Contacts of the helix formed by residues 178 - 189 (chain B) in PDB entry 2NO5
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 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ASL 3.5 27.5 + - - +
13B TYR 4.0 2.4 + - - -
14B GLY* 5.0 0.6 - - - -
42B ARG* 3.0 27.4 + - - +
176B SER* 2.8 5.9 + - - +
177B SER* 1.3 85.8 - - - +
179B ALA* 1.3 67.5 + - - +
180B TRP* 3.0 23.7 + - + +
181B ASP* 2.8 21.7 + - + +
182B LEU* 3.0 13.0 + - - +
1016B CNR 2.9 29.9 - - - +
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Residues in contact with ALA 179 (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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177B SER 3.7 4.8 + - - -
178B ASN* 1.3 70.3 - - - +
180B TRP* 1.3 56.8 + - - +
182B LEU* 3.4 12.9 + - - +
183B GLY* 2.9 22.2 + - - -
194B ARG* 3.7 21.2 - - - +
203B GLU* 3.5 36.1 - - + +
204B TYR* 3.4 20.5 - - + +
1016B CNR 3.7 8.4 - - + +
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Residues in contact with TRP 180 (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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47A GLU* 3.5 8.7 - - - +
51A THR* 4.3 8.1 - - + -
55A MET* 3.6 8.3 - - - +
11B ASL 3.8 28.5 - - + -
42B ARG* 4.8 0.2 - - - -
46B LEU* 3.8 25.0 - - + +
50B TRP* 3.6 32.9 - + - -
120B ASN* 4.0 14.4 - - - -
152B LYS* 3.9 25.4 - - + -
153B PRO* 4.0 9.6 - - + +
178B ASN* 2.8 17.8 + - + +
179B ALA* 1.3 73.5 - - - +
181B ASP* 1.3 83.3 + - + +
183B GLY 3.3 0.3 + - - -
184B GLY* 2.9 24.8 + - - -
204B TYR* 3.4 33.7 - - + +
1016B CNR 3.4 39.7 + - + -
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Residues in contact with ASP 181 (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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11B ASL 3.2 14.4 - - - +
152B LYS* 2.8 41.1 + - - +
158B TYR* 2.5 32.5 + - - -
174B PHE* 3.3 17.9 - - - -
176B SER* 3.9 7.2 - - - +
178B ASN* 2.8 19.2 + - + +
180B TRP* 1.3 90.3 - - + +
182B LEU* 1.3 58.8 + - - +
185B ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 182 (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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174B PHE* 3.9 12.1 - - + +
176B SER* 3.2 38.8 - - - +
178B ASN 3.0 22.0 + - - +
179B ALA* 3.8 6.5 - - - +
181B ASP* 1.3 73.7 - - - +
183B GLY* 1.3 60.3 + - - +
185B ALA* 4.4 3.6 - - - -
186B GLY* 2.8 26.7 + - - -
192B THR* 3.5 16.4 + - - +
193B VAL 3.2 29.8 - - - +
194B ARG* 3.6 27.8 - - + -
207B ALA* 4.6 3.8 - - - +
209B LEU* 4.0 15.7 - - + -
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Residues in contact with GLY 183 (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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55A MET* 3.9 8.5 - - - +
179B ALA 2.9 16.2 + - - -
180B TRP 3.3 1.7 + - - -
181B ASP 3.3 0.4 - - - -
182B LEU* 1.3 76.4 - - - +
184B GLY* 1.3 57.7 + - - +
187B LYS* 2.9 30.1 + - - +
204B TYR* 4.2 16.4 - - - -
207B ALA* 3.4 22.3 - - - +
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Residues in contact with GLY 184 (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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55A MET* 3.6 15.7 - - - +
153B PRO* 3.7 26.9 - - - +
155B PRO* 5.7 0.3 - - - +
158B TYR* 3.3 14.1 - - - -
180B TRP 2.9 10.9 + - - -
181B ASP 3.8 0.9 - - - -
183B GLY* 1.3 76.8 - - - +
185B ALA* 1.3 59.7 + - - +
187B LYS* 3.6 2.5 + - - +
188B PHE* 3.2 18.2 + - - +
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Residues in contact with ALA 185 (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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158B TYR* 3.6 20.3 - - + -
174B PHE* 3.3 35.4 - - + -
181B ASP 2.9 21.7 + - - +
182B LEU 3.9 2.5 - - - +
184B GLY* 1.3 71.1 - - - +
186B GLY* 1.3 60.5 + - - +
188B PHE* 3.1 6.1 - - - +
189B GLY 2.9 21.3 + - - -
190B PHE* 3.2 15.2 + - + +
192B THR* 3.9 5.6 - - + -
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Residues in contact with GLY 186 (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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182B LEU 2.8 16.2 + - - -
183B GLY 3.9 0.7 - - - -
185B ALA* 1.3 75.1 - - - +
187B LYS* 1.3 67.2 + - - +
189B GLY* 2.7 15.2 + - - -
190B PHE 3.8 7.5 - - - +
192B THR* 3.5 15.7 - - - +
207B ALA* 4.4 9.9 - - - -
208B PRO 5.8 1.1 - - - -
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Residues in contact with LYS 187 (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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55A MET* 3.1 33.2 - - + +
56A HIS* 3.3 17.9 + - - -
57A GLN* 2.5 36.5 + - + +
183B GLY 2.9 19.5 + - - +
184B GLY* 4.0 5.4 - - - +
185B ALA 3.4 0.2 - - - -
186B GLY* 1.3 75.8 - - - +
188B PHE* 1.3 62.2 + - - +
189B GLY* 4.5 0.2 - - - -
206B PHE* 4.8 5.2 - - + -
207B ALA* 3.9 9.4 - - + +
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Residues in contact with PHE 188 (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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155B PRO* 3.7 36.3 - - + -
158B TYR* 3.5 22.0 - - + -
159B GLN* 3.2 43.5 - - + -
162B CYS* 3.8 10.8 - - - -
169B PRO* 3.9 16.3 - - + +
184B GLY 3.2 12.4 + - - +
185B ALA 3.1 9.6 - - - +
187B LYS* 1.3 79.8 - - - +
189B GLY* 1.3 60.6 + - - +
190B PHE* 3.6 32.1 - + - -
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Residues in contact with GLY 189 (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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169B PRO* 3.7 27.2 - - - +
170B ASN* 3.9 7.4 + - - +
185B ALA 2.9 1.4 + - - -
186B GLY 2.7 18.0 + - - -
187B LYS 4.5 0.4 - - - -
188B PHE* 1.3 76.0 - - - +
190B PHE* 1.3 67.5 + - - +
191B ASN* 3.7 1.6 + - - +
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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