Contacts of the helix formed by residues 213 - 226 (chain B) in PDB entry 1O5K
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 ALA 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B VAL* 2.8 16.7 + - + +
210B SER* 3.8 4.0 - - - -
212B VAL* 1.3 79.3 - - - +
214B PRO* 1.3 64.4 - - - +
215B LYS 3.4 0.2 + - - -
216B GLN* 3.3 23.8 + - - +
217B MET* 3.3 22.5 + - - +
239B LEU* 4.3 9.2 - - + -
242B LEU* 4.0 22.2 - - + -
293B LEU* 4.1 5.6 - - + -
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Residues in contact with PRO 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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29B TYR* 3.5 27.4 - - + +
30B GLN* 3.8 5.6 - - - +
33B ASN* 3.7 26.2 - - + +
35B VAL* 3.7 21.0 - - + +
210B SER* 3.2 28.0 - - - +
212B VAL 3.3 9.0 - - - +
213B ALA* 1.3 88.9 - - - +
215B LYS* 1.3 64.5 + - - +
216B GLN* 4.6 1.1 - - - +
217B MET* 3.4 1.4 + - - +
218B VAL* 3.0 30.0 + - - +
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 3.8 32.9 - - + +
213B ALA 3.4 0.6 - - - -
214B PRO* 1.3 82.6 - - - +
216B GLN* 1.3 71.2 + - + +
218B VAL* 3.4 4.4 + - + +
219B GLU* 2.9 31.8 + - + +
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Residues in contact with GLN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 5.6 0.2 + - - -
213B ALA* 3.3 33.9 - - + +
214B PRO* 4.6 1.2 - - - +
215B LYS* 1.3 89.5 - - + +
217B MET* 1.3 60.6 + - - +
219B GLU* 3.3 13.8 + - - +
220B LEU* 3.0 23.2 + - - +
235B VAL* 3.3 15.1 - - + +
239B LEU* 4.1 25.8 - - + -
291B SER 5.2 5.9 - - - +
293B LEU* 4.5 14.9 - - - +
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Residues in contact with MET 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.4 19.0 - - + +
191B ASP* 3.8 19.5 - - - +
194B THR* 4.1 13.0 - - + +
205B VAL* 3.8 22.0 - - + -
207B SER* 3.9 12.8 - - - +
209B VAL* 4.2 9.6 - - + -
210B SER* 4.0 14.8 - - - +
213B ALA 3.3 15.8 + - - +
214B PRO 4.0 2.7 - - - +
216B GLN* 1.3 73.2 - - - +
218B VAL* 1.3 66.8 + - - +
220B LEU* 3.4 19.2 + - + +
221B CYS* 3.3 19.1 + - - -
239B LEU* 3.6 23.1 - - + -
243B MET* 3.9 14.6 - - + -
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.7 18.6 - - + -
33B ASN 3.6 15.9 - - - +
34B GLY* 3.5 31.2 - - - +
35B VAL* 3.9 7.6 - - + +
36B ASN* 5.2 4.3 - - - +
214B PRO 3.0 19.0 + - - +
215B LYS* 3.5 7.0 - - + +
217B MET* 1.3 77.0 - - - +
219B GLU* 1.3 56.0 + - - +
221B CYS* 3.3 3.9 + - - +
222B ALA* 2.8 33.6 + - + +
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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 LYS* 2.9 21.5 + - + +
216B GLN* 3.4 19.7 - - - +
217B MET 3.2 0.2 - - - -
218B VAL* 1.3 73.6 - - - +
220B LEU* 1.3 66.2 + - - +
222B ALA* 4.2 6.3 - - + -
223B GLU* 2.8 46.8 + - + +
235B VAL* 3.9 23.4 - - + +
238B LYS* 5.0 7.7 + - - -
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Residues in contact with LEU 220 (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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194B THR* 3.9 18.6 - - + -
195B PHE* 4.3 8.7 - - - +
198B LEU* 3.7 19.7 - - + -
216B GLN 3.0 12.4 + - - +
217B MET* 3.5 26.2 - - + +
219B GLU* 1.3 77.0 - - - +
221B CYS* 1.3 62.9 + - - +
224B TYR* 3.4 4.0 + - - +
232B SER* 2.7 47.4 + - - +
235B VAL* 3.9 13.6 - - + +
236B HIS* 3.9 29.4 - - + +
239B LEU* 4.4 4.7 - - + -
243B MET* 4.3 11.9 - - + -
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Residues in contact with CYS 221 (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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4B GLY* 4.1 18.6 - - - -
5B VAL* 3.9 15.0 - - + -
194B THR* 4.2 25.1 - - - -
198B LEU* 4.1 11.7 - - + -
204B GLY* 4.3 5.2 - - - -
205B VAL* 4.3 2.7 - - - -
217B MET 3.3 13.1 + - - +
218B VAL* 3.7 6.1 - - - +
219B GLU 3.2 0.4 - - - -
220B LEU* 1.3 78.2 - - - +
222B ALA* 1.3 59.3 + - - +
224B TYR* 3.1 4.0 + - - +
225B PHE* 2.8 50.7 + - + -
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Residues in contact with ALA 222 (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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218B VAL* 2.8 28.5 + - + +
219B GLU* 3.8 7.6 - - - +
221B CYS* 1.3 72.1 - - - +
223B GLU* 1.3 59.9 + - + +
225B PHE* 3.2 9.0 + - - +
226B SER* 2.8 32.6 + - - -
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Residues in contact with GLU 223 (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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219B GLU* 2.8 41.1 + - + +
222B ALA* 1.3 73.6 - - + +
224B TYR* 1.3 66.6 + - - +
226B SER* 2.9 9.7 + - - -
228B ASN* 2.7 60.2 + - - +
231B LYS* 3.7 27.8 - - + +
232B SER* 3.8 22.4 - - - +
235B VAL* 5.0 1.3 - - + -
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Residues in contact with TYR 224 (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 PHE* 4.7 5.4 - + - -
198B LEU* 3.1 49.0 + - + -
199B CYS* 3.5 36.5 + - - -
202B GLY 5.8 0.7 - - - -
220B LEU 3.4 12.3 + - - +
221B CYS 3.1 8.8 + - - +
223B GLU* 1.3 78.6 - - - +
225B PHE* 1.3 73.9 + + - +
227B GLY* 2.8 23.7 + - - -
228B ASN 4.5 2.9 - - - +
229B LEU* 4.1 19.3 - - + +
232B SER* 3.7 18.3 - - - +
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Residues in contact with PHE 225 (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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3B ARG* 3.6 43.5 - - + +
4B GLY* 3.8 26.9 - - - -
198B LEU* 3.6 30.3 - - + -
202B GLY 4.3 0.7 - - - -
203B ASP 3.7 18.2 - - - -
221B CYS* 2.8 27.2 + - + +
222B ALA* 3.8 7.4 - - - +
224B TYR* 1.3 87.2 - + - +
226B SER* 1.3 60.4 + - - +
227B GLY 3.2 1.1 + - - -
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Residues in contact with SER 226 (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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222B ALA 2.8 15.4 + - - -
223B GLU* 2.9 13.2 + - - -
225B PHE* 1.3 77.1 - - - +
227B GLY* 1.3 56.0 + - - +
228B ASN* 2.7 34.0 + - - +
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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