Contacts of the helix formed by residues 226 - 242 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN* 4.3 9.7 + - - +
198A GLU* 3.8 11.7 + - - -
225A LEU* 1.3 78.1 - - - +
227A VAL* 1.3 69.9 + - - +
228A SER* 3.0 33.5 + - - +
229A VAL* 3.1 22.9 + - + +
230A ALA* 3.0 26.2 + - - +
111F ALA* 6.2 3.6 - - + -
114F ARG* 3.4 28.8 - - - +
115F SER* 6.0 0.2 + - - -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 4.4 18.8 - - + -
108A ASN* 3.6 41.1 - - + +
112A CYS* 4.7 2.9 - - - -
195A MSE 4.8 8.0 - - + +
196A GLY 4.0 19.5 - - - +
197A ALA* 5.2 0.9 - - - -
198A GLU* 3.5 25.3 + - + +
225A LEU 3.7 0.9 + - - -
226A ASN* 1.3 79.9 - - - +
228A SER* 1.3 68.2 + - - +
230A ALA* 3.1 7.0 + - + +
231A THR* 2.8 40.1 + - - +
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Residues in contact with SER 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN* 4.6 5.6 + - - -
111A ALA* 3.3 34.2 - - - +
112A CYS* 4.1 18.6 - - - -
115A SER* 4.3 3.5 + - - -
226A ASN* 3.0 13.5 + - - -
227A VAL* 1.3 85.2 - - - +
229A VAL* 1.3 60.2 + - - +
231A THR* 3.9 2.7 - - - -
232A GLY 3.3 13.5 + - - -
229F VAL* 3.7 22.8 - - - +
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 4.4 4.3 - - + -
226A ASN* 3.1 30.7 + - + +
227A VAL 3.1 0.6 - - - -
228A SER* 1.3 79.8 - - - +
230A ALA* 1.3 67.1 + - - +
231A THR 3.3 0.2 - - - -
232A GLY* 3.3 1.4 + - - +
233A ILE* 3.0 37.8 + - + +
111F ALA 5.7 0.7 - - - +
115F SER* 3.4 24.0 - - - +
228F SER* 3.3 35.4 - - - +
229F VAL* 4.1 9.3 - - - +
232F GLY* 4.0 12.3 - - - -
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A MSE 3.6 19.1 - - + -
216A ILE* 4.0 18.8 - - + -
225A LEU* 4.4 16.1 - - + +
226A ASN 3.0 18.2 + - - +
227A VAL* 3.5 7.4 - - - +
229A VAL* 1.3 74.9 - - - +
231A THR* 1.3 65.6 + - - +
233A ILE* 3.2 3.1 + - - +
234A CYS* 3.0 27.7 + - - -
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Residues in contact with THR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.9 23.3 - - + -
100A LEU* 4.5 0.3 - - - +
112A CYS* 3.5 28.5 - - + +
115A SER* 4.9 2.2 - - - -
193A LEU* 4.3 0.5 - - - +
195A MSE 3.4 28.4 - - - +
227A VAL* 2.8 20.6 + - - +
228A SER 3.9 5.2 - - - +
230A ALA* 1.3 76.1 - - - +
232A GLY* 1.3 57.4 + - - +
234A CYS* 3.2 1.9 + - - +
235A LEU* 2.8 53.8 + - + +
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Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 4.5 10.1 - - - -
228A SER 3.3 5.5 + - - -
229A VAL 3.3 5.7 + - - -
230A ALA 3.3 0.4 - - - -
231A THR* 1.3 79.7 - - - +
233A ILE* 1.3 55.6 + - - +
235A LEU* 3.2 4.8 + - - -
236A PHE* 2.8 36.9 + - - +
229F VAL* 3.9 20.6 - - - -
233F ILE* 3.8 9.9 - - - -
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Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 3.8 17.4 - - + +
183A TYR* 4.2 2.4 + - - +
216A ILE* 4.6 9.0 - - + -
225A LEU* 3.5 26.9 - - + -
229A VAL* 3.0 28.6 + - + +
230A ALA* 3.7 4.7 - - - +
232A GLY* 1.3 74.0 - - - +
234A CYS* 1.3 62.7 + - - +
236A PHE* 4.1 1.1 - - - +
237A GLU* 3.2 22.3 + - - +
232F GLY 3.7 22.9 - - - +
233F ILE* 4.0 8.7 - - - +
236F PHE* 3.4 46.4 - - + -
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Residues in contact with CYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 3.6 27.1 - - - -
182A LEU* 4.1 20.6 - - + -
187A MSE 4.3 6.1 - - - +
193A LEU* 3.6 26.5 - - + -
195A MSE 4.2 3.8 - - - -
214A ILE* 4.6 0.4 - - - -
216A ILE* 3.6 24.5 - - - -
230A ALA 3.0 18.9 + - - +
231A THR 3.7 0.7 - - - +
233A ILE* 1.3 76.3 - - - +
235A LEU* 1.3 66.5 + - - +
237A GLU* 3.2 12.5 + - - +
238A ALA* 3.2 12.0 + - - +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 4.1 11.1 - - + -
97A LEU 5.4 0.2 - - - +
98A LEU* 4.0 11.7 - - + -
115A SER* 4.1 7.2 - - - +
116A ALA* 4.0 24.5 - - - +
119A ALA* 3.8 20.0 - - + -
121A VAL* 4.0 17.9 - - + -
193A LEU* 3.2 27.1 - - + -
231A THR* 2.8 44.2 + - + +
232A GLY 3.6 3.4 - - - +
234A CYS* 1.3 72.9 - - - +
236A PHE* 1.3 61.5 + - + +
238A ALA* 3.1 10.0 + - - +
239A VAL* 2.9 26.8 + - - +
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Residues in contact with PHE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 4.0 18.8 - - - -
118A ALA* 3.9 28.0 - - + -
119A ALA* 4.0 6.5 - - + -
232A GLY* 2.8 22.3 + - - +
233A ILE* 4.6 1.6 - - - +
235A LEU* 1.3 75.9 - - + +
237A GLU* 1.3 61.2 + - - +
239A VAL* 3.5 18.1 - - + +
240A ARG* 2.8 24.9 + - - +
183F TYR* 3.2 28.7 + + - +
216F ILE* 3.6 19.3 - - + -
217F PRO* 3.4 22.9 - - + -
218F MSE 3.9 7.9 - - + -
225F LEU* 4.1 7.0 - - + -
233F ILE* 3.3 35.4 - - + -
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 3.6 37.4 - - + +
183A TYR* 3.3 30.2 - - + +
187A MSE 4.2 5.2 - - - -
233A ILE 3.2 15.0 + - - +
234A CYS 3.2 10.9 + - - +
236A PHE* 1.3 77.5 - - - +
238A ALA* 1.3 63.9 + - - +
240A ARG* 2.8 44.4 + - - +
241A GLN* 2.9 34.1 + - - +
183F TYR* 5.7 0.4 - - - -
237F GLU* 4.5 1.7 - - - +
240F ARG* 3.7 2.6 - - - -
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PHE* 3.5 26.9 - - + -
187A MSE 3.9 32.9 - - + -
191A LEU* 4.5 0.4 - - + -
234A CYS 3.2 7.6 + - - +
235A LEU* 3.1 12.0 + - - +
237A GLU* 1.3 76.6 - - - +
239A VAL* 1.3 57.8 + - - +
241A GLN* 2.9 2.8 + - - -
242A ARG* 2.7 42.8 + - - +
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 4.5 4.5 - - + -
119A ALA* 3.6 39.5 - - + +
235A LEU 2.9 18.4 + - - +
236A PHE* 3.2 23.1 + - + +
238A ALA* 1.3 75.7 - - - +
240A ARG* 1.3 63.6 + - - +
242A ARG* 3.4 8.7 + - - +
243A SER* 3.2 25.2 + - - +
183F TYR* 4.7 2.2 - - + -
217F PRO* 4.3 25.6 - - + +
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Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A PHE 2.8 13.2 + - - +
237A GLU* 2.8 49.8 + - - +
239A VAL* 1.3 78.6 - - - +
241A GLN* 1.3 88.0 + - - +
243A SER* 2.9 24.0 + - - -
183F TYR* 3.5 36.4 - - + +
237F GLU* 3.6 19.5 + - - -
240F ARG* 3.0 36.5 - - - +
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Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LEU 4.6 4.8 + - - -
183A TYR 4.7 5.9 + - - -
185A SER 3.3 20.8 + - - +
186A LYS* 3.6 2.4 - - - -
187A MSE 2.8 33.5 + - + +
188A THR* 3.5 22.5 + - + +
237A GLU* 2.9 32.8 + - - +
238A ALA* 2.9 8.9 + - - +
240A ARG* 1.3 97.2 - - - +
242A ARG* 1.3 60.5 + - - +
243A SER* 3.3 6.2 + - - +
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Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLN* 4.2 15.3 + - - -
95A PRO 3.6 12.9 + - - -
96A PHE* 3.0 54.7 - - - +
122A HIS* 5.4 0.6 - - - -
187A MSE 3.1 25.4 + - - +
188A THR* 4.3 8.8 - - - +
189A GLY 2.6 32.5 + - - +
191A LEU* 4.0 6.5 - - - +
238A ALA 2.7 33.7 + - - +
239A VAL* 3.8 5.8 - - - +
241A GLN* 1.3 73.6 - - - +
243A SER* 1.3 59.3 + - - +
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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