Contacts of the helix formed by residues 193 - 206 (chain B) in PDB entry 2G9I
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 CYS 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.2 32.1 - - - +
158A ARG 4.1 2.9 - - - +
160A VAL 3.0 9.8 + - - +
161A VAL* 3.9 8.9 - - + +
172B ALA 3.7 9.2 - - - -
173B MSE 3.7 14.5 - - - -
191B VAL 4.0 2.0 + - - -
192B GLU* 1.3 66.7 - - - +
194B VAL* 1.3 64.8 + - - +
196B ASP* 3.2 16.3 + - - -
197B GLU* 3.1 27.2 + - - +
232B ILE* 3.5 32.3 - - - -
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.9 21.0 - - + +
170B VAL* 4.2 4.3 - - + -
171B LYS* 3.6 17.0 - - + +
172B ALA 3.2 9.0 + - - +
173B MSE 4.6 0.4 - - - +
174B LYS* 3.8 34.1 - - + +
192B GLU* 3.1 8.6 + - + +
193B CYS* 1.3 71.5 - - - +
195B ALA* 1.3 66.2 + - - +
197B GLU* 3.1 11.5 + - - +
198B ILE* 3.1 41.5 + - + +
223B VAL* 3.8 20.0 - - + -
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 3.7 19.0 - - + +
164B ALA* 4.1 4.1 - - + +
167B ILE* 4.1 25.8 - - + -
170B VAL* 4.6 4.7 - - + -
172B ALA* 3.6 13.7 + - - +
193B CYS 3.3 1.0 - - - -
194B VAL* 1.3 81.8 - - - +
196B ASP* 1.3 59.2 + - - +
198B ILE 3.6 0.3 + - - -
199B ALA* 2.9 27.4 + - - +
232B ILE* 4.2 17.9 - - + -
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Residues in contact with ASP 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 2.7 41.2 + - - +
157A ARG* 2.7 35.6 + - - -
161A VAL* 4.4 4.3 - - + -
200A ALA* 4.7 0.9 - - - +
162B GLY 4.0 2.6 - - - +
163B PHE* 3.9 10.7 - - + -
164B ALA* 3.0 20.0 + - - +
193B CYS* 3.2 15.3 + - - +
195B ALA* 1.3 73.7 - - - +
197B GLU* 1.3 61.7 + - - +
199B ALA* 3.9 5.4 - - - -
200B ALA* 3.1 26.7 + - - +
232B ILE* 4.8 0.3 - - - +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A VAL* 3.4 15.2 - - + -
162A GLY 3.2 13.5 + - - -
200A ALA* 3.1 37.5 - - + +
201A PHE* 3.9 7.9 + - - +
203A ASN* 2.8 25.6 - - - +
204A LEU* 3.6 17.5 - - + +
192B GLU* 2.5 32.1 - - - +
193B CYS 3.1 12.7 + - - +
194B VAL* 3.1 8.6 + - - +
196B ASP* 1.3 74.2 - - - +
198B ILE* 1.3 65.9 + - - +
200B ALA* 3.2 2.9 + - - +
201B PHE* 3.2 22.3 + - - +
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Residues in contact with ILE 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PHE* 4.0 10.1 - - + -
204A LEU* 3.7 9.4 - - + -
35B VAL* 4.2 8.1 - - + -
37B VAL* 3.7 28.0 - - + -
147B ILE* 3.7 19.1 - - + -
170B VAL* 4.8 1.3 - - + -
194B VAL* 3.1 40.1 + - + +
195B ALA 3.9 2.2 - - - +
197B GLU* 1.3 71.9 - - - +
199B ALA* 1.3 69.9 + - - +
200B ALA 3.0 0.3 + - - -
201B PHE* 3.2 2.6 + - - +
202B ALA* 2.8 21.7 + - - +
218B VAL* 4.3 11.0 - - + -
221B LEU* 3.7 31.2 - - + -
223B VAL* 4.5 9.0 - - + -
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.7 1.3 - - - -
147B ILE* 4.3 2.0 - - + +
149B THR* 3.4 31.6 - - + +
162B GLY* 4.0 3.0 - - - -
163B PHE* 3.4 8.5 - - - +
164B ALA* 3.4 25.6 - - + +
195B ALA 2.9 16.7 + - - +
196B ASP 4.0 2.5 - - - +
197B GLU 3.3 0.2 - - - -
198B ILE* 1.3 81.7 - - - +
200B ALA* 1.3 61.6 + - - +
202B ALA* 3.2 4.8 + - - +
203B ASN* 3.1 22.5 + - - +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASP 5.0 0.2 - - - +
197A GLU* 3.2 42.0 - - + +
200A ALA* 4.0 17.9 - - + -
161B VAL* 4.9 5.4 - - + -
162B GLY* 3.4 20.2 - - - +
196B ASP 3.1 19.8 + - - +
197B GLU 3.7 4.3 - - - +
198B ILE 3.1 0.8 - - - -
199B ALA* 1.3 77.7 - - - +
201B PHE* 1.3 63.2 + - - +
203B ASN 3.3 3.8 + - - -
204B LEU 3.5 0.3 + - - -
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Residues in contact with PHE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.9 20.6 - - + -
5A VAL* 4.2 5.4 - - + -
197A GLU* 3.6 13.1 + - - -
198A ILE* 4.0 16.2 - - + -
201A PHE* 3.4 53.4 - + + -
218A VAL* 4.1 15.9 - - + -
221A LEU* 4.4 4.0 - - + -
5B VAL* 3.6 32.3 - - + -
197B GLU 3.2 2.5 + - - +
198B ILE 3.2 2.1 + - - +
200B ALA* 1.3 76.8 - - - +
202B ALA* 1.3 68.1 + - - +
203B ASN 3.0 2.1 + - - -
204B LEU* 3.0 39.5 + - + +
205B LEU* 3.5 21.4 + - + +
218B VAL* 5.9 0.7 - - + -
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 5.2 0.9 - - - -
37B VAL* 3.5 40.6 - - + -
149B THR* 5.3 0.2 - - + -
198B ILE* 2.8 21.4 + - + +
199B ALA 3.6 2.0 - - - +
201B PHE* 1.3 73.7 - - - +
203B ASN* 1.3 62.0 + - - +
205B LEU* 3.1 14.6 + - - -
206B MSE 3.1 15.5 + - + +
216B VAL* 3.7 25.7 - - + +
218B VAL* 5.4 1.3 - - + -
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Residues in contact with ASN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLU* 3.6 19.8 + - - +
197A GLU* 2.9 24.7 + - - +
149B THR* 5.0 6.3 + - - +
150B ASP 5.5 0.3 - - - -
151B THR* 3.1 35.1 - - - +
161B VAL* 4.3 0.6 - - - +
162B GLY* 3.7 10.3 - - - +
199B ALA 3.1 12.2 + - - +
200B ALA 3.5 3.8 - - - +
201B PHE 3.0 0.8 - - - -
202B ALA* 1.3 72.7 - - - +
204B LEU* 1.3 67.9 + - - +
206B MSE 3.2 31.4 + - - +
207B GLY 3.9 2.1 + - - -
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LYS* 4.6 10.6 + - - +
192A GLU* 3.3 13.7 + - - +
194A VAL* 3.9 24.7 - - + +
197A GLU* 3.5 22.9 - - + +
198A ILE* 3.6 31.9 - - + +
221A LEU* 3.8 25.4 - - + -
223A VAL* 4.9 5.6 - - + -
200B ALA 3.5 4.2 + - - +
201B PHE* 3.0 26.6 + - + +
203B ASN* 1.3 78.5 - - - +
205B LEU* 1.3 59.6 + - + +
207B GLY* 3.2 24.1 + - - -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 4.5 18.3 - - + +
3A VAL* 3.6 28.9 - - + -
221A LEU* 4.4 7.4 - - + -
5B VAL* 4.1 26.7 - - + +
6B PHE* 4.6 5.4 - - - -
7B PRO* 4.7 6.6 - - + +
201B PHE* 3.6 41.1 - - + +
202B ALA 3.1 9.3 + - - +
204B LEU* 1.3 80.4 - - + +
206B MSE 1.3 56.7 + - - +
207B GLY* 2.9 16.8 + - - +
213B ILE* 4.1 18.4 - - - +
216B VAL* 3.8 13.1 - - + +
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Residues in contact with MSE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 3.4 43.7 - - + +
39B CYS* 3.9 28.5 - - - +
149B THR* 4.2 8.7 - - - +
202B ALA* 3.1 15.0 + - + +
203B ASN* 3.2 25.8 + - - +
205B LEU* 1.3 74.8 - - - +
207B GLY* 1.4 53.7 + - - +
212B GLY* 4.6 5.0 + - - -
213B ILE* 2.8 42.1 + - - +
214B PRO 3.6 11.7 - - - +
215B ALA* 3.9 4.9 - - - -
216B VAL* 4.2 13.7 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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