Contacts of the helix formed by residues 206 - 219 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A GLU* 3.6 6.2 + - - -
205A LEU* 1.3 73.7 - - - +
207A PHE* 1.3 69.8 + - + +
208A SER* 3.2 31.0 - - - +
209A ASP* 2.7 32.5 + - - +
210A TYR* 2.9 12.8 + - - -
253A LYS* 4.3 12.2 + - - -
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ILE* 5.4 16.3 - - + +
184A ARG* 3.3 60.1 - - + -
187A GLN* 3.5 28.0 - - + -
188A ALA* 4.9 10.8 - - + -
205A LEU 4.0 0.8 + - - -
206A THR* 1.3 69.8 - - + +
208A SER* 1.3 71.6 + - - +
209A ASP 2.4 15.4 + - - -
210A TYR* 2.5 26.5 + - + -
211A LYS* 2.9 36.2 + - + -
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A THR* 3.2 18.3 - - - +
207A PHE* 1.3 87.6 - - - +
209A ASP* 1.3 58.3 + - - +
211A LYS* 3.6 13.1 + - - +
212A THR* 2.9 22.7 + - - +
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Residues in contact with ASP 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 4.1 14.6 - - + -
206A THR* 2.7 44.4 + - - +
207A PHE 2.4 8.3 + - - -
208A SER* 1.3 68.5 + - - +
210A TYR* 1.3 67.6 + - - +
211A LYS 3.0 1.1 - - - -
212A THR* 2.6 28.2 - - + +
213A LEU* 2.7 15.6 + - + +
253A LYS* 3.6 21.7 - - - +
254A ASN* 5.6 0.5 - - - +
257A LEU* 3.7 24.9 - - + +
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Residues in contact with TYR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER* 5.6 1.6 - - - -
151A ILE* 4.6 11.4 - - + +
152A ARG* 3.1 51.3 + - + +
188A ALA* 3.6 28.0 - - + -
191A ALA* 3.8 18.6 - - + +
196A VAL* 5.8 1.3 - - + -
202A GLN* 3.5 21.7 + - - +
205A LEU* 3.2 42.4 - - + +
206A THR 2.9 26.7 + - - -
207A PHE* 2.5 18.1 + - + +
209A ASP* 1.3 72.0 - - - +
211A LYS* 1.3 68.2 + - - +
213A LEU* 2.8 24.3 + - + +
214A CYS* 3.0 10.5 + - - +
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Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLN* 3.4 29.6 - - + +
207A PHE* 2.9 30.7 + - + +
208A SER* 3.6 15.7 + - - +
210A TYR* 1.3 77.4 - - - +
212A THR* 1.3 56.4 - - - +
213A LEU 2.1 20.4 + - - -
214A CYS* 2.8 19.3 + - - -
215A ALA* 2.9 13.2 + - + -
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A SER 2.9 17.5 - - - +
209A ASP* 2.6 37.2 + - + +
211A LYS* 1.3 77.1 - - - +
213A LEU* 1.3 57.5 + - - +
215A ALA* 3.5 13.2 - - - +
216A VAL* 2.8 26.2 - - - +
257A LEU* 4.4 16.3 - - + +
261A THR* 4.7 10.7 - - - +
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ALA* 4.4 17.9 - - + -
192A PRO* 4.1 3.9 - - + +
195A LEU* 4.6 25.9 - - + +
196A VAL* 5.0 4.7 - - + -
199A PHE* 4.4 11.7 - - + -
205A LEU* 4.7 14.4 - - + -
209A ASP* 2.7 6.8 + - + +
210A TYR* 3.0 22.4 - - + +
211A LYS 2.1 18.0 + - - -
212A THR* 1.3 67.5 - - - +
214A CYS* 1.3 48.9 + - - +
215A ALA 2.8 4.3 - - - -
216A VAL* 2.6 12.1 + - + +
217A GLY* 2.5 30.0 + - - -
257A LEU* 3.7 29.2 - - + -
260A ILE* 3.9 25.1 - - + -
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Residues in contact with CYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLN* 3.9 27.4 - - - -
190A SER* 3.9 12.3 - - - +
191A ALA* 3.9 10.3 - - - +
192A PRO* 3.3 24.8 - - + +
210A TYR 3.0 9.7 + - - -
211A LYS* 2.8 19.8 + - - -
213A LEU* 1.3 69.6 - - - +
215A ALA* 1.3 73.6 + - - +
217A GLY* 2.7 8.5 + - - -
218A ASP* 3.1 18.4 + - - +
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LYS* 2.9 21.1 + - + +
212A THR* 3.5 16.2 - - - +
214A CYS* 1.3 85.1 - - - +
216A VAL* 1.3 58.9 + - + +
218A ASP* 3.0 9.6 - - - +
219A GLU* 2.7 34.8 + - + +
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Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 4.1 18.8 - - + -
212A THR* 2.8 28.0 - - - +
213A LEU* 2.6 17.6 + - + +
215A ALA* 1.3 70.7 - - + +
217A GLY* 1.3 67.8 + - - +
219A GLU* 3.9 12.7 + - + +
220A MSE 4.2 10.8 - - + +
227A PHE* 4.6 2.8 - - - -
230A LEU* 5.2 0.9 - - + -
260A ILE* 4.8 1.6 - - + -
261A THR* 4.3 24.9 - - + -
264A ALA* 3.9 30.7 - - + +
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Residues in contact with GLY 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A PRO* 3.2 31.0 - - - -
195A LEU* 5.0 0.6 - - - +
213A LEU 2.5 13.7 + - - -
214A CYS 2.7 10.7 + - - -
216A VAL* 1.3 76.8 - - - +
218A ASP* 1.3 59.9 + - - +
220A MSE 3.8 5.7 + - - +
222A ASN* 3.5 18.3 + - - +
227A PHE* 3.8 12.4 - - - -
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Residues in contact with ASP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A CYS* 3.1 10.1 + - - +
215A ALA* 3.0 10.3 - - - +
217A GLY* 1.3 69.4 - - - +
219A GLU* 1.3 79.2 + - - +
220A MSE 2.1 24.8 + - - -
221A GLY* 2.8 16.6 + - - -
222A ASN* 3.1 26.5 + - + +
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ALA* 2.7 37.4 + - + +
216A VAL* 4.2 8.1 - - + -
217A GLY 3.6 0.6 - - - -
218A ASP* 1.3 83.9 + - - +
220A MSE 1.3 49.3 + - + -
221A GLY 3.8 1.1 - - - -
268A THR* 2.5 33.3 + - - +
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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