Contacts of the helix formed by residues 192 - 201 (chain H) in PDB entry 2I2R
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 LEU 192 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H HIS* 5.8 0.7 - - + -
128H ARG* 3.6 35.7 - - + +
131H PHE* 3.4 53.4 - - + -
132H ASN* 5.4 1.8 - - - +
140H GLY* 4.1 3.1 + - - +
191H THR* 1.3 74.4 - - - +
193H ASP* 1.3 55.2 + - - +
195H PHE* 3.1 3.3 + - + -
196H LEU* 2.6 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 193 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H LYS* 5.4 0.4 + - - -
191H THR* 3.3 5.7 + - - +
192H LEU* 1.3 75.4 - - - +
194H GLU* 1.3 65.8 - - - +
196H LEU* 3.9 18.7 - - - +
197H GLU* 3.1 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H MET 3.4 17.4 - - - +
183H ASP* 3.2 5.5 - - - +
184H LYS* 2.7 45.6 + - + +
185H ASN* 2.9 23.1 + - - +
189H ILE 3.0 8.7 - - - +
190H VAL* 3.5 4.4 - - + -
191H THR* 3.1 24.9 + - - +
193H ASP* 1.3 80.2 - - - +
195H PHE* 1.3 55.8 + - - +
197H GLU* 4.4 0.7 - - - +
198H SER* 2.9 31.5 + - - -
510H CA 2.4 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 195 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE 3.8 15.9 - - - -
127H LEU* 3.6 35.0 - - + -
130H THR* 3.8 24.2 - - + -
131H PHE* 3.7 33.7 - + + -
134H TYR* 4.1 4.5 - + - -
142H ILE* 5.3 2.0 - - + -
178H PHE* 4.0 15.3 - + - -
182H MET* 3.6 27.4 - - + -
190H VAL* 4.2 6.2 - - + +
191H THR 2.8 15.9 + - - +
192H LEU* 3.5 6.3 - - + +
194H GLU* 1.3 74.6 - - - +
196H LEU* 1.3 66.8 + - - +
198H SER* 3.8 3.1 - - - -
199H CYS* 3.1 49.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H HIS* 3.6 41.7 - - + +
127H LEU* 3.6 35.9 - - + -
128H ARG 4.5 0.7 - - - +
192H LEU* 2.6 46.4 + - + +
193H ASP* 3.9 20.2 - - - +
195H PHE* 1.3 73.0 - - + +
197H GLU* 1.3 66.4 + - - +
199H CYS* 3.2 4.9 + - - +
200H GLN* 2.9 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H LYS* 4.8 13.9 - - - +
193H ASP* 3.1 24.0 + - - +
194H GLU 4.5 1.1 - - - +
196H LEU* 1.3 86.5 - - - +
198H SER* 1.3 59.2 - - - +
200H GLN* 3.6 14.8 + - + +
201H GLU* 3.1 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181H LYS 3.3 11.4 + - - -
182H MET* 3.0 45.5 + - - +
184H LYS* 5.9 0.8 - - - +
194H GLU 2.9 22.8 + - - -
195H PHE 3.8 4.3 - - - -
196H LEU 3.2 0.2 - - - -
197H GLU* 1.3 78.9 - - - +
199H CYS* 1.3 59.7 + - - +
201H GLU* 3.5 26.3 + - - +
202H ASP* 3.7 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 199 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE* 5.3 3.8 - - - -
18D GLY* 5.6 3.1 - - - -
127H LEU* 4.0 23.8 - - + -
182H MET* 4.2 11.4 - - - -
195H PHE* 3.1 53.2 - - - +
196H LEU 3.2 4.1 + - - +
198H SER* 1.3 74.3 - - - +
200H GLN* 1.3 61.3 + - - +
201H GLU 3.1 1.8 - - - -
202H ASP* 3.0 24.4 + - - +
205H ILE* 3.8 15.6 - - + +
206H MET* 3.3 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H VAL* 4.3 11.3 - - - +
124H HIS* 5.3 6.9 - - - +
127H LEU* 3.6 20.8 - - - +
196H LEU* 2.9 41.0 + - - +
197H GLU* 3.8 16.4 + - + +
198H SER 3.5 0.2 - - - -
199H CYS* 1.3 75.6 - - - +
201H GLU* 1.3 62.1 + - + +
202H ASP 3.4 1.0 + - - -
203H ASP* 5.5 0.5 - - - -
206H MET* 3.7 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H LYS* 5.9 3.3 + - - +
197H GLU* 3.1 23.7 + - + +
198H SER* 3.5 19.8 + - - +
199H CYS 3.1 0.4 - - - -
200H GLN* 1.3 78.2 - - + +
202H ASP* 1.3 56.4 + - - +
203H ASP* 3.3 8.5 + - - +
----------------------------------------------------------
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