Contacts of the helix formed by residues 209 - 219 (chain B) in PDB entry 2O2C
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 ASP 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B ASN* 4.4 5.6 + - - +
204B GLY 3.3 16.7 - - - +
205B ILE* 3.8 7.4 - - - -
206B GLY 3.0 5.9 + - - +
207B GLY 3.3 1.8 + - - -
208B SER* 1.3 80.0 - - - +
210B LEU* 1.3 78.9 + - - +
211B GLY 3.4 1.6 - - - -
212B PRO* 3.4 8.4 - - - +
213B VAL* 3.0 46.5 + - - +
231B PHE* 3.8 16.1 - - - +
232B VAL 5.0 0.2 - - - +
233B SER* 3.7 26.0 + - - -
439C ASN* 4.2 5.9 + - - -
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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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206B GLY* 2.8 24.6 + - - +
207B GLY* 5.6 0.2 - - - -
209B ASP* 1.3 87.6 - - - +
211B GLY* 1.3 58.5 + - - +
213B VAL* 3.8 7.4 - - + +
214B MET* 2.9 32.6 + - - +
400B ARG* 5.1 10.3 - - - +
403B ALA* 3.6 36.8 - - + +
404B TYR* 3.7 15.5 - - + +
407B GLN* 3.3 29.2 - - + +
439C ASN* 5.7 5.2 - - + +
443C ALA* 4.5 12.1 - - + -
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Residues in contact with GLY 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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206B GLY 4.7 0.8 + - - -
207B GLY* 4.8 4.1 + - - -
209B ASP 4.7 0.2 - - - +
210B LEU* 1.3 76.4 - - - +
212B PRO* 1.4 66.7 - - - +
214B MET* 3.8 1.2 - - - +
215B ALA* 2.9 34.3 + - - +
329B MET* 4.1 12.8 - - - -
337B ILE* 4.5 5.4 - - - -
404B TYR* 3.4 25.7 - - - -
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Residues in contact with PRO 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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202B ASN* 4.6 3.4 - - - +
207B GLY 4.6 1.6 - - - +
208B SER 4.6 3.6 - - - +
209B ASP* 3.4 20.0 - - - +
211B GLY* 1.4 87.6 - - - +
213B VAL* 1.3 53.8 + - - +
216B THR* 2.8 39.6 + - - +
231B PHE* 3.7 20.4 - - + -
329B MET* 4.9 3.4 - - + -
333B ILE* 3.6 40.4 - - + +
336B PRO* 3.9 15.3 - - + -
337B ILE* 3.9 13.7 - - + -
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Residues in contact with VAL 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 ASP* 3.0 34.7 + - - +
210B LEU* 3.8 10.5 - - + +
212B PRO* 1.3 75.2 - - - +
214B MET* 1.3 65.1 + - - +
216B THR* 3.2 7.3 + - - -
217B GLU* 3.1 33.3 + - + +
231B PHE* 3.5 35.2 - - + -
399B TRP* 5.7 1.3 - - + -
400B ARG* 3.8 30.3 - - + +
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Residues in contact with MET 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 22.0 + - - +
211B GLY 4.1 1.6 - - - +
213B VAL* 1.3 73.0 - - - +
215B ALA* 1.3 64.8 + - - +
217B GLU* 3.7 1.9 - - - +
218B ALA* 2.9 32.6 + - + +
329B MET* 3.8 29.8 - - + -
397B TYR 4.6 1.2 - - - +
398B LEU* 4.9 2.6 - - + -
400B ARG* 3.9 33.5 - - + +
401B LEU* 3.9 18.4 - - + +
404B TYR* 3.9 18.2 - - + -
539B LEU* 3.9 24.2 - - + -
543B ILE* 3.7 24.5 - - + -
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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 GLY 2.9 21.0 + - - +
214B MET* 1.3 77.6 - - - +
216B THR* 1.3 60.4 + - - +
219B LEU* 2.9 36.6 + - + +
329B MET* 4.1 17.3 - - + -
337B ILE* 3.6 32.5 - - + +
349B LEU* 5.0 0.7 - - + -
539B LEU* 4.0 11.4 - - + -
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Residues in contact with THR 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 PRO* 2.8 26.4 + - + +
213B VAL 3.2 7.3 + - - -
215B ALA* 1.3 76.2 - - - +
217B GLU* 1.3 64.8 + - - +
219B LEU* 3.8 2.3 - - - -
220B LYS* 3.3 24.6 + - - +
229B LEU* 4.7 6.3 - - + -
231B PHE* 3.4 26.2 - - + -
336B PRO 4.1 4.0 - - - +
337B ILE* 3.9 30.1 - - + +
340B SER* 4.1 23.9 + - - -
341B ILE* 5.7 2.2 - - - +
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Residues in contact with GLU 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 VAL* 3.1 30.0 + - + +
214B MET* 3.7 4.9 - - - +
216B THR* 1.3 83.3 + - - +
218B ALA* 1.3 61.7 + - - +
219B LEU 3.5 0.5 + - - -
220B LYS* 3.6 27.8 + - - +
231B PHE* 5.6 4.7 - - + -
397B TYR* 3.3 35.7 - - - +
399B TRP* 2.8 42.0 + - + +
400B ARG* 4.7 3.6 - - + -
7006B GOL 4.4 8.1 + - - -
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Residues in contact with ALA 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 MET* 2.9 18.9 + - - +
215B ALA 3.7 3.8 - - - +
217B GLU* 1.3 78.0 - - - +
219B LEU* 1.3 63.9 + - + +
220B LYS 3.5 1.7 + - - -
221B PRO* 4.2 3.6 - - - +
397B TYR* 3.3 26.9 - - - +
398B LEU* 3.8 27.1 - - + -
534B LEU* 3.9 12.5 - - + +
539B LEU* 3.9 19.3 - - + -
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Residues in contact with LEU 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 2.9 19.1 + - - +
216B THR 3.8 3.8 - - - -
218B ALA* 1.3 84.6 - - + +
220B LYS* 1.3 62.4 + - - +
221B PRO* 3.3 4.9 - - - -
222B PHE* 3.0 26.9 + - + +
223B SER* 3.6 4.6 + - - -
337B ILE* 5.0 1.1 - - + -
341B ILE* 3.7 40.5 - - + +
349B LEU* 4.5 10.1 - - + -
534B LEU* 4.3 7.0 - - + +
535B THR 3.9 8.1 - - - +
536B PRO* 3.7 38.4 - - + -
539B LEU* 3.9 25.8 - - + -
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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