Contacts of the helix formed by residues 226 - 242 (chain B) in PDB entry 1GZ0
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 ASN 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ASN* 3.7 22.0 + - - +
198B GLU* 3.5 14.2 + - - +
225B LEU* 1.3 75.3 - - - +
227B VAL* 1.3 60.5 + - - +
228B SER* 2.7 13.5 + - - -
229B VAL* 2.7 45.2 + - + +
230B ALA* 2.8 26.2 + - - +
111G ALA* 6.3 3.6 - - + -
114G ARG* 3.7 23.5 - - - +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 4.3 22.7 - - + -
108B ASN* 5.0 15.9 - - - +
112B CYS* 4.7 3.6 - - - -
195B MSE 4.7 9.4 - - + -
196B GLY 3.4 20.0 - - - +
197B ALA* 3.9 2.2 - - - -
198B GLU* 3.0 43.3 + - + +
225B LEU 3.7 1.8 + - - -
226B ASN* 1.3 73.8 - - - +
228B SER* 1.3 53.9 + - - +
230B ALA* 3.9 6.2 - - + +
231B THR* 2.5 46.1 + - - +
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASN* 3.8 17.0 + - - -
111B ALA* 2.8 35.7 - - - +
112B CYS* 4.2 10.2 - - - +
115B SER* 4.6 3.1 + - - -
226B ASN* 2.7 24.0 + - - +
227B VAL* 1.3 71.4 - - - +
229B VAL* 1.3 63.0 + - - -
231B THR* 3.2 3.8 + - - -
232B GLY* 3.0 19.4 + - - -
229G VAL* 4.1 17.4 - - - +
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 4.4 7.4 - - + -
226B ASN* 2.7 33.6 + - + +
228B SER* 1.3 72.1 - - - +
230B ALA* 1.3 62.5 + - - +
232B GLY* 3.3 1.6 + - - -
233B ILE* 3.0 41.1 + - + +
111G ALA* 5.4 2.7 - - + +
115G SER* 3.6 22.2 - - - +
228G SER* 3.7 32.3 - - - +
229G VAL* 4.2 14.1 - - + +
232G GLY* 3.8 14.1 - - - -
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B MSE 3.9 12.6 - - + -
216B ILE* 4.0 16.8 - - + +
225B LEU* 4.0 23.7 - - + +
226B ASN 2.8 16.5 + - - +
227B VAL* 3.9 7.4 - - - +
229B VAL* 1.3 77.7 - - - +
231B THR* 1.3 61.0 + - - +
233B ILE* 3.4 2.8 + - - +
234B CYS* 3.1 29.8 + - - -
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Residues in contact with THR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.1 13.9 - - + -
100B LEU* 4.8 0.2 - - + -
112B CYS* 3.6 28.3 - - + +
115B SER* 5.1 1.3 - - - -
193B LEU* 4.7 0.2 - - - +
195B MSE 3.5 32.7 - - + +
227B VAL* 2.5 27.1 + - - +
228B SER 3.2 4.7 + - - -
230B ALA* 1.3 73.9 - - - +
232B GLY* 1.3 60.9 + - - +
234B CYS* 3.5 1.2 + - - +
235B LEU* 2.9 52.2 + - + +
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Residues in contact with GLY 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER* 4.4 10.0 + - - -
228B SER 3.0 13.8 + - - -
229B VAL 3.7 2.9 - - - -
230B ALA 3.3 0.2 - - - -
231B THR* 1.3 77.8 - - - +
233B ILE* 1.3 56.6 + - - +
235B LEU* 3.2 5.0 + - - +
236B PHE* 2.8 37.8 + - - +
229G VAL* 4.2 7.6 - - - -
233G ILE* 3.7 19.7 - - - -
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Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.8 8.5 - - + -
183B TYR* 4.4 6.5 - - - +
216B ILE* 4.8 11.0 - - + -
225B LEU* 3.5 28.3 - - + -
229B VAL* 3.0 30.9 + - + +
230B ALA* 3.6 4.9 - - - +
232B GLY* 1.3 77.2 - - - +
234B CYS* 1.3 63.5 + - - +
236B PHE* 3.4 2.7 + - - +
237B GLU* 3.2 19.8 + - - +
232G GLY* 3.9 21.3 - - - +
233G ILE* 3.9 8.9 - - - +
236G PHE* 3.8 42.2 - - + -
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Residues in contact with CYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 3.6 22.0 - - - -
182B LEU* 3.4 24.7 - - + -
187B MSE 3.2 22.5 - - + +
193B LEU* 3.6 25.6 - - + +
195B MSE 4.1 4.7 - - - -
214B ILE* 4.8 1.8 - - + -
216B ILE* 3.4 32.5 - - - -
230B ALA 3.1 13.9 + - - +
231B THR 4.1 0.2 - - - +
233B ILE* 1.3 73.9 - - - +
235B LEU* 1.3 63.9 + - - +
238B ALA* 3.3 7.4 + - - +
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Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 4.1 16.6 - - + -
98B LEU* 4.2 13.5 - - + -
115B SER* 4.1 18.8 - - - +
116B ALA* 4.1 14.1 - - - +
119B ALA* 3.7 17.9 - - + -
121B VAL* 3.9 20.6 - - + -
193B LEU* 3.6 19.9 - - + +
231B THR* 2.9 39.9 + - + +
232B GLY* 3.6 4.7 - - - +
234B CYS* 1.3 77.8 - - - +
236B PHE* 1.3 61.6 + - + +
237B GLU 3.2 0.2 - - - -
238B ALA* 3.2 7.9 - - - +
239B VAL* 2.9 27.5 + - - +
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Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER* 4.1 21.3 - - - -
118B ALA* 3.9 26.2 - - + -
119B ALA* 4.1 7.0 - - + -
232B GLY* 2.8 22.3 + - - +
233B ILE* 3.8 3.6 - - - +
235B LEU* 1.3 81.2 - - + +
237B GLU* 1.3 61.6 + - - +
238B ALA 3.2 0.4 - - - -
239B VAL* 3.7 17.7 - - + -
240B ARG* 3.3 10.7 + - - +
183G TYR* 2.7 41.9 + - - +
216G ILE* 3.6 20.0 - - + -
217G PRO* 3.4 25.8 - - + -
218G MSE 4.9 0.2 - - - -
225G LEU* 3.9 12.6 - - + -
233G ILE* 3.5 30.1 - - + -
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 3.7 22.2 - - + +
183B TYR* 3.5 30.7 - - + +
187B MSE 3.2 26.7 - - + -
233B ILE 3.2 15.2 + - - +
235B LEU 3.2 0.4 - - - -
236B PHE* 1.3 75.8 - - - +
238B ALA* 1.3 66.2 + - - +
240B ARG* 3.2 28.6 + - - +
241B GLN* 2.8 43.5 + - - +
183G TYR* 5.9 0.4 - - - -
237G GLU* 5.1 0.9 - - - +
240G ARG* 3.9 8.1 - - - -
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Residues in contact with ALA 238 (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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96B PHE* 3.6 25.1 - - + -
187B MSE 3.6 30.5 - - + -
191B LEU* 4.3 2.0 - - + -
193B LEU* 5.7 1.1 - - + -
234B CYS 3.3 10.3 + - - +
235B LEU* 3.2 11.6 + - + +
237B GLU* 1.3 78.4 - - - +
239B VAL* 1.3 55.6 + - - +
241B GLN* 3.0 1.7 + - - -
242B ARG* 2.8 45.2 + - - +
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Residues in contact with VAL 239 (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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96B PHE* 4.6 3.4 - - + -
118B ALA 5.0 0.4 - - - +
119B ALA* 3.4 40.6 - - + +
235B LEU 2.9 19.7 + - - +
236B PHE* 3.8 21.3 - - + +
238B ALA* 1.3 76.4 - - - +
240B ARG* 1.3 63.4 + - - +
242B ARG* 3.4 12.8 + - - +
243B SER* 3.4 19.2 + - - +
183G TYR* 4.1 19.5 - - + +
217G PRO* 4.4 12.6 - - + +
219G ALA* 6.1 0.4 - - + -
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Residues in contact with ARG 240 (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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236B PHE 3.3 8.4 + - - +
237B GLU* 3.2 31.6 + - - +
238B ALA 3.2 0.8 - - - -
239B VAL* 1.3 81.1 - - - +
241B GLN* 1.3 79.1 + - - +
243B SER* 3.4 18.1 + - - -
183G TYR* 3.5 55.4 - - + +
237G GLU* 3.9 1.6 - - - -
240G ARG* 3.1 51.4 - - - +
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Residues in contact with GLN 241 (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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182B LEU 4.1 2.0 + - - -
183B TYR 5.3 2.4 + - - -
185B SER* 3.1 26.1 + - - +
186B LYS* 3.7 1.2 - - - -
187B MSE 2.5 51.1 + - + +
188B THR* 3.5 21.2 + - + +
237B GLU* 2.8 38.5 + - - +
238B ALA 3.0 3.3 + - - +
240B ARG* 1.3 87.9 - - - +
242B ARG* 1.3 59.1 + - - +
243B SER* 3.3 8.3 + - - +
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLN* 3.3 32.4 + - - +
95B PRO 3.9 5.3 + - - -
96B PHE* 3.6 38.3 - - - +
122B HIS* 5.9 0.8 - - - -
187B MSE 3.0 30.0 + - - +
188B THR* 4.2 8.7 - - + +
189B GLY 3.0 27.9 + - - +
191B LEU* 4.4 3.8 - - - +
238B ALA* 2.8 34.3 + - - +
239B VAL* 3.4 4.9 + - - +
240B ARG 3.3 0.4 - - - -
241B GLN* 1.3 80.0 - - - +
243B SER* 1.3 57.8 + - - +
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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
------------------------------------------------------------
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