Contacts of the helix formed by residues 197 - 215 (chain B) in PDB entry 5HQ0
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 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 3.8 7.6 - - - +
194B ARG 5.0 4.0 - - - +
195B GLU 3.6 8.9 + - - +
196B VAL* 1.3 78.1 - - - +
198B GLY* 1.3 58.3 + - - +
199B ASN* 3.7 10.6 + - - +
200B MET* 3.2 28.8 + - - +
201B ARG* 2.9 28.8 + - - +
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Residues in contact with GLY 198 (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 LEU* 4.0 3.6 - - - +
197B THR* 1.3 73.9 - - - +
199B ASN* 1.3 58.4 + - - +
201B ARG* 3.3 6.6 + - - +
202B ALA* 2.9 27.9 + - - +
331B LEU 4.9 0.3 - - - +
333B TYR* 3.7 47.0 - - - +
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Residues in contact with ASN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 3.2 9.4 + - - +
198B GLY* 1.3 78.3 - - - +
200B MET* 1.3 56.7 + - + +
202B ALA* 3.1 8.8 + - - +
203B ILE* 3.0 36.0 + - + +
396B HIS* 4.6 4.1 - - + -
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Residues in contact with MET 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU 3.8 13.9 - - - +
196B VAL* 3.9 3.1 - - + -
197B THR* 3.2 34.8 + - - +
199B ASN* 1.3 73.9 - - + +
201B ARG* 1.3 66.6 + - - +
203B ILE* 3.3 17.0 + - + +
204B LEU* 3.0 22.7 + - - +
240B LYS* 3.7 42.6 - - + +
243B LEU* 4.0 23.8 - - + +
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Residues in contact with ARG 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR* 3.6 13.4 + - - +
191B LEU* 4.4 8.1 - - + -
196B VAL* 4.5 2.7 - - + +
197B THR 2.9 13.6 + - - +
198B GLY* 3.4 8.5 - - - +
200B MET* 1.3 78.2 - - - +
202B ALA* 1.3 55.8 + - - +
204B LEU* 3.3 11.7 + - + +
205B ILE* 3.0 46.4 + - + +
226B VAL* 3.8 6.9 - - - +
229B ILE* 5.6 7.0 - - + -
230B ASP* 2.8 39.8 + - - +
233B MET* 6.3 2.9 - - - -
243B LEU* 4.5 6.2 - - + +
329B THR 5.3 0.4 + - - -
330B MET* 2.9 28.7 + - - +
331B LEU 3.4 19.2 + - - -
332B ASP 4.0 4.9 - - - +
333B TYR* 4.1 18.7 - - - +
336B VAL* 3.4 21.6 - - - +
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Residues in contact with ALA 202 (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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198B GLY 2.9 12.3 + - - +
199B ASN* 3.1 10.9 + - - +
201B ARG* 1.3 74.1 - - - +
203B ILE* 1.3 65.9 + - - +
205B ILE* 3.2 3.7 + - - +
206B ASP* 3.0 26.9 + - - +
331B LEU* 3.4 32.6 + - + +
396B HIS* 3.7 21.8 - - + +
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Residues in contact with ILE 203 (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 ASN* 3.0 20.0 + - + +
200B MET* 3.6 16.8 - - + +
202B ALA* 1.3 75.3 - - - +
204B LEU* 1.3 64.6 + - - +
206B ASP* 3.8 1.8 - - - +
207B TRP* 3.0 25.4 + - + +
396B HIS* 3.6 24.6 + - + +
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Residues in contact with LEU 204 (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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200B MET 3.0 12.5 + - - +
201B ARG* 3.5 12.3 - - + +
202B ALA 3.2 0.2 - - - -
203B ILE* 1.3 79.3 - - - +
205B ILE* 1.3 59.7 + - + +
207B TRP* 3.2 20.5 + - + +
208B LEU* 2.8 46.2 + - + +
229B ILE* 4.4 16.6 - - + -
243B LEU* 3.6 40.2 - - + +
244B GLN* 3.8 26.5 - - + +
247B GLY* 4.1 14.8 - - - +
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ARG* 3.0 64.2 + - + +
202B ALA 3.2 2.9 + - - +
204B LEU* 1.3 74.8 - - + +
206B ASP* 1.3 61.1 + - - +
208B LEU* 3.0 16.7 + - + +
209B VAL* 2.9 30.3 + - + +
222B MET* 5.3 1.3 - - - -
226B VAL* 4.2 24.0 - - + -
229B ILE* 4.9 9.6 - - + -
230B ASP* 5.4 0.4 - - - +
330B MET* 3.5 26.0 - - + +
331B LEU* 4.0 20.9 - - + -
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Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ALA 3.0 16.7 + - - +
203B ILE 3.8 3.4 - - - +
205B ILE* 1.3 75.9 - - - +
207B TRP* 1.3 63.5 + - - +
209B VAL* 3.1 17.4 + - - +
210B GLN* 3.2 27.9 + - - +
331B LEU* 3.7 16.7 - - + +
395B LYS 5.1 1.2 - - - +
396B HIS* 3.6 32.7 - - + +
397B MET 4.9 0.3 + - - -
398B THR* 2.8 41.1 + - - -
399B VAL* 4.7 0.9 + - - +
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Residues in contact with TRP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 3.0 18.8 + - + +
204B LEU* 3.4 19.3 - - + +
206B ASP* 1.3 76.9 + - - +
208B LEU* 1.3 90.6 + - + +
210B GLN* 3.1 28.0 + - + +
211B VAL* 3.1 39.1 + - + +
244B GLN* 3.3 36.6 - - + +
248B VAL* 3.4 34.1 - - + -
271B VAL* 3.5 27.4 + - + -
272B THR* 4.0 1.3 - - + -
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 2.8 24.9 + - + +
205B ILE* 3.0 15.0 + - + +
207B TRP* 1.3 102.0 - - + +
209B VAL* 1.3 54.9 + - - +
211B VAL* 3.3 4.8 + - + +
212B GLN 2.9 23.0 + - - -
222B MET* 3.1 16.3 - - - +
225B THR* 4.0 9.4 - - + -
226B VAL* 6.1 0.7 - - + -
229B ILE* 3.6 30.5 - - + -
247B GLY* 3.8 25.6 - - - +
248B VAL* 4.2 2.7 - - + +
251B MET* 3.4 27.5 - - + +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 2.9 28.2 + - + +
206B ASP* 3.1 9.8 + - - +
208B LEU* 1.3 73.3 - - - +
210B GLN* 1.3 57.5 + - - +
212B GLN* 3.1 15.1 + - - +
213B MET* 2.9 38.6 + - - +
222B MET* 3.6 22.7 - - + -
327B GLU* 4.8 3.4 - - + +
330B MET* 4.9 5.2 - - - -
331B LEU* 5.0 1.1 - - + -
398B THR* 3.6 18.8 - - + -
399B VAL* 4.0 26.2 - - + -
402B LYS* 4.4 7.6 - - + -
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Residues in contact with GLN 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 ASP* 3.2 30.3 + - - +
207B TRP* 3.1 26.1 + - + +
209B VAL* 1.3 77.5 - - - +
211B VAL* 1.3 56.8 + - + +
213B MET* 3.4 7.6 + - - +
214B LYS* 3.0 28.4 + - - +
398B THR* 3.4 25.1 + - + +
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Residues in contact with VAL 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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207B TRP* 3.1 52.2 + - + +
208B LEU* 3.6 7.9 - - + +
209B VAL 3.2 0.2 - - - -
210B GLN* 1.3 73.0 - - + +
212B GLN* 1.3 65.9 + - - +
214B LYS* 3.2 7.1 + - - +
215B PHE* 3.0 47.7 + - + +
248B VAL* 6.0 0.7 - - + -
251B MET* 3.6 21.3 - - - -
268B PHE* 4.5 2.7 - - + -
271B VAL* 4.1 20.6 - - + -
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Residues in contact with GLN 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 LEU 2.9 6.5 + - - -
209B VAL* 3.2 15.4 - - - +
211B VAL* 1.3 77.6 - - - +
213B MET* 1.3 58.5 + - - +
215B PHE 3.5 0.3 + - - -
216B ARG* 2.9 23.9 + - - -
217B LEU* 3.0 56.6 + - + +
218B LEU 3.5 10.5 + - - -
219B GLN* 3.0 27.3 + - - +
221B THR* 6.3 0.2 - - + -
222B MET* 3.0 39.1 - - + +
251B MET* 4.3 1.7 - - + +
402B LYS* 3.4 19.5 + - - +
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Residues in contact with MET 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 VAL* 2.9 26.5 + - + +
210B GLN* 3.8 7.0 - - - +
211B VAL 3.2 0.2 - - - -
212B GLN* 1.3 78.2 - - - +
214B LYS* 1.3 67.3 + - - +
216B ARG* 3.1 25.5 + - - +
398B THR* 4.3 11.4 - - - +
401B ASN* 5.7 0.7 - - + -
402B LYS* 3.8 51.6 - - + +
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Residues in contact with LYS 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 GLN 3.0 18.0 + - - +
211B VAL* 3.2 4.7 + - - +
213B MET* 1.3 77.9 - - - +
215B PHE* 1.3 82.8 + - + +
216B ARG* 3.5 6.1 + - - +
270B PHE* 5.3 14.7 - - - -
271B VAL* 4.0 26.7 - - + +
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Residues in contact with PHE 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 VAL* 3.0 32.3 + - + +
214B LYS* 1.3 101.6 - - + +
216B ARG* 1.3 69.4 + - - +
217B LEU* 3.3 24.2 + - + +
263B PRO* 3.8 21.2 - - + +
267B ASP* 3.6 41.1 - - + -
268B PHE* 3.6 31.0 - + - -
271B VAL* 4.3 11.2 - - + -
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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
------------------------------------------------------------
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