Contacts of the helix formed by residues 226 - 243 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D HIS* 6.1 2.6 - - - -
111D ALA* 5.0 11.3 - - - +
114D ARG* 3.3 28.4 - - - +
141D VAL* 6.0 2.6 - - - +
228D SER* 5.6 0.6 - - - -
108E ASN* 4.6 6.8 - - - +
198E GLU* 3.4 14.6 - - - +
225E LEU* 1.3 75.1 - - - +
227E VAL* 1.3 63.6 + - - +
228E SER* 2.8 27.8 + - - -
229E VAL* 3.1 33.8 + - - +
230E ALA* 3.1 9.6 + - - +
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Residues in contact with VAL 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E VAL* 4.6 17.5 - - + -
108E ASN* 4.9 17.0 + - + +
112E CYS* 4.1 12.8 - - - -
195E MSE 4.8 7.9 - - + -
196E GLY 3.8 15.0 - - - +
197E ALA* 3.9 2.7 - - - -
198E GLU* 3.1 44.0 + - + +
225E LEU 3.6 1.8 + - - -
226E ASN* 1.3 73.1 + - - +
228E SER* 1.3 56.6 + - - +
230E ALA* 3.9 6.3 - - - +
231E THR* 2.8 44.2 + - - +
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Residues in contact with SER 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D VAL* 3.4 22.7 - - - +
108E ASN* 4.5 9.7 + - - -
111E ALA* 3.3 36.6 + - - +
112E CYS* 4.2 12.6 - - - +
115E SER* 4.4 2.6 + - - -
226E ASN* 2.8 18.2 + - - -
227E VAL* 1.3 70.7 - - - +
229E VAL* 1.3 63.8 + - - -
231E THR* 3.4 2.8 + - - -
232E GLY* 3.1 18.7 + - - -
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Residues in contact with VAL 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ALA* 5.6 2.0 - - + +
115D SER* 3.6 24.0 - - - +
228D SER* 4.0 29.8 - - - +
229D VAL* 4.3 12.8 - - + +
232D GLY* 3.9 12.1 - - - -
225E LEU* 4.4 9.2 - - + -
226E ASN* 3.1 30.9 + - - +
228E SER* 1.3 74.4 - - - +
230E ALA* 1.3 58.6 + - - +
232E GLY* 3.2 1.9 + - - -
233E ILE* 2.9 49.7 + - + +
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E MSE 3.6 16.6 - - + -
216E ILE* 3.9 20.0 - - + -
225E LEU* 4.2 13.4 - - + +
226E ASN 3.1 15.5 + - - +
227E VAL* 3.9 6.1 - - - +
229E VAL* 1.3 76.4 - - - +
231E THR* 1.3 65.5 + - - +
233E ILE* 3.4 6.3 + - - +
234E CYS* 2.9 29.6 + - - +
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Residues in contact with THR 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E LEU* 3.8 26.2 - - + -
100E LEU* 4.4 0.2 - - - +
112E CYS* 3.5 25.9 - - + +
115E SER* 5.0 1.6 - - - -
193E LEU* 4.4 0.2 - - - +
195E MSE 3.3 27.6 - - - +
227E VAL* 2.8 23.6 + - - +
228E SER 3.7 4.5 - - - -
230E ALA* 1.3 74.9 - - - +
232E GLY* 1.3 58.7 + - - +
234E CYS* 3.8 0.9 - - - +
235E LEU* 2.8 53.3 + - + +
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Residues in contact with GLY 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D VAL* 3.9 16.2 - - - -
233D ILE* 3.9 9.6 - - - -
115E SER* 4.2 13.0 - - - -
228E SER 3.1 14.5 + - - -
229E VAL 3.6 3.1 - - - -
230E ALA 3.2 0.4 - - - -
231E THR* 1.3 76.7 - - - +
233E ILE* 1.3 52.8 + - - +
235E LEU* 3.1 3.2 + - - -
236E PHE* 2.7 39.8 + - - +
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Residues in contact with ILE 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D GLY 3.7 20.6 - - - +
233D ILE* 3.9 8.9 - - - +
236D PHE* 3.4 49.6 - - + -
182E LEU* 4.2 15.3 - - + -
183E TYR* 4.4 2.2 - - + +
216E ILE* 4.9 8.1 - - + -
225E LEU* 3.8 23.3 - - + -
229E VAL* 2.9 36.3 + - + +
230E ALA* 3.8 5.6 - - - +
232E GLY* 1.3 71.4 - - - +
234E CYS* 1.3 62.7 + - - +
236E PHE* 3.9 2.0 - - - +
237E GLU* 3.2 21.5 + - - +
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Residues in contact with CYS 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E THR* 3.6 31.0 - - - -
182E LEU* 3.9 19.5 - - + -
187E MSE 4.2 6.9 - - - +
193E LEU* 3.7 24.1 - - + +
195E MSE 4.2 3.4 - - - -
214E ILE* 4.3 5.4 - - + -
216E ILE* 3.6 19.1 - - - -
230E ALA 2.9 21.0 + - - +
231E THR 3.9 0.7 - - - +
233E ILE* 1.3 75.4 - - - +
235E LEU* 1.3 64.6 + - - +
237E GLU* 3.2 11.8 + - - +
238E ALA* 3.3 11.6 + - - +
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Residues in contact with LEU 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E PHE* 3.8 13.2 - - + -
98E LEU* 4.2 13.5 - - + -
115E SER* 4.0 6.5 - - - -
116E ALA* 3.7 29.2 - - - +
119E ALA* 3.8 18.6 - - + -
121E VAL* 4.1 17.0 - - + -
193E LEU* 3.4 24.2 - - + -
231E THR* 2.8 41.7 + - + +
232E GLY* 3.5 4.7 - - - +
234E CYS* 1.3 71.9 - - - +
236E PHE* 1.3 61.9 + - + +
238E ALA* 3.1 9.7 - - - +
239E VAL* 3.0 26.5 + - - +
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Residues in contact with PHE 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D TYR* 3.2 30.1 + - - +
216D ILE* 3.6 18.2 - - + -
217D PRO* 3.3 28.0 - - + -
218D MSE 3.9 10.5 - - + -
225D LEU* 4.3 5.2 - - + -
233D ILE* 3.5 28.5 - - + -
115E SER* 4.2 8.7 - - - -
118E ALA* 3.9 22.9 - - + -
119E ALA* 3.9 18.2 - - + -
232E GLY* 2.7 25.3 + - - +
233E ILE 3.9 2.5 - - - +
235E LEU* 1.3 75.0 - - + +
237E GLU* 1.3 58.9 + - - +
238E ALA 3.1 1.3 - - - -
239E VAL* 3.5 20.6 - - + +
240E ARG* 3.0 20.8 + - - +
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Residues in contact with GLU 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D TYR* 5.3 0.4 - - - -
237D GLU* 5.0 0.7 - - - +
240D ARG* 3.7 5.1 + - - -
182E LEU* 3.7 33.7 - - + +
183E TYR* 3.7 28.9 - - + +
187E MSE 4.7 5.8 - - - -
233E ILE 3.2 14.1 + - - +
234E CYS 3.2 9.1 + - - +
236E PHE* 1.3 74.7 - - - +
238E ALA* 1.3 62.1 + - - +
240E ARG* 3.3 32.0 + - - +
241E GLN* 2.8 49.7 + - - +
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Residues in contact with ALA 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E PHE* 3.6 24.9 - - + -
187E MSE 4.0 33.8 - - + +
191E LEU* 4.5 2.7 - - + -
234E CYS 3.3 8.1 + - - +
235E LEU* 3.1 12.5 + - - +
237E GLU* 1.3 78.7 - - - +
239E VAL* 1.3 66.3 + - - +
241E GLN* 3.0 3.5 + - - +
242E ARG* 2.8 30.0 + - - +
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Residues in contact with VAL 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D TYR* 4.6 1.8 - - + -
217D PRO* 4.2 26.7 - - + +
96E PHE* 4.5 4.0 - - + -
119E ALA* 3.7 38.4 - - + +
235E LEU 3.0 19.9 + - - +
236E PHE* 3.5 23.1 - - + +
238E ALA* 1.3 75.5 - - - +
240E ARG* 1.3 57.0 + - - +
242E ARG* 3.2 8.2 + - - +
243E SER* 2.8 35.2 + - - +
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Residues in contact with ARG 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D TYR* 3.6 32.9 - - + +
237D GLU* 3.6 19.3 - - - -
240D ARG* 3.0 45.1 - - - +
236E PHE 3.0 17.3 + - - +
237E GLU* 3.3 24.8 + - - +
239E VAL* 1.3 73.7 - - - +
241E GLN* 1.3 98.9 + - - +
242E ARG 3.0 4.5 - - - -
243E SER* 3.0 23.8 + - - -
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Residues in contact with GLN 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E LEU 3.9 6.9 + - - -
183E TYR 5.1 2.4 + - - -
185E SER 3.3 22.1 + - - +
186E LYS* 3.8 1.4 - - - -
187E MSE 2.7 38.6 + - - +
188E THR* 3.1 29.4 + - + +
237E GLU* 2.8 35.1 + - - +
238E ALA 3.0 4.7 + - - +
240E ARG* 1.3 100.6 - - - +
242E ARG* 1.3 58.3 + - - +
243E SER 4.2 3.2 - - - +
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Residues in contact with ARG 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLN* 3.7 21.4 + - + +
95E PRO 3.6 2.2 + - - -
96E PHE* 3.1 47.5 - - - +
187E MSE 3.0 21.2 + - - +
188E THR* 4.2 8.2 - - - +
189E GLY 2.7 28.7 + - - +
191E LEU* 3.2 34.4 - - - +
238E ALA* 2.8 21.8 + - - +
239E VAL* 3.5 6.5 - - - +
241E GLN* 1.3 77.0 - - - +
243E SER* 1.3 65.5 + - - +
28F LEU* 5.5 0.7 - - - +
31F ARG* 4.7 11.3 - - + +
32F GLU* 3.4 19.4 + - - +
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Residues in contact with SER 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D TYR* 5.3 8.9 - - - -
217D PRO* 5.4 4.5 - - - +
239E VAL* 2.8 23.7 + - - +
240E ARG* 3.0 16.8 + - - +
241E GLN 4.2 4.0 - - - +
242E ARG* 1.3 83.8 - - - +
28F LEU* 5.3 3.6 - - - +
32F GLU* 4.1 13.4 + - - +
33F ASP* 4.3 20.9 - - - +
34F LYS* 5.9 3.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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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