Contacts of the helix formed by residues 189 - 201 (chain B) in PDB entry 2A8I
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 THR 189 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO* 3.8 30.8 + - + -
103B MSE 3.9 17.9 - - + -
104B GLY* 3.8 23.7 + - - +
187B MSE 4.0 0.2 + - - -
188B THR* 1.3 79.3 - - - +
190B ARG* 1.3 65.0 + - - +
191B PHE* 3.5 9.2 + - - +
192B SER* 3.1 34.6 + - - -
193B LEU* 3.3 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR* 1.3 75.6 - - - +
191B PHE* 1.3 60.6 + - - +
193B LEU* 3.8 6.7 + - - +
194B ALA* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 5.2 14.6 - - - -
97B PRO 5.5 7.2 - - - +
106B ASN* 6.0 2.5 - - - -
189B THR* 3.1 9.0 + - - +
190B ARG* 1.3 80.6 - - - +
192B SER* 1.3 65.9 + - - +
194B ALA* 3.3 5.2 + - + +
195B ALA* 2.8 43.6 + - + +
198B ARG* 5.0 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLY* 4.2 9.6 - - - -
105B SER 3.9 13.3 + - - -
106B ASN* 5.1 2.7 - - - -
107B LEU* 3.8 24.2 + - - +
188B THR* 3.7 8.3 - - - +
189B THR* 3.1 33.2 + - - -
191B PHE* 1.3 83.7 - - - +
193B LEU* 1.3 57.7 + - - +
195B ALA* 3.4 7.0 + - - +
196B PHE* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.3 14.8 - - + -
185B ASN* 5.9 2.9 - - - +
188B THR* 3.5 23.1 - - + -
189B THR 3.3 12.0 + - - +
190B ARG* 4.0 7.2 - - - +
191B PHE 3.2 0.2 - - - -
192B SER* 1.3 79.1 + - - +
194B ALA* 1.3 65.0 + - - +
196B PHE* 3.2 6.8 + - + +
197B LYS* 3.1 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ARG 3.3 16.7 + - - +
191B PHE* 3.8 5.6 - - + +
193B LEU* 1.3 78.8 - - - +
195B ALA* 1.3 57.3 + - - +
197B LYS* 3.4 7.0 + - - +
198B ARG* 2.9 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASN* 5.8 4.3 - - - +
191B PHE* 2.8 33.4 + - + +
192B SER* 3.6 9.0 - - - +
194B ALA* 1.3 78.0 - - - +
196B PHE* 1.3 51.3 + - - +
198B ARG* 3.0 18.2 - - - +
199B ASN* 2.6 51.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 3.6 27.1 - - + +
108B ASN 3.4 23.1 - - - -
109B LEU 3.7 4.0 - - - -
110B LEU 4.3 1.6 - - - -
111B GLY* 3.4 20.4 - - - -
192B SER 2.9 18.7 + - - +
193B LEU* 3.4 8.3 - - + +
194B ALA 3.2 0.2 - - - -
195B ALA* 1.3 72.7 - - - +
197B LYS* 1.3 87.9 + - + +
199B ASN* 3.1 8.6 + - - +
200B LYS* 2.7 64.8 + - + +
257B LEU* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.1 28.0 + - + +
194B ALA* 3.8 6.5 - - - +
196B PHE* 1.3 106.9 - - - +
198B ARG* 1.3 65.9 + - - +
200B LYS* 3.5 9.6 + - + +
201B ARG* 3.2 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B PHE* 5.0 7.3 + - - -
194B ALA* 2.9 27.9 + - - +
195B ALA* 3.0 46.1 - - - +
197B LYS* 1.3 75.6 - - - +
199B ASN* 1.3 65.8 + - - +
201B ARG* 2.7 38.5 + - - +
202B LYS* 4.0 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU 5.4 0.9 - - - +
195B ALA* 2.6 36.4 + - - +
196B PHE* 3.5 6.5 - - - +
198B ARG* 1.3 84.9 - - - +
200B LYS* 1.3 59.5 + - - +
202B LYS* 3.0 32.8 - - - +
256B ALA* 3.6 25.1 - - - +
257B LEU* 3.8 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.2 38.1 + - - +
110B LEU* 5.1 2.4 - - - +
196B PHE* 2.7 50.2 + - + +
197B LYS* 3.9 11.2 - - + +
199B ASN* 1.3 72.4 - - - +
201B ARG* 1.3 57.5 + - - +
202B LYS 3.1 12.0 + - - +
257B LEU* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LYS 3.2 11.0 + - - +
198B ARG* 2.7 20.9 + - - +
200B LYS* 1.3 71.6 - - - +
202B LYS* 1.3 74.4 + - - +
----------------------------------------------------------
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