Contacts of the helix formed by residues 226 - 242 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASN* 3.4 20.0 + - - +
198C GLU* 3.4 11.4 + - - -
225C LEU* 1.3 76.9 - - - +
227C VAL* 1.3 57.3 + - - +
228C SER* 2.9 37.6 + - - -
229C VAL* 3.4 19.2 + - + +
230C ALA* 3.0 24.4 + - - +
111H ALA* 6.2 3.4 - - + -
114H ARG* 3.4 27.7 - - - +
115H SER* 5.9 0.2 + - - -
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C VAL* 4.7 17.3 - - + -
108C ASN* 3.6 35.0 - - + +
112C CYS* 4.6 1.6 - - - -
195C MSE 4.6 5.4 - - + +
196C GLY 3.4 25.4 - - - +
197C ALA* 4.2 2.5 - - - -
198C GLU* 3.2 33.3 + - + +
225C LEU 3.7 0.9 + - - +
226C ASN* 1.3 69.8 + - - +
228C SER* 1.3 58.5 + - - +
230C ALA* 3.4 5.4 + - + +
231C THR* 2.7 41.7 + - - +
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Residues in contact with SER 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ASN* 3.6 21.1 + - - -
111C ALA* 3.0 36.8 - - - +
112C CYS* 4.0 11.6 + - - +
115C SER* 4.4 2.4 + - - -
226C ASN* 2.9 14.7 + - - -
227C VAL* 1.3 75.0 - - - +
229C VAL* 1.3 58.5 + - - +
231C THR* 3.2 2.8 + - - -
232C GLY* 2.8 27.4 + - - -
229H VAL* 4.2 17.1 - - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C LEU* 4.3 5.2 - - + -
226C ASN* 3.4 26.6 + - + +
227C VAL 3.3 0.4 - - - -
228C SER* 1.3 77.2 - - - +
230C ALA* 1.3 57.4 + - - +
232C GLY* 3.2 1.4 + - - -
233C ILE* 2.8 41.6 + - + +
111H ALA* 5.6 2.2 - - + +
115H SER* 3.5 23.8 - - - +
228H SER* 4.0 31.4 - - - +
229H VAL* 4.1 13.3 - - + +
232H GLY* 3.7 23.6 - - - -
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C MSE 3.5 18.8 - - + -
216C ILE* 3.8 17.3 - - + -
225C LEU* 4.2 15.4 - - + +
226C ASN 3.0 16.9 + - - +
227C VAL* 3.9 4.9 - - + +
229C VAL* 1.3 75.6 - - - +
231C THR* 1.3 59.3 + - - +
233C ILE* 3.2 7.3 + - - +
234C CYS* 2.8 35.0 + - - -
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Residues in contact with THR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 4.1 23.6 - - + -
112C CYS* 3.6 25.9 - - + +
115C SER* 4.8 2.7 - - - -
193C LEU* 4.3 0.6 - - + +
195C MSE 3.3 27.5 - - - +
227C VAL* 2.7 24.8 + - - +
228C SER 3.3 5.8 - - - +
230C ALA* 1.3 76.9 - - - +
232C GLY* 1.3 58.5 + - - +
234C CYS* 3.1 2.6 + - - +
235C LEU* 2.8 52.2 + - + +
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Residues in contact with GLY 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C SER* 4.2 13.2 - - - -
228C SER 2.8 18.4 + - - -
229C VAL 3.7 2.9 - - - -
231C THR* 1.3 73.6 - - - +
233C ILE* 1.3 56.2 + - - +
235C LEU* 4.5 2.2 - - - -
236C PHE* 3.0 36.3 + - - +
229H VAL* 4.2 7.4 - - - -
233H ILE* 3.6 18.1 - - - +
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Residues in contact with ILE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C LEU* 4.0 9.8 - - + +
183C TYR* 3.8 21.2 + - - +
216C ILE* 4.5 6.5 - - + -
225C LEU* 3.9 14.8 - - + -
229C VAL* 2.8 31.4 + - + +
230C ALA* 3.2 5.8 + - - +
232C GLY* 1.3 75.8 - - - +
234C CYS* 1.3 62.7 + - - +
236C PHE* 4.1 1.5 - - - +
237C GLU* 3.2 21.5 + - - +
232H GLY 3.5 25.8 - - - +
233H ILE* 3.8 8.5 - - - +
236H PHE* 3.4 42.6 - - + -
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Residues in contact with CYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C THR* 3.9 17.0 - - - -
182C LEU* 4.0 26.9 - - + -
187C MSE 4.3 4.7 - - - +
193C LEU* 3.5 26.5 - - + -
195C MSE 4.1 5.4 - - - -
214C ILE* 4.9 1.1 - - - -
216C ILE* 3.7 24.2 - - - -
230C ALA 2.8 20.0 + - - +
231C THR 3.7 0.7 - - - +
233C ILE* 1.3 74.5 - - - +
235C LEU* 1.3 66.8 + - - +
236C PHE 3.1 1.1 - - - -
237C GLU* 3.0 13.7 + - - +
238C ALA* 3.1 11.6 + - - +
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PHE* 4.0 14.3 - - + -
97C LEU 5.3 0.2 - - - +
98C LEU* 4.3 10.8 - - + -
115C SER* 4.4 3.8 - - - -
116C ALA* 4.1 23.8 - - - +
119C ALA* 3.7 22.4 - - + -
121C VAL* 4.0 18.2 - - + -
193C LEU* 3.4 25.1 - - + -
231C THR* 2.8 46.3 + - + +
232C GLY* 4.0 3.6 - - - +
234C CYS* 1.3 72.4 - - - +
236C PHE* 1.3 60.8 + - + +
238C ALA* 3.0 9.3 - - + +
239C VAL* 2.7 28.8 + - - +
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Residues in contact with PHE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C SER* 4.1 7.0 - - - -
118C ALA* 3.9 14.4 - - + -
119C ALA* 4.1 16.6 - - + -
232C GLY 3.0 26.8 + - - +
233C ILE 4.5 1.8 - - - +
235C LEU* 1.3 80.5 - - + +
237C GLU* 1.3 61.2 + - - +
238C ALA 2.9 1.3 - - - -
239C VAL* 3.5 16.8 - - + +
240C ARG* 2.8 24.8 + - - +
183H TYR* 3.3 28.2 + - - +
216H ILE* 3.4 20.0 - - + -
217H PRO* 3.3 26.7 - - + -
218H MSE 3.7 19.5 - - + -
225H LEU* 4.1 9.6 - - + -
233H ILE* 3.5 26.0 - - + -
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Residues in contact with GLU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C LEU* 3.6 33.7 - - + +
183C TYR* 3.1 30.9 - - + +
187C MSE 4.2 1.6 - - - -
233C ILE 3.2 15.0 + - - +
234C CYS 3.0 9.9 + - - +
236C PHE* 1.3 77.4 - - - +
238C ALA* 1.3 58.1 + - - +
240C ARG* 2.8 25.0 + - - +
241C GLN* 2.6 56.1 + - - +
183H TYR* 6.1 0.2 - - - -
237H GLU* 4.6 1.4 - - - +
240H ARG* 3.2 12.6 - - - -
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Residues in contact with ALA 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PHE* 3.7 25.1 - - + -
187C MSE 4.2 35.1 - - + +
191C LEU* 4.9 0.4 - - + -
234C CYS 3.1 10.7 + - - +
235C LEU* 3.0 14.8 - - - +
237C GLU* 1.3 74.6 - - - +
239C VAL* 1.3 63.8 + - - +
240C ARG 3.1 1.9 + - - -
241C GLN* 3.1 1.6 + - - -
242C ARG* 2.8 31.2 + - - +
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Residues in contact with VAL 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PHE* 4.6 3.6 - - + -
118C ALA 5.9 0.4 - - - +
119C ALA* 3.6 40.4 - - + +
235C LEU 2.7 22.9 + - - +
236C PHE* 3.2 27.1 + - + +
238C ALA* 1.3 72.0 - - - +
240C ARG* 1.3 63.8 + - - +
242C ARG* 3.3 8.4 + - - +
243C SER* 3.0 24.9 + - - -
183H TYR* 5.0 2.0 - - + -
217H PRO* 4.5 18.6 - - + +
219H ALA* 6.3 2.0 - - + -
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Residues in contact with ARG 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C PHE 2.8 17.5 + - - +
237C GLU* 2.8 38.1 + - - +
239C VAL* 1.3 77.1 - - - +
241C GLN* 1.3 83.8 + - - +
243C SER* 2.6 27.8 + - - +
183H TYR* 3.8 36.9 - - + +
237H GLU* 3.8 15.7 - - - -
240H ARG* 3.0 44.3 - - - +
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Residues in contact with GLN 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C LEU 4.2 4.8 + - - -
183C TYR* 5.1 3.4 + - - +
185C SER 3.2 21.3 + - - +
186C LYS* 3.6 2.8 - - - -
187C MSE 3.0 31.6 + - - +
188C THR* 3.5 23.4 + - + +
237C GLU* 2.6 42.4 + - - +
238C ALA* 3.9 4.5 - - - +
240C ARG* 1.3 98.4 - - - +
242C ARG* 1.3 59.3 + - - +
243C SER* 3.3 3.9 + - - +
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Residues in contact with ARG 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN* 3.7 23.2 + - - +
95C PRO 3.5 14.6 + - - -
96C PHE* 3.8 44.9 - - - +
122C HIS* 5.5 1.2 - - - -
187C MSE 3.5 24.1 + - - +
188C THR* 4.4 9.1 - - - +
189C GLY 2.5 34.0 + - - +
191C LEU* 4.5 2.4 - - - +
238C ALA 2.8 25.2 + - - +
239C VAL* 3.6 5.8 - - - +
241C GLN* 1.3 76.7 - - - +
243C SER* 1.3 63.9 + - - +
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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