Contacts of the helix formed by residues 226 - 242 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A HIS* 6.0 4.2 - - - -
111A ALA* 6.2 3.1 - - + +
114A ARG* 3.6 21.0 - - - +
108F ASN* 4.2 13.8 + - - +
198F GLU* 3.6 17.0 + - - -
225F LEU* 1.3 72.9 - - - +
227F VAL* 1.3 55.4 + - - +
228F SER* 2.6 41.5 + - - -
229F VAL* 3.2 19.0 + - + +
230F ALA* 2.8 33.7 + - - +
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Residues in contact with VAL 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F LEU* 5.2 0.2 - - + -
103F VAL* 4.2 22.4 - - + -
108F ASN* 4.8 18.6 - - + +
112F CYS* 4.4 7.0 - - - -
195F MSE 4.6 8.7 - - + -
196F GLY 3.6 19.1 - - - +
197F ALA* 4.2 3.8 - - + -
198F GLU* 3.5 39.8 + - + +
225F LEU 3.9 1.6 + - - -
226F ASN* 1.3 73.8 + - - +
228F SER* 1.3 56.2 + - - +
230F ALA* 4.0 5.3 - - - +
231F THR* 2.4 46.6 + - - +
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Residues in contact with SER 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 3.3 22.8 - - - +
108F ASN* 4.8 6.9 + - - -
111F ALA* 3.3 36.7 + - - +
112F CYS* 4.1 13.2 - - - +
115F SER* 4.5 3.3 + - - -
226F ASN* 2.6 20.8 + - - -
227F VAL* 1.3 73.2 - - - +
229F VAL* 1.3 58.4 + - - -
231F THR* 3.4 1.9 + - - -
232F GLY* 2.8 26.2 + - - -
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Residues in contact with VAL 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 5.3 4.0 - - + +
115A SER* 3.6 23.8 - - - +
228A SER* 3.7 38.8 - - - +
229A VAL* 4.1 12.0 - - + +
232A GLY* 3.9 17.5 - - - -
225F LEU* 4.5 4.5 - - + -
226F ASN* 3.2 28.1 + - + +
228F SER* 1.3 75.2 - - - +
230F ALA* 1.3 58.8 + - - +
232F GLY* 3.0 2.6 + - - -
233F ILE* 2.8 42.3 + - + +
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Residues in contact with ALA 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F THR* 5.9 0.2 - - + -
195F MSE 3.8 16.6 - - + -
216F ILE* 4.0 18.1 - - + +
225F LEU* 4.0 18.5 - - + +
226F ASN 2.8 23.5 + - - +
227F VAL* 4.0 4.0 - - - +
229F VAL* 1.3 73.9 - - - +
231F THR* 1.3 56.5 + - - +
233F ILE* 3.2 5.3 + - - +
234F CYS* 3.0 34.0 + - - -
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Residues in contact with THR 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F LEU* 4.0 27.6 - - + -
100F LEU* 4.4 0.8 - - + +
112F CYS* 3.8 22.7 - - + +
115F SER* 5.1 1.3 - - - -
193F LEU* 4.6 0.7 - - + +
195F MSE 3.4 29.2 - - + +
227F VAL* 2.4 28.0 + - - +
228F SER 3.6 3.8 - - - -
230F ALA* 1.3 72.7 - - - +
232F GLY* 1.3 67.6 + - - +
234F CYS* 4.0 0.5 - - - +
235F LEU* 3.0 46.6 + - + +
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Residues in contact with GLY 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 4.0 16.4 - - - -
233A ILE* 3.8 9.0 - - - -
115F SER* 4.0 13.0 + - - -
228F SER 2.8 15.5 + - - -
229F VAL 3.0 3.1 + - - -
231F THR* 1.3 77.7 - - - +
233F ILE* 1.3 55.8 + - - +
235F LEU* 3.7 1.5 - - - +
236F PHE* 3.0 37.7 + - - +
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Residues in contact with ILE 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A GLY 3.8 21.3 - - - +
233A ILE* 4.0 9.6 - - + +
236A PHE* 3.3 48.2 - - + -
182F LEU* 4.3 11.4 - - + -
183F TYR* 4.5 4.5 - - + +
216F ILE* 4.7 10.1 - - + -
225F LEU* 3.6 25.4 - - + -
229F VAL* 2.8 30.8 + - + +
230F ALA* 3.5 7.6 - - - +
232F GLY* 1.3 73.4 - - - +
234F CYS* 1.3 63.7 + - - +
236F PHE* 3.4 1.9 + - - +
237F GLU* 3.2 20.1 + - - +
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Residues in contact with CYS 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F THR* 3.6 20.9 - - - -
182F LEU* 3.6 17.9 - - + -
187F MSE 4.2 6.2 - - + +
193F LEU* 3.6 24.0 - - + -
195F MSE 4.1 4.7 - - - -
214F ILE* 4.7 7.0 - - + -
216F ILE* 3.5 29.4 - - - -
230F ALA 3.0 20.0 + - - +
231F THR 4.1 0.7 - - - +
233F ILE* 1.3 73.1 - - - +
235F LEU* 1.3 67.5 + - - +
237F GLU* 3.2 4.0 + - - +
238F ALA* 3.2 20.3 + - - +
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Residues in contact with LEU 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F PHE* 4.0 15.6 - - + -
98F LEU* 4.1 13.7 - - + -
115F SER* 4.0 9.2 - - - -
116F ALA* 3.8 29.8 - - - +
119F ALA* 3.8 17.0 - - + -
121F VAL* 3.8 18.6 - - + -
193F LEU* 3.7 23.0 - - + +
231F THR* 3.0 36.0 + - + +
232F GLY 3.7 2.7 - - - +
234F CYS* 1.3 75.7 - - - +
236F PHE* 1.3 62.7 + - + +
238F ALA* 3.2 8.8 - - - +
239F VAL* 3.1 26.4 + - - +
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Residues in contact with PHE 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 3.1 31.1 + + - +
216A ILE* 3.8 19.3 - - + -
217A PRO* 3.4 23.1 - - + -
218A MSE 4.1 5.4 - - + -
225A LEU* 4.2 5.8 - - + -
233A ILE* 3.4 26.7 - - + -
115F SER* 4.1 12.1 - - - -
118F ALA* 3.9 32.3 - - + -
119F ALA* 4.0 14.4 - - + -
232F GLY 3.0 23.4 + - - +
233F ILE 4.2 2.2 - - - +
235F LEU* 1.3 79.9 - - + +
237F GLU* 1.3 63.9 + - - +
238F ALA 3.0 1.1 - - - -
239F VAL* 3.5 18.0 - - + +
240F ARG* 3.0 18.7 + - - +
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Residues in contact with GLU 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 5.0 1.1 - - - -
237A GLU* 4.5 2.1 - - - +
240A ARG* 3.6 11.8 + - - -
182F LEU* 3.4 41.1 - - + +
183F TYR* 3.7 21.5 - - + +
187F MSE 4.0 6.7 - - - -
233F ILE 3.2 7.7 + - - +
234F CYS 3.2 4.2 + - - +
236F PHE* 1.3 76.2 - - - +
238F ALA* 1.3 63.3 + - - +
240F ARG* 2.7 42.7 + - - +
241F GLN* 2.8 42.8 + - - +
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Residues in contact with ALA 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F PHE* 3.8 23.6 - - + -
187F MSE 4.1 36.1 - - + +
191F LEU* 4.7 0.7 - - + -
193F LEU* 6.1 0.2 - - + -
234F CYS 3.2 10.8 + - - +
235F LEU* 3.2 11.7 - - - +
237F GLU* 1.3 79.0 - - - +
239F VAL* 1.3 63.9 + - - +
241F GLN* 3.0 4.9 + - - +
242F ARG* 2.8 27.5 + - - +
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Residues in contact with VAL 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 4.8 2.7 - - + -
217A PRO* 4.6 18.2 - - + +
96F PHE* 4.3 5.2 - - + -
119F ALA* 3.7 37.9 - - + +
235F LEU 3.1 15.8 + - - +
236F PHE* 3.3 26.4 + - + +
238F ALA* 1.3 79.5 - - - +
240F ARG* 1.3 64.8 + - - +
242F ARG* 3.2 15.5 + - - +
243F SER* 2.9 31.9 + - - +
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Residues in contact with ARG 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR* 3.7 37.5 - - + -
237A GLU* 3.7 18.8 - - - -
240A ARG* 3.0 41.8 - - - +
236F PHE 3.0 13.6 + - - +
237F GLU* 2.7 45.3 + - - +
239F VAL* 1.3 79.1 - - - +
241F GLN* 1.3 86.5 + - - +
242F ARG 3.4 0.2 + - - -
243F SER* 3.4 16.4 + - - +
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Residues in contact with GLN 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F LEU 3.9 4.0 + - - -
183F TYR 4.8 3.8 + - - -
185F SER 3.0 21.1 + - - +
186F LYS* 3.6 2.4 - - - +
187F MSE 2.6 43.3 + - + +
188F THR* 3.5 20.7 + - + +
237F GLU* 2.8 28.5 + - - +
238F ALA* 3.0 10.6 + - - +
240F ARG* 1.3 102.2 - - - +
242F ARG* 1.3 56.6 + - - +
243F SER 3.3 5.4 + - - +
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Residues in contact with ARG 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F GLN* 3.5 26.4 + - - +
95F PRO 3.6 7.1 + - - -
96F PHE* 3.7 28.8 - - + +
187F MSE 3.2 27.1 + - - -
188F THR* 3.2 20.2 + - + +
189F GLY 2.7 32.7 + - - +
191F LEU* 3.6 11.7 - - - +
238F ALA* 2.8 24.9 + - - +
239F VAL* 3.2 8.0 + - - +
241F GLN* 1.3 75.3 - - - +
243F SER* 1.3 60.7 + - - +
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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
------------------------------------------------------------
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