Contacts of the helix formed by residues 211 - 223 (chain F) in PDB entry 2POZ
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 211 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275E GLY 4.9 0.2 - - - -
301E ASN* 3.4 23.1 - - - +
302E MSE 3.9 20.0 - - - +
303E ARG* 3.5 28.6 + - + +
327E ASN* 6.1 0.9 - - + -
174F ARG 5.7 0.4 - - - +
175F ARG* 3.5 22.1 + - + +
176F SER* 5.6 1.6 - - - +
210F LEU* 1.3 82.2 - - - +
212F THR* 1.3 67.9 + - - +
213F ASP* 2.6 22.8 + - - -
214F GLU* 3.3 6.8 + - - +
215F THR* 3.1 17.4 + - - -
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Residues in contact with THR 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E CYS 5.7 1.6 - - - -
275E GLY* 5.5 5.8 - - - -
300E TYR 4.6 1.9 + - - -
301E ASN* 3.1 36.1 + - - +
302E MSE 6.5 0.2 - - - -
211F THR* 1.3 72.3 - - - +
213F ASP* 1.3 65.2 + - - +
215F THR* 3.3 5.6 + - - -
216F ILE* 3.0 47.2 + - + +
241F ALA* 3.6 10.3 - - - +
244F VAL* 4.1 18.2 - - + -
245F ILE* 4.1 14.5 - - + +
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Residues in contact with ASP 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E PRO* 3.9 30.8 - - + +
275E GLY* 4.2 18.8 - - - +
276E ILE* 3.7 13.5 - - - +
303E ARG* 2.8 31.9 + - - -
211F THR* 2.6 30.2 + - - -
212F THR* 1.3 78.1 - - - +
214F GLU* 1.3 69.0 + - - +
216F ILE* 3.3 7.7 + - - +
217F ARG* 3.0 21.9 + - - +
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Residues in contact with GLU 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E CYS* 5.2 2.4 - - - -
303E ARG* 2.7 41.9 + - - +
182F ILE* 3.8 22.8 - - + +
210F LEU* 3.6 30.6 - - + +
211F THR* 3.3 4.2 + - - +
213F ASP* 1.3 82.4 + - - +
215F THR* 1.3 61.3 + - - +
217F ARG* 2.7 41.6 + - - +
218F PHE* 3.0 28.9 + - - +
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Residues in contact with THR 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F LEU* 4.1 15.3 - - + -
210F LEU* 3.0 32.6 + - - +
211F THR 3.1 13.1 + - - -
212F THR* 3.8 4.2 - - - -
214F GLU* 1.3 73.9 - - - +
216F ILE* 1.3 61.5 + - - +
218F PHE* 3.2 5.5 + - - +
219F CYS* 2.9 33.4 + - - -
233F PRO* 3.2 38.2 + - + +
245F ILE* 4.1 12.8 - - + -
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Residues in contact with ILE 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F THR* 3.0 40.1 + - + +
213F ASP* 3.6 6.5 - - - +
215F THR* 1.3 76.8 - - - +
217F ARG* 1.3 63.8 + - - +
219F CYS* 3.3 1.6 + - - +
220F ARG* 3.0 60.4 + - - +
244F VAL* 4.5 6.1 - - + -
245F ILE* 4.2 14.6 - - + -
248F GLN* 3.8 32.1 - - + +
249F ILE* 3.9 13.0 - - + +
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Residues in contact with ARG 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ASP* 4.5 12.9 + - - -
227E ILE 2.8 30.3 + - - -
228E CYS* 3.5 15.2 + - - +
251E LEU* 5.7 0.8 - - - +
252E PRO* 3.5 26.6 - - + +
182F ILE* 6.2 3.8 - - + -
213F ASP 3.0 15.5 + - - +
214F GLU* 2.7 45.4 + - - +
216F ILE* 1.3 80.3 - - - +
218F PHE* 1.3 62.0 + - - +
220F ARG* 3.4 8.6 + - - +
221F LYS* 3.0 26.5 + - + +
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Residues in contact with PHE 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F PRO* 4.4 5.6 - - + -
161F LEU* 4.4 8.5 - - + -
177F MSE 5.9 1.8 - - + -
182F ILE* 4.1 23.6 - - + -
185F ALA* 3.8 26.5 - - + -
186F TYR* 3.6 31.4 - - + -
189F VAL* 4.2 6.5 - - + -
206F LEU* 4.0 34.8 - - + -
210F LEU* 5.5 4.0 - - + -
214F GLU 3.0 17.2 + - - +
215F THR* 3.7 5.2 - - - +
217F ARG* 1.3 76.3 - - - +
219F CYS* 1.3 67.1 + - - +
221F LYS* 3.1 11.7 + - + +
222F ILE* 3.0 52.2 + - + +
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Residues in contact with CYS 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F LEU* 4.1 17.0 - - - -
215F THR* 2.9 35.3 + - - +
218F PHE* 1.3 78.9 - - - +
220F ARG* 1.3 62.0 + - - +
222F ILE* 3.4 12.7 - - - +
223F GLY* 3.2 17.7 + - - -
230F VAL* 4.2 12.8 - - - -
233F PRO* 5.0 0.9 - - - -
249F ILE* 3.7 40.6 - - + -
250F PRO* 4.5 2.7 - - - +
251F LEU* 3.7 13.8 - - + +
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Residues in contact with ARG 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E ILE 5.1 3.2 + - - -
250E PRO* 3.8 33.3 + - - +
216F ILE* 3.0 35.4 + - - +
217F ARG* 3.6 7.3 - - - +
219F CYS* 1.3 74.7 - - - +
221F LYS* 1.3 64.4 + - - +
223F GLY* 3.0 13.7 + - - -
224F GLU* 4.5 1.6 + - - +
248F GLN* 2.7 53.5 + - - +
249F ILE* 4.8 0.7 - - - -
250F PRO* 4.0 23.3 - - + +
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Residues in contact with LYS 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F ILE* 6.2 3.4 - - + -
183F GLU* 4.1 14.4 + - - +
186F TYR* 3.4 60.9 - - + -
187F ARG* 5.6 2.2 - - - +
217F ARG* 3.0 18.8 + - + +
218F PHE* 3.1 15.5 + - + +
220F ARG* 1.3 78.4 - - - +
222F ILE* 1.3 60.0 + - + +
223F GLY 3.3 0.7 + - - -
224F GLU* 3.9 15.6 - - - +
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Residues in contact with ILE 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F TYR* 3.9 19.3 - - + -
189F VAL* 4.2 16.2 - - + -
204F VAL* 4.3 20.6 - - + -
206F LEU* 5.9 0.2 - - + -
218F PHE* 3.0 51.5 + - + +
219F CYS* 3.4 18.8 - - - +
221F LYS* 1.3 72.0 - - - +
223F GLY* 1.3 64.3 + - - +
224F GLU 3.2 3.1 - - - -
225F LEU* 2.9 30.0 + - + +
227F ILE* 3.5 17.3 - - + +
230F VAL* 5.7 2.0 - - + -
251F LEU* 4.0 18.6 - - + -
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Residues in contact with GLY 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F CYS 3.2 10.5 + - - -
220F ARG 3.0 15.0 + - - -
222F ILE* 1.3 78.2 - - - +
224F GLU* 1.3 59.3 + - - +
225F LEU 3.1 1.5 + - - -
226F ASP* 3.6 10.9 + - - -
227F ILE 4.8 1.2 + - - -
250F PRO* 4.6 9.9 - - - -
251F LEU* 4.3 17.4 - - - +
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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