Contacts of the helix formed by residues 191 - 204 (chain B) in PDB entry 1NOY
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 GLU 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B GLU* 3.2 22.9 - - + +
130B ILE* 3.1 23.4 + - - +
148B LEU* 3.5 24.1 - - + +
190B ASN* 1.3 70.4 - - - +
192B ARG* 1.3 59.0 + - + +
194B MET* 2.7 32.7 + - + +
195B LEU* 2.8 29.4 + - + +
226B ARG* 2.9 48.7 + - - +
230B ILE* 3.3 13.8 - - + +
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Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ASN* 3.3 12.1 - - + +
191B GLU* 1.3 78.8 - - + +
193B ASP* 1.3 65.2 + - - +
195B LEU* 3.4 4.0 + - - +
196B MET* 3.1 24.5 + - - +
230B ILE* 3.7 42.7 + - + +
231B LEU* 4.2 14.8 - - + +
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B PHE* 3.8 20.7 - - + -
190B ASN* 2.9 44.4 + - - +
192B ARG* 1.3 77.2 - - - +
194B MET* 1.3 60.3 + - - +
196B MET* 3.7 9.4 - - - +
197B GLU* 3.5 16.6 + - - +
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Residues in contact with MET 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 2.9 46.7 - - + +
131B ASP 4.5 1.3 - - - +
132B ALA* 5.1 0.2 - - - -
133B ILE* 4.7 8.7 - - + -
146B PHE* 4.1 23.9 - - + +
147B ASP 4.1 5.2 - - - -
148B LEU* 3.8 30.3 - - + -
188B PHE* 3.6 28.9 - - + -
190B ASN 3.2 10.8 + - - +
191B GLU* 2.7 29.3 + - + +
193B ASP* 1.3 71.4 - - - +
195B LEU* 1.3 65.3 + - + +
197B GLU* 3.1 6.1 + - - +
198B TYR* 3.1 20.4 + - - +
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 4.2 22.4 - - + -
133B ILE* 4.9 7.9 - - + -
191B GLU* 2.8 44.3 + - + +
192B ARG* 3.9 3.4 - - - +
194B MET* 1.3 79.4 - - + +
196B MET* 1.3 62.3 + - - +
198B TYR* 3.1 8.3 + - + +
199B ILE* 3.0 30.0 + - - +
223B ILE* 5.8 3.1 - - + -
226B ARG* 3.9 20.0 - - + -
227B VAL* 4.1 22.2 - - + -
230B ILE* 4.1 8.3 - - + -
231B LEU* 4.0 25.1 - - + -
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Residues in contact with MET 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ARG 3.1 18.1 + - - +
193B ASP* 3.7 11.2 - - - +
195B LEU* 1.3 78.1 - - - +
197B GLU* 1.3 61.8 + - + +
199B ILE* 3.9 8.1 + - + +
200B ASN* 3.3 25.5 + - + +
203B GLU* 5.8 0.4 - - - +
231B LEU* 4.2 19.7 - - + +
238B ARG* 3.9 24.7 - - - +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B PHE* 3.9 15.7 - - + -
186B MET* 3.5 18.5 - - - +
188B PHE* 3.6 24.0 - - + -
193B ASP 3.5 7.5 + - - +
194B MET 3.1 9.4 + - - +
196B MET* 1.3 80.1 - - + +
198B TYR* 1.3 58.4 + - - +
200B ASN* 3.1 29.3 + - - +
201B LEU* 2.9 26.7 + - - +
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Residues in contact with TYR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B CYS* 3.7 14.4 - - - +
133B ILE* 4.0 27.6 - - + -
135B HIS* 2.6 44.5 + + + -
146B PHE* 3.7 26.8 - + + -
194B MET 3.1 11.7 + - - +
195B LEU* 3.1 11.4 + - + +
197B GLU* 1.3 73.2 - - - +
199B ILE* 1.3 66.9 + - + +
201B LEU* 2.8 17.9 + - + +
202B TRP* 2.9 40.9 + + - -
210B PHE* 3.7 5.2 - - - -
223B ILE* 3.6 30.3 - - + -
239B PHE* 4.3 15.3 - + - -
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Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU 3.0 17.0 + - - +
196B MET* 4.0 9.6 - - + +
198B TYR* 1.3 75.0 - - - +
200B ASN* 1.3 55.9 - - - +
202B TRP* 3.5 3.3 + - - +
203B GLU* 3.1 46.9 + - - +
227B VAL* 3.6 27.6 - - + -
231B LEU* 3.7 18.4 - - + -
235B SER* 3.6 21.1 - - - +
238B ARG* 3.6 22.8 - - + +
239B PHE* 3.6 29.8 - - + +
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Residues in contact with ASN 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B MET* 3.3 19.2 + - + +
197B GLU* 3.1 33.6 + - - +
198B TYR 3.0 1.0 - - - -
199B ILE* 1.3 78.0 - - - +
201B LEU* 1.3 59.9 + - - +
203B GLU* 3.4 15.2 - - - +
204B GLN* 2.8 56.7 + - - +
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B HIS* 3.5 38.6 - - + +
144B TYR* 3.6 49.4 - - + -
146B PHE* 4.2 15.3 - - + -
186B MET* 6.0 0.2 - - - -
197B GLU 2.9 10.2 + - - +
198B TYR* 2.8 12.1 + - + +
200B ASN* 1.3 75.7 - - - +
202B TRP* 1.3 64.9 + - + +
204B GLN* 3.0 5.7 + - - +
205B LYS* 2.6 57.2 + - + +
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Residues in contact with TRP 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B HIS* 3.5 8.1 - + - -
198B TYR* 2.9 51.0 + + - +
199B ILE 3.8 7.2 - - - +
201B LEU* 1.3 83.0 - - + +
203B GLU* 1.3 58.6 + - - +
205B LYS 3.9 6.5 - - - -
206B ARG* 2.8 44.8 + - - +
207B PRO* 3.9 22.4 - - + -
210B PHE* 3.6 49.8 - + + -
220B VAL* 6.6 0.4 - - + -
223B ILE* 6.2 1.1 - - + -
224B MET* 5.5 4.9 - - + -
239B PHE* 3.5 46.0 - + + -
262B ILE* 4.4 27.1 - - + -
265B VAL* 4.5 7.0 - - + -
267B ILE* 5.8 2.5 - - + -
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Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ILE* 3.1 20.2 + - - +
200B ASN* 3.4 20.4 - - - +
201B LEU 3.1 0.4 - - - -
202B TRP* 1.3 78.7 - - - +
204B GLN* 1.3 67.9 + - - +
205B LYS 3.4 0.2 + - - -
206B ARG* 3.8 29.1 + - - +
238B ARG* 2.9 64.7 + - - +
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Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG* 5.2 0.7 + - - -
200B ASN* 2.8 50.9 + - - +
201B LEU* 3.0 7.6 + - - +
203B GLU* 1.3 80.1 - - - +
205B LYS* 1.3 74.7 + - + +
206B ARG 4.0 0.2 - - - -
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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
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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