Contacts of the helix formed by residues 206 - 219 (chain B) in PDB entry 2NTZ
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 THR 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B GLU 3.5 4.9 + - - -
205B LEU* 1.3 74.8 - - - +
207B PHE* 1.3 62.9 + - + +
208B SER* 3.3 23.3 - - - +
209B ASP* 2.4 56.6 + - - +
210B TYR* 3.1 5.9 + - - -
253B LYS* 4.6 3.8 + - - -
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Residues in contact with PHE 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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151B ILE* 4.2 23.7 - - + +
184B ARG* 2.8 61.9 - - + -
187B GLN* 3.6 20.0 - - + -
188B ALA* 4.0 12.1 - - + -
205B LEU 4.1 1.2 + - - -
206B THR* 1.3 75.3 - - + +
208B SER* 1.3 66.8 + - - +
210B TYR* 3.2 11.4 + - - +
211B LYS* 2.9 48.8 + - + -
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 2.9 16.1 - - - +
207B PHE* 1.3 82.3 - - - +
209B ASP* 1.3 54.5 + - - +
211B LYS* 3.1 8.8 + - - +
212B THR* 2.6 51.0 + - - +
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Residues in contact with ASP 209 (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 PHE* 6.3 0.4 - - + -
205B LEU* 4.4 14.4 - - + -
206B THR* 2.4 51.3 + - - +
208B SER* 1.3 73.6 + - - +
210B TYR* 1.3 61.6 + - - +
212B THR* 2.7 25.7 + - - +
213B LEU* 2.8 16.4 + - + +
253B LYS* 2.9 29.5 + - - -
257B LEU* 3.5 24.1 - - + +
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Residues in contact with TYR 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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150B SER 4.5 4.1 + - - -
151B ILE* 4.0 18.2 - - + -
152B ARG* 3.3 46.1 - - + +
188B ALA* 3.8 41.3 - - + +
191B ALA* 3.8 8.8 - - + +
196B VAL* 4.6 6.7 - - + -
202B GLN* 3.4 17.2 + - - +
205B LEU* 3.0 48.9 - - + +
206B THR 3.1 11.9 + - - -
207B PHE* 3.7 6.3 - - - +
209B ASP* 1.3 77.5 - - - +
211B LYS* 1.3 57.3 + - - +
213B LEU* 3.0 14.2 + - + +
214B CYS* 2.9 33.3 + - - -
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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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187B GLN* 3.2 31.4 + - - +
188B ALA* 5.6 0.8 - - - +
207B PHE* 2.9 41.2 + - + +
208B SER* 3.3 11.9 - - - +
210B TYR* 1.3 73.5 - - - +
212B THR* 1.3 68.8 + - + +
214B CYS* 2.8 26.2 + - + +
215B ALA* 3.1 11.0 + - - +
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Residues in contact with THR 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 SER* 2.6 35.2 + - - +
209B ASP* 2.7 22.2 + - - +
211B LYS* 1.3 73.6 - - + +
213B LEU* 1.3 58.2 + - - +
215B ALA* 3.0 11.2 + - - +
216B VAL* 2.8 33.1 + - - +
257B LEU* 3.8 25.3 - - + +
261B THR* 5.4 4.7 - - - -
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Residues in contact with LEU 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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191B ALA* 4.2 10.3 - - + -
192B PRO* 3.6 13.8 - - + +
195B LEU* 4.8 16.8 - - + +
196B VAL* 4.8 7.4 - - + +
199B PHE* 4.3 26.9 - - + -
205B LEU* 5.2 3.4 - - + -
209B ASP* 2.8 25.6 + - + +
210B TYR* 3.1 31.2 - - + +
211B LYS 3.0 0.2 - - - -
212B THR* 1.3 83.7 + - - +
214B CYS* 1.3 62.7 + - - +
216B VAL* 3.2 6.6 + - + +
217B GLY* 3.0 17.7 + - - -
257B LEU* 4.0 21.8 - - + -
260B ILE* 4.7 15.7 - - + -
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Residues in contact with CYS 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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187B GLN* 3.7 26.0 - - - -
190B SER* 4.5 6.7 - - - +
191B ALA* 3.8 16.6 - - - -
192B PRO* 4.1 9.4 - - - +
210B TYR 2.9 29.3 + - - -
211B LYS* 2.8 17.4 + - + +
213B LEU* 1.3 75.6 - - - +
215B ALA* 1.3 57.2 + - - +
217B GLY* 3.2 2.6 + - - -
218B ASP* 3.1 39.0 + - - +
222B ASN* 4.7 0.3 - - - +
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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 3.1 6.7 + - - +
212B THR* 3.0 17.0 + - - +
213B LEU 3.0 0.2 - - - -
214B CYS* 1.3 74.5 - - - +
216B VAL* 1.3 56.8 + - + +
217B GLY 2.7 14.0 + - - -
218B ASP* 3.2 17.2 + - - -
219B GLU* 3.2 22.3 + - - +
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Residues in contact with VAL 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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195B LEU* 4.4 8.7 - - + -
212B THR 2.8 22.8 + - - +
213B LEU* 3.2 11.4 + - + +
215B ALA* 1.3 72.5 - - + +
217B GLY* 1.3 55.7 + - - +
219B GLU* 4.3 12.0 - - - +
220B MSE 3.2 26.7 + - - +
230B LEU* 4.9 5.4 - - + -
260B ILE* 3.4 41.3 - - + +
261B THR* 3.7 31.9 - - + -
264B ALA* 3.5 14.6 - - + +
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Residues in contact with GLY 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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192B PRO* 4.1 14.8 - - - -
213B LEU 3.0 11.4 + - - -
214B CYS 3.5 4.5 - - - -
215B ALA 2.7 3.6 + - - -
216B VAL* 1.3 78.0 - - - +
218B ASP* 1.3 64.2 + - - -
220B MSE 2.9 15.6 + - - +
221B GLY 3.1 8.1 + - - -
222B ASN* 3.3 18.2 + - - -
227B PHE* 4.4 8.7 - - - -
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Residues in contact with ASP 218 (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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214B CYS* 3.1 23.4 + - - +
215B ALA* 3.2 5.9 + - - +
217B GLY* 1.3 67.8 - - - +
219B GLU* 1.3 56.1 + - - +
220B MSE 2.7 5.3 + - - -
221B GLY* 2.5 32.5 + - - +
222B ASN* 3.2 15.6 - - - +
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Residues in contact with GLU 219 (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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215B ALA* 3.2 18.8 + - - +
216B VAL* 4.3 8.3 + - - +
218B ASP* 1.3 77.5 - - - +
220B MSE 1.3 57.1 + - - +
221B GLY 3.4 0.8 + - - -
264B ALA* 3.1 35.2 - - - +
265B SER* 3.8 7.6 + - - -
268B THR* 3.5 25.0 + - + +
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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