Contacts of the helix formed by residues 206 - 217 (chain B) in PDB entry 7NPA
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 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B LYS* 2.7 31.4 + - - -
34B ASP* 5.0 4.0 - - - +
135B THR* 4.4 0.2 - - - -
136B VAL* 3.7 13.6 - - - +
205B PHE* 1.3 74.3 - - - +
207B TYR* 1.3 66.4 + - - +
208B ASP* 4.6 2.2 - - + +
209B GLU* 3.2 20.2 + - + +
210B LEU* 3.0 21.3 + - - +
251B GLU* 5.0 3.2 + - - +
252B LEU 5.5 1.6 - - - +
253B SER* 3.2 28.6 + - - +
254B ALA 5.0 1.2 + - - -
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Residues in contact with TYR 207 (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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112B CYS 3.9 11.4 + - - -
113B TRP 3.7 25.8 - - - -
114B LYS* 3.7 38.8 - - + -
115B PRO* 5.6 1.6 - - + -
135B THR* 3.9 20.7 - - - +
136B VAL* 5.2 1.6 - - - +
205B PHE 3.7 2.6 + - - -
206B GLU* 1.3 72.2 + - - +
208B ASP* 1.3 73.5 + - - +
210B LEU* 3.3 2.9 + - - +
211B LYS* 2.8 72.7 + - + +
221B MET* 3.7 26.0 - - + +
222B ASP* 3.9 5.7 + - - -
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Residues in contact with ASP 208 (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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206B GLU* 3.3 3.2 - - + +
207B TYR* 1.3 93.8 - - - +
209B GLU* 1.3 60.9 + - - +
211B LYS* 3.8 10.1 + - - +
212B GLU* 3.0 49.2 + - - +
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PHE* 5.4 0.2 - - + -
206B GLU* 3.2 24.7 + - + +
208B ASP* 1.3 77.2 - - - +
210B LEU* 1.3 54.8 + - - +
212B GLU* 3.9 15.5 - - - +
213B THR* 2.7 43.1 + - - +
250B ILE* 5.5 0.9 - - + -
251B GLU* 3.7 57.1 + - + +
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Residues in contact with LEU 210 (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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134B TYR* 4.8 5.2 - - + +
135B THR* 3.7 23.1 - - + -
205B PHE* 4.1 21.4 - - + +
206B GLU 3.0 12.7 + - - +
207B TYR 3.7 7.6 - - - +
209B GLU* 1.3 74.4 - - - +
211B LYS* 1.3 59.1 + - - +
213B THR* 3.2 4.5 + - - -
214B LEU* 2.9 44.2 + - + +
221B MET* 3.7 18.8 - - + -
227B PHE* 4.3 15.7 - - + -
234B LEU* 3.7 28.0 - - + -
250B ILE* 4.4 17.7 - - + -
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Residues in contact with LYS 211 (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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114B LYS* 5.1 4.2 - - - +
207B TYR* 2.8 54.4 + - + +
208B ASP* 3.8 14.9 + - - +
210B LEU* 1.3 74.5 - - - +
212B GLU* 1.3 58.5 + - + +
214B LEU* 3.3 4.6 + - - +
215B ALA* 3.0 27.4 + - + +
219B ILE 4.8 0.7 - - - +
220B ASN* 5.3 2.7 - - - -
221B MET* 3.7 29.2 + - + +
222B ASP* 3.8 21.3 + - - -
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Residues in contact with GLU 212 (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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208B ASP* 3.0 35.9 + - - +
209B GLU* 3.9 19.0 - - - +
211B LYS* 1.3 73.8 - - + +
213B THR* 1.3 66.4 + - - +
215B ALA* 3.2 9.8 + - + +
216B LYS* 3.2 30.8 + - + +
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Residues in contact with THR 213 (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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209B GLU* 2.7 31.6 + - - +
210B LEU* 3.2 8.7 + - + -
212B GLU* 1.3 76.7 - - - +
214B LEU* 1.3 61.6 + - - +
216B LYS* 3.2 19.2 + - + +
217B TYR* 3.2 38.6 - - + -
245B ILE* 4.9 4.0 - - + -
249B GLU* 4.2 11.9 + - + +
250B ILE* 4.0 37.5 - - + +
251B GLU 5.2 0.3 + - - -
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Residues in contact with LEU 214 (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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210B LEU* 2.9 28.7 + - + +
211B LYS* 3.6 7.6 - - - +
213B THR* 1.3 75.7 - - + +
215B ALA* 1.3 53.7 + - - +
217B TYR* 3.0 16.7 + - - -
219B ILE* 2.8 47.9 + - + +
221B MET* 3.7 27.6 - - + +
224B VAL* 4.3 6.7 - - + -
227B PHE* 3.5 31.4 - - + -
234B LEU* 4.6 0.7 - - + -
236B VAL* 4.0 16.2 - - + -
245B ILE* 3.8 25.8 - - + -
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Residues in contact with ALA 215 (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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211B LYS* 3.0 13.9 + - + +
212B GLU* 3.2 14.5 + - + +
214B LEU* 1.3 76.8 - - - +
216B LYS* 1.3 57.0 + - + +
218B ASN* 3.0 25.4 + - - +
219B ILE 3.5 10.2 + - - +
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Residues in contact with LYS 216 (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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212B GLU* 3.2 20.0 + - - +
213B THR* 3.2 16.8 + - + +
215B ALA* 1.3 75.3 - - + +
217B TYR* 1.3 66.8 + - + +
218B ASN* 3.2 8.8 + - - +
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Residues in contact with TYR 217 (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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213B THR* 3.2 24.2 - - + -
214B LEU 3.0 9.1 + - - +
216B LYS* 1.3 80.5 - - + +
218B ASN* 1.3 69.5 + - - +
219B ILE* 3.2 21.8 + - + +
243B HIS* 4.9 11.8 - - + +
244B LYS 5.1 3.8 - - - -
245B ILE* 3.6 44.9 - - + +
246B PRO* 5.4 1.1 - - + -
249B GLU* 2.5 36.0 + - + +
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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