Contacts of the helix formed by residues 226 - 243 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D ASN* 3.7 24.2 + - - +
198D GLU* 3.6 11.0 + - - +
225D LEU* 1.3 75.1 - - - +
227D VAL* 1.3 69.2 + - - +
228D SER* 2.8 10.6 + - - +
229D VAL* 2.8 35.7 + - + +
230D ALA* 2.9 20.7 + - - +
111E ALA* 6.4 1.6 - - + -
114E ARG* 3.5 22.4 - - - +
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D VAL* 3.9 23.1 - - + -
108D ASN* 3.8 30.3 - - + +
112D CYS* 4.7 3.4 - - - -
195D MSE 4.6 6.0 - - + +
196D GLY 3.6 23.3 - - - +
197D ALA* 5.0 1.1 - - - -
198D GLU* 3.6 31.7 + - + +
225D LEU 3.7 2.2 + - - -
226D ASN* 1.3 71.7 - - - +
228D SER* 1.3 54.4 + - - +
230D ALA* 3.5 6.2 + - - +
231D THR* 2.7 44.1 + - - +
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Residues in contact with SER 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ASN* 3.7 18.7 + - - -
111D ALA* 2.9 36.4 - - - +
112D CYS* 4.1 11.4 - - - +
115D SER* 4.5 2.3 + - - -
226D ASN* 2.8 17.4 + - - +
227D VAL* 1.3 71.9 - - - +
229D VAL* 1.3 60.5 + - - -
231D THR* 3.3 1.6 + - - -
232D GLY* 2.8 27.0 + - - -
226E ASN* 5.6 0.7 - - - -
229E VAL* 4.0 16.6 - - - +
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D LEU* 4.6 4.0 - - + -
226D ASN* 2.8 36.5 + - + +
228D SER* 1.3 72.0 - - - +
230D ALA* 1.3 57.7 + - - +
232D GLY* 3.2 2.3 + - - -
233D ILE* 2.8 51.4 + - + +
111E ALA* 5.6 1.3 - - + +
115E SER* 3.4 24.0 - - - +
228E SER* 3.4 33.2 - - - +
229E VAL* 4.3 13.5 - - + +
232E GLY* 3.9 13.7 - - - -
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Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D THR* 5.9 0.9 - - + -
195D MSE 3.4 17.5 - - + +
216D ILE* 3.8 23.3 - - + -
225D LEU* 4.2 13.6 - - + +
226D ASN 2.9 16.2 + - - +
227D VAL* 3.7 6.7 - - - +
229D VAL* 1.3 79.0 - - - +
231D THR* 1.3 61.2 + - - +
233D ILE* 3.4 5.8 + - - +
234D CYS* 3.0 24.1 + - - +
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Residues in contact with THR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 4.0 24.9 - - + -
100D LEU* 4.2 0.7 - - + +
112D CYS* 3.6 27.6 - - + -
115D SER* 4.9 1.3 - - - -
193D LEU* 4.6 0.2 - - - +
195D MSE 3.4 27.0 - - + +
227D VAL* 2.7 28.6 + - - +
228D SER 3.6 4.3 - - - -
230D ALA* 1.3 72.3 - - - +
232D GLY* 1.3 58.1 + - - +
234D CYS* 3.4 1.6 + - - +
235D LEU* 2.9 53.0 + - + +
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Residues in contact with GLY 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D SER* 4.2 13.4 + - - -
228D SER 2.8 15.1 + - - -
229D VAL 3.6 3.4 - - - -
231D THR* 1.3 78.6 - - - +
233D ILE* 1.3 61.4 + - - +
235D LEU* 3.3 1.5 + - - -
236D PHE* 2.9 30.4 + - - +
229E VAL* 3.9 16.6 - - - -
233E ILE* 3.7 9.4 - - - -
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Residues in contact with ILE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D LEU* 3.8 19.9 - - + +
183D TYR* 4.1 0.7 - - - +
216D ILE* 4.5 7.2 - - + -
225D LEU* 3.7 25.4 - - + -
229D VAL* 2.8 35.6 + - + +
230D ALA* 3.7 5.4 - - - +
232D GLY* 1.3 73.0 - - - +
234D CYS* 1.3 63.4 + - - +
236D PHE* 3.4 2.6 + - - +
237D GLU* 3.3 18.7 + - - +
232E GLY 3.9 21.5 - - - +
233E ILE* 3.9 8.0 - - - +
236E PHE* 3.5 46.7 - - + -
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Residues in contact with CYS 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D THR* 3.7 20.9 - - - -
182D LEU* 3.8 23.8 - - + -
187D MSE 3.2 25.1 - - - +
193D LEU* 3.8 22.2 - - + -
195D MSE 4.0 5.2 - - - -
214D ILE* 4.5 3.4 - - - -
216D ILE* 3.7 25.6 - - - -
230D ALA 3.0 20.5 + - - +
231D THR 3.8 1.1 - - - +
233D ILE* 1.3 74.9 - - - +
235D LEU* 1.3 65.7 + - - +
237D GLU* 3.3 5.5 + - - +
238D ALA* 3.3 1.0 + - - +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PHE* 3.8 24.7 - - + -
98D LEU* 4.1 18.2 - - + -
115D SER* 4.1 20.9 - - - +
116D ALA* 4.2 2.0 - - - +
119D ALA* 3.6 19.3 - - + -
121D VAL* 3.8 10.8 - - + -
193D LEU* 3.4 23.5 - - + +
231D THR* 2.9 41.3 + - + +
232D GLY 3.7 4.5 - - - +
234D CYS* 1.3 76.0 - - - +
236D PHE* 1.3 62.1 + - + +
238D ALA* 3.1 9.4 - - - +
239D VAL* 2.9 26.7 + - - +
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Residues in contact with PHE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D SER* 4.1 20.2 - - - -
118D ALA* 3.7 30.7 - - + -
119D ALA* 3.9 6.5 - - + -
232D GLY 2.9 22.9 + - - +
233D ILE 4.0 2.7 - - - +
234D CYS 3.2 0.2 - - - -
235D LEU* 1.3 76.3 - - + +
237D GLU* 1.3 59.6 + - - +
238D ALA 3.1 1.1 - - - -
239D VAL* 3.5 18.6 - - + +
240D ARG* 2.9 20.6 + - - +
183E TYR* 2.8 38.5 + + - +
216E ILE* 3.8 17.3 - - + -
217E PRO* 3.5 22.2 - - + -
225E LEU* 4.0 12.1 - - + -
233E ILE* 3.4 31.0 - - + -
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Residues in contact with GLU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D LEU* 3.6 37.2 - - + +
183D TYR* 3.4 29.8 - - + +
187D MSE 3.7 5.8 - - + -
233D ILE 3.3 5.3 + - - +
234D CYS 3.3 11.2 + - - +
236D PHE* 1.3 76.9 - - - +
238D ALA* 1.3 57.3 + - - +
240D ARG* 2.8 32.2 + - - +
241D GLN* 2.8 57.2 + - - +
183E TYR* 6.0 0.2 - - - -
237E GLU* 5.0 0.9 - - - +
240E ARG* 3.6 6.6 - - - -
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Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PHE* 3.7 25.8 - - + -
187D MSE 3.7 33.1 - - + +
191D LEU* 4.1 2.5 - - + -
193D LEU* 6.0 0.4 - - + -
234D CYS 3.3 8.3 + - - +
235D LEU* 3.1 15.2 + - + +
237D GLU* 1.3 80.9 - - - +
239D VAL* 1.3 53.8 + - - +
241D GLN* 3.3 1.0 + - - -
242D ARG* 2.8 39.2 + - - +
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Residues in contact with VAL 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PHE* 4.7 2.2 - - + -
118D ALA 5.1 0.4 - - - +
119D ALA* 3.4 41.7 - - + +
235D LEU 2.9 19.0 + - - +
236D PHE* 3.7 21.8 - - + +
237D GLU 3.3 0.4 - - - -
238D ALA* 1.3 73.8 - - - +
240D ARG* 1.3 65.2 + - - +
242D ARG* 3.3 5.9 + - - +
243D SER* 3.0 29.7 + - - -
183E TYR* 4.2 13.0 - - + -
217E PRO* 4.4 16.4 - - + +
219E ALA* 6.4 1.8 - - + -
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Residues in contact with ARG 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D PHE 2.9 18.5 + - - +
237D GLU* 2.8 39.1 + - - +
239D VAL* 1.3 79.5 - - - +
241D GLN* 1.3 80.4 + - - +
243D SER* 3.3 15.2 + - - -
183E TYR* 3.7 37.4 + - + -
237E GLU* 3.7 17.7 + - - -
240E ARG* 3.0 44.5 - - - +
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Residues in contact with GLN 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D LEU 4.2 4.0 + - - -
183D TYR 5.2 2.4 + - - -
185D SER 3.3 22.7 + - - +
186D LYS* 3.5 2.8 - - - +
187D MSE 2.7 39.7 + - + +
188D THR* 3.6 25.0 + - + +
237D GLU* 2.8 51.3 + - - +
238D ALA 3.8 3.4 - - - +
240D ARG* 1.3 85.5 - - - +
242D ARG* 1.3 59.6 + - - +
243D SER* 3.5 4.0 + - - +
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Residues in contact with ARG 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLN* 3.2 30.4 + - - +
95D PRO 3.9 0.6 + - - -
96D PHE* 3.4 38.0 - - - +
122D HIS* 5.2 0.6 - - - -
187D MSE 2.8 39.4 + - - +
188D THR* 3.7 13.3 - - - -
189D GLY 2.9 24.2 + - - +
191D LEU* 3.8 9.7 - - - +
238D ALA* 2.8 36.3 + - - +
239D VAL* 4.0 4.0 - - - +
241D GLN* 1.3 71.5 - - - +
243D SER* 1.3 63.8 + - - +
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Residues in contact with SER 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D VAL* 3.0 20.2 + - - -
240D ARG* 3.3 19.1 + - - +
241D GLN 4.2 4.2 - - - +
242D ARG* 1.3 81.9 - - - +
183E TYR* 4.9 6.8 - - - +
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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