Contacts of the helix formed by residues 226 - 242 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B HIS* 5.9 5.1 - - - -
111B ALA* 6.2 4.0 - - + -
114B ARG* 3.6 25.7 - - - +
108G ASN* 4.1 13.0 + - - +
198G GLU* 3.7 14.6 + - - -
225G LEU* 1.3 76.0 - - - +
227G VAL* 1.3 59.8 + - - +
228G SER* 2.9 35.5 + - - -
229G VAL* 3.2 21.3 + - + +
230G ALA* 2.8 26.9 + - - +
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Residues in contact with VAL 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G LEU* 5.6 0.2 - - + -
103G VAL* 4.6 15.3 - - + -
108G ASN* 4.8 14.6 - - + +
112G CYS* 4.4 10.1 - - - -
195G MSE 5.0 6.5 - - + -
196G GLY 3.9 16.2 - - - +
197G ALA* 4.3 1.6 - - - -
198G GLU* 3.2 52.3 + - + +
225G LEU 4.5 0.4 - - - +
226G ASN* 1.3 74.8 + - - +
228G SER* 1.3 54.3 + - - +
230G ALA* 3.9 5.0 - - - +
231G THR* 2.6 46.3 + - - +
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Residues in contact with SER 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B VAL* 3.7 17.4 - - - +
108G ASN* 4.4 8.8 + - - -
111G ALA* 3.0 42.9 + - - +
112G CYS* 4.1 13.3 - - - -
115G SER* 4.5 2.3 + - - -
226G ASN* 2.9 15.6 + - - -
227G VAL* 1.3 72.3 - - - +
229G VAL* 1.3 62.7 + - - +
231G THR* 3.3 1.9 + - - -
232G GLY* 2.9 26.5 + - - -
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Residues in contact with VAL 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA* 5.4 4.7 - - + +
115B SER* 3.6 23.8 - - - +
228B SER* 4.1 31.6 - - - +
229B VAL* 4.2 12.6 - - + +
232B GLY* 4.2 10.1 - - - -
225G LEU* 4.3 5.8 - - + -
226G ASN* 3.2 27.8 + - + +
228G SER* 1.3 77.7 - - - +
230G ALA* 1.3 57.0 + - - +
232G GLY* 3.3 0.7 + - - -
233G ILE* 2.9 47.3 + - + +
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Residues in contact with ALA 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G MSE 3.7 14.1 - - + -
216G ILE* 3.7 24.5 - - + -
225G LEU* 4.1 15.5 - - + +
226G ASN 2.8 17.9 + - - +
227G VAL* 3.9 3.8 - - - +
229G VAL* 1.3 74.0 - - - +
231G THR* 1.3 66.2 + - - +
233G ILE* 3.7 4.3 - - - +
234G CYS* 3.0 31.0 + - - -
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Residues in contact with THR 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G LEU* 3.8 28.3 - - + -
100G LEU* 4.7 0.2 - - + -
112G CYS* 3.6 25.1 - - + -
115G SER* 5.1 1.1 - - - -
193G LEU* 4.5 0.3 - - - +
195G MSE 3.4 27.2 - - + +
227G VAL* 2.6 24.1 + - - +
228G SER 3.3 4.2 + - - -
230G ALA* 1.3 76.5 - - - +
232G GLY* 1.3 56.7 + - - +
234G CYS* 3.9 0.9 - - - +
235G LEU* 2.8 52.4 + - + +
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Residues in contact with GLY 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B VAL* 3.8 17.7 - - - -
233B ILE* 3.9 8.3 - - - -
115G SER* 4.2 10.5 + - - -
228G SER 2.9 15.3 + - - -
229G VAL 3.7 2.5 - - - -
230G ALA 3.2 0.2 - - - -
231G THR* 1.3 76.5 - - - +
233G ILE* 1.3 56.9 + - - +
235G LEU* 3.2 5.2 + - - -
236G PHE* 2.9 38.0 + - - +
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Residues in contact with ILE 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLY* 3.7 23.1 - - - +
233B ILE* 3.9 10.4 - - + +
236B PHE* 3.5 44.6 - - + -
182G LEU* 3.9 19.0 - - + +
216G ILE* 4.6 8.1 - - + -
225G LEU* 3.6 23.6 - - + -
229G VAL* 2.9 35.4 + - + +
230G ALA* 3.7 4.7 - - - +
232G GLY* 1.3 70.9 - - - +
234G CYS* 1.3 64.3 + - - +
236G PHE* 3.6 2.5 + - - +
237G GLU* 3.3 20.3 + - - +
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Residues in contact with CYS 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G THR* 3.9 19.1 - - - -
182G LEU* 3.6 29.6 - - + +
187G MSE 4.6 2.6 - - - +
193G LEU* 3.6 24.0 - - + -
195G MSE 4.2 3.1 - - - -
214G ILE* 4.3 2.0 - - - -
216G ILE* 3.8 25.1 - - - -
230G ALA 3.0 21.4 + - - +
233G ILE* 1.3 74.7 - - - +
235G LEU* 1.3 70.5 + - - +
237G GLU* 2.7 15.4 + - - +
238G ALA* 3.1 10.4 + - - +
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Residues in contact with LEU 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G PHE* 3.9 14.0 - - + -
98G LEU* 3.9 14.6 - - + -
115G SER* 3.9 7.6 - - - -
116G ALA* 3.8 28.9 - - - +
119G ALA* 4.0 18.4 - - + -
121G VAL* 3.9 17.3 - - + -
193G LEU* 3.5 23.8 - - + -
231G THR* 2.8 40.2 + - + +
232G GLY* 3.5 5.6 - - - +
234G CYS* 1.3 73.7 - - - +
236G PHE* 1.3 60.4 + - + +
238G ALA* 3.2 8.5 - - - +
239G VAL* 3.1 25.9 + - - +
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Residues in contact with PHE 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 2.7 40.0 + + - +
216B ILE* 3.9 10.8 - - + -
217B PRO* 3.5 26.7 - - + -
218B MSE 4.5 4.5 - - + -
225B LEU* 4.5 6.7 - - + -
233B ILE* 3.8 34.3 - - + -
115G SER* 4.3 9.6 - - - -
118G ALA* 3.9 28.9 - - + -
119G ALA* 3.6 20.4 - - + -
232G GLY* 2.9 21.2 + - - +
233G ILE 3.9 2.9 - - - +
235G LEU* 1.3 77.8 - - + +
237G GLU* 1.3 59.5 + - - +
238G ALA 3.2 0.9 - - - -
239G VAL* 3.6 19.6 - - + +
240G ARG* 3.1 15.2 + - - +
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Residues in contact with GLU 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 6.1 0.2 - - - -
237B GLU* 5.1 0.7 - - - +
240B ARG* 3.9 1.7 - - - -
182G LEU* 3.4 34.3 - - + +
183G TYR* 3.4 28.5 - - - -
187G MSE 4.8 2.7 - - - -
233G ILE 3.3 12.4 + - - +
234G CYS 2.7 13.2 + - - +
236G PHE* 1.3 72.4 - - - +
238G ALA* 1.3 59.7 - - - +
240G ARG* 3.1 36.0 + - - +
241G GLN* 2.5 55.7 + - - +
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Residues in contact with ALA 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G PHE* 4.0 17.3 - - + -
187G MSE 3.9 34.3 - - + +
191G LEU* 4.1 11.4 - - + -
193G LEU* 6.1 0.7 - - + -
234G CYS 3.1 8.5 + - - +
235G LEU* 3.2 12.8 - - - +
237G GLU* 1.3 76.7 - - - +
239G VAL* 1.3 58.3 + - - +
241G GLN* 3.7 1.1 - - - +
242G ARG* 2.8 36.8 + - - +
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Residues in contact with VAL 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 4.6 7.6 - - + -
217B PRO* 4.7 12.6 - - + -
96G PHE* 4.2 6.1 - - + -
119G ALA* 3.3 47.3 - - + +
235G LEU 3.1 12.7 + - - +
236G PHE* 3.7 26.7 - - + +
237G GLU 3.3 0.2 - - - -
238G ALA* 1.3 78.0 - - - +
240G ARG* 1.3 61.5 + - - +
242G ARG* 3.3 7.0 + - - +
243G SER* 2.8 29.6 + - - +
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Residues in contact with ARG 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 3.6 33.0 - - + -
237B GLU* 3.9 16.4 - - - -
240B ARG* 3.1 40.8 - - - +
183G TYR* 4.9 6.5 + - - +
236G PHE 3.1 18.3 + - - +
237G GLU* 3.1 38.3 + - - +
238G ALA 3.3 0.2 - - - -
239G VAL* 1.3 77.7 - - - +
241G GLN* 1.3 77.8 + - - +
243G SER* 3.3 21.6 - - - -
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Residues in contact with GLN 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G LEU 4.0 7.7 + - - -
183G TYR 4.5 3.6 + - - -
185G SER* 3.2 21.3 + - - +
186G LYS* 3.9 0.9 - - - -
187G MSE 2.9 33.6 + - - +
188G THR* 3.3 26.6 - - + +
237G GLU* 2.5 46.4 + - - +
238G ALA* 3.3 4.7 + - - +
240G ARG* 1.3 97.1 - - - +
242G ARG* 1.3 58.4 + - - +
243G SER* 3.1 9.5 + - - +
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Residues in contact with ARG 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G GLN* 3.6 21.6 + - - +
95G PRO 3.2 18.6 + - - -
96G PHE* 3.3 44.9 - - + +
122G HIS* 6.0 0.2 - - - -
187G MSE 2.8 30.3 + - - -
188G THR* 3.8 9.9 - - - +
189G GLY 3.1 30.1 + - - +
191G LEU* 4.2 2.8 - - - +
238G ALA* 2.8 21.0 + - - +
239G VAL* 3.6 7.9 - - - +
241G GLN* 1.3 74.1 - - - +
243G SER* 1.3 66.7 + - - +
32H GLU 5.3 4.3 - - - +
34H LYS* 5.6 2.9 - - - +
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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