2.8 35.4 - - - +
48B VAL* 3.5 29.4 - - + -
49B THR* 4.0 7.0 - - - +
193B ILE* 2.9 36.4 + - + +
194B GLN* 4.2 14.5 - - + +
196B THR* 1.3 70.8 - - - +
198B ASN* 1.3 56.1 + - - +
199B VAL 3.2 1.6 - - - -
200B THR* 3.7 9.2 - - - +
201B LEU* 3.1 36.1 - - + +
400B TRP* 4.0 27.3 - - + +
----------------------------------------------------------
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