Contacts of the helix formed by residues 191 - 209 (chain B) in PDB entry 5A6C
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 ARG 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B GLY* 3.8 6.5 + - - +
190B ASP* 1.3 76.7 + - - +
192B ALA* 1.3 69.5 + - - +
193B ALA 3.1 1.1 - - - -
194B GLN* 2.9 35.0 + - - +
195B GLY* 2.9 22.2 + - - -
198B PHE* 5.5 1.8 - - - -
220B GLN* 5.8 2.0 - - - +
223B LEU* 3.9 20.0 - - - +
224B ILE* 3.8 21.8 - - + +
227B GLU* 3.2 40.4 + - - +
228B PHE* 4.1 11.9 - - + -
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A SER* 5.3 4.9 - - - +
190B ASP* 3.6 6.8 + - - +
191B ARG* 1.3 77.3 - - - +
193B ALA* 1.3 57.5 + - - +
195B GLY* 3.3 1.2 + - - -
196B ARG* 3.0 41.2 + - - +
221B ARG* 5.1 1.9 + - - -
224B ILE* 4.4 7.9 - - - +
228B PHE* 3.9 28.4 - - + -
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 6.1 0.2 - - - -
181B ASN* 4.7 2.5 - - - +
185B VAL* 4.2 19.5 - - + -
190B ASP* 3.1 34.5 + - + +
192B ALA* 1.3 75.9 - - - +
194B GLN* 1.3 65.4 + - - +
196B ARG* 3.1 5.4 + - - +
197B ALA* 2.9 23.2 + - - +
380B GLU* 4.4 19.1 - - - +
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Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 3.8 11.6 - - + +
185B VAL* 2.8 39.8 - - + +
186B THR* 3.1 27.5 + - - +
189B GLY* 4.6 2.6 - - - -
190B ASP 2.9 16.3 + - - +
191B ARG* 2.9 45.8 + - - +
193B ALA* 1.3 79.5 - - - +
195B GLY* 1.3 56.1 + - - +
197B ALA* 3.5 3.4 + - - +
198B PHE* 2.9 45.2 + - + -
224B ILE* 4.6 1.3 - - + -
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Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ARG 2.9 11.4 + - - -
192B ALA 3.7 2.9 - - - -
194B GLN* 1.3 73.4 - - - +
196B ARG* 1.3 61.1 + - - +
198B PHE* 3.3 6.1 + - - +
199B GLY 2.9 24.3 + - - -
221B ARG* 3.3 22.1 - - - -
224B ILE* 3.8 27.1 - - - +
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Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 3.9 20.0 - - + +
192B ALA* 3.0 22.9 + - - +
193B ALA* 3.1 8.5 + - - +
195B GLY* 1.3 76.3 - - - +
197B ALA* 1.3 63.1 + - - +
199B GLY 3.2 1.6 + - - -
200B ASN* 3.1 22.9 + - - +
221B ARG* 4.2 7.0 - - - +
377B GLU* 3.4 35.2 + - + +
378B GLU* 3.5 30.2 + - - +
379B GLU 5.5 1.8 + - - -
380B GLU* 3.8 36.8 + - - +
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Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 4.4 12.0 - - + -
178B TYR* 4.3 19.6 - - + +
181B ASN* 3.6 25.8 - - - +
182B LEU* 4.4 13.0 - - + -
193B ALA 2.9 9.6 + - - +
194B GLN* 3.6 9.0 - - - +
196B ARG* 1.3 77.8 - - - +
198B PHE* 1.3 56.9 + - - +
200B ASN* 4.1 0.9 - - - +
201B LEU* 2.9 34.0 + - - +
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Residues in contact with PHE 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 3.6 39.7 - - + -
186B THR* 5.9 1.1 - - - -
191B ARG* 5.5 0.9 - - - -
194B GLN* 2.9 40.9 + - + +
195B GLY* 3.5 8.3 - - - +
196B ARG 3.3 0.4 - - - -
197B ALA* 1.3 71.7 - - - +
199B GLY* 1.3 69.8 + - - +
201B LEU* 3.4 6.4 + - + -
202B GLY* 2.9 17.7 + - - -
216B ILE* 6.0 1.6 - - + -
217B ALA* 3.5 41.0 - - + +
218B HIS 4.5 0.2 + - - -
220B GLN* 3.4 41.7 - - + -
221B ARG 3.9 6.1 - - - +
224B ILE* 4.2 5.6 - - + -
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Residues in contact with GLY 199 (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 GLY 2.9 14.4 + - - -
196B ARG 3.2 4.0 + - - -
198B PHE* 1.3 73.5 - - - +
200B ASN* 1.3 56.9 + - - +
202B GLY* 2.7 25.3 + - - -
203B ASN* 2.9 13.6 + - - +
218B HIS* 3.6 12.8 - - - -
221B ARG* 3.7 16.7 - - - +
240B ASN* 5.9 0.7 - - - -
375B TYR 5.8 0.7 - - - -
377B GLU* 4.2 8.3 - - - -
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Residues in contact with ASN 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 3.4 15.2 + - - -
143B ASN* 3.2 14.8 + - - +
146B HIS* 4.5 3.4 + - + -
178B TYR* 3.1 36.5 + - + +
196B ARG 3.1 13.0 + - - +
197B ALA 4.3 0.2 - - - +
199B GLY* 1.3 73.1 - - - +
201B LEU* 1.3 52.7 + - - +
203B ASN* 3.7 8.7 - - - +
204B THR* 2.6 37.6 + - - -
376B ASN* 3.6 13.4 - - - +
377B GLU* 2.7 36.2 + - - +
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 3.8 30.5 - - + +
178B TYR* 3.5 32.7 - - + +
179B GLU* 4.2 20.4 - - + +
182B LEU* 4.9 14.4 - - + -
197B ALA 2.9 20.8 + - - +
198B PHE* 3.9 7.2 - - + +
200B ASN* 1.3 74.8 - - - +
202B GLY* 1.3 66.5 + - - +
204B THR* 4.2 1.6 - - - -
205B HIS* 3.0 54.0 + - + +
217B ALA* 4.8 7.2 - - + -
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Residues in contact with GLY 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 PHE 2.9 9.3 + - - -
199B GLY 2.7 8.4 + - - -
201B LEU* 1.3 77.0 - - - +
203B ASN* 1.3 55.5 + - - +
205B HIS 3.2 1.7 + - - -
206B TYR* 2.8 28.9 + - - +
214B ALA* 3.3 19.0 - - - +
217B ALA* 4.2 5.6 - - - +
218B HIS* 3.2 24.2 - - - -
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Residues in contact with ASN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B HIS* 4.0 5.6 - - + +
199B GLY 2.9 12.2 + - - +
200B ASN* 3.7 9.8 + - - +
202B GLY* 1.3 77.6 - - - +
204B THR* 1.3 56.8 + - - +
206B TYR* 3.1 9.8 - - + +
207B LEU* 2.9 35.0 + - + +
218B HIS* 3.3 4.9 + - - -
240B ASN* 2.4 25.9 + - - +
374B ALA* 4.0 11.6 - - - +
375B TYR 2.9 26.9 + - - +
376B ASN* 2.8 33.5 + - - +
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Residues in contact with THR 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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146B HIS* 3.6 16.6 + - - -
171B LEU* 3.3 39.2 - - + +
174B ALA* 3.8 13.7 - - + -
175B VAL* 3.6 13.9 - - + +
178B TYR* 3.5 13.9 - - - -
200B ASN 2.6 23.8 + - - -
201B LEU* 3.9 7.0 - - - -
202B GLY 3.3 0.4 - - - -
203B ASN* 1.3 73.2 - - - +
205B HIS* 1.3 61.2 + - - +
207B LEU* 3.8 3.5 + - - +
208B LEU* 3.0 30.2 + - - +
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Residues in contact with HIS 205 (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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175B VAL* 4.2 26.4 - - + +
179B GLU* 4.7 5.6 + - - -
201B LEU* 3.0 48.7 + - + +
202B GLY* 3.5 4.7 - - - +
204B THR* 1.3 74.5 - - - +
206B TYR* 1.3 58.7 + - - +
208B LEU* 2.7 25.5 + - - +
209B GLY 2.8 12.3 + - - -
210B ASN* 3.2 33.7 + - - +
213B ASP* 3.8 40.4 - - + +
214B ALA* 3.6 6.1 - - + -
217B ALA* 4.9 2.2 - - + -
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Residues in contact with TYR 206 (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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157B PRO* 3.2 47.9 - - + +
202B GLY 2.8 13.9 + - - +
203B ASN* 3.1 17.5 - - + +
205B HIS* 1.3 77.7 - - - +
207B LEU* 1.3 82.9 + - + +
209B GLY 3.3 6.8 + - - -
211B PHE* 3.6 24.6 - + - -
214B ALA* 3.8 11.3 - - + +
218B HIS* 4.7 4.9 - - + +
240B ASN 5.9 0.7 - - - -
243B ASN* 4.0 23.0 - - + +
244B ALA* 4.8 8.1 - - + -
247B PHE* 3.7 25.3 - + - -
372B PHE* 3.8 18.9 + - - +
374B ALA* 4.0 26.7 - - + -
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Residues in contact with LEU 207 (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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146B HIS* 3.6 27.6 - - + +
150B LYS* 3.9 25.6 - - + -
155B PRO* 4.1 7.9 - - + +
156B GLY* 3.5 34.2 - - - +
157B PRO* 3.8 6.6 - - - +
158B GLN 3.8 18.9 + - - -
163B PHE* 6.1 0.2 - - - +
171B LEU* 3.7 24.4 - - + +
203B ASN* 2.9 19.1 + - + +
204B THR 4.1 1.6 - - - +
206B TYR* 1.3 91.5 - - + +
208B LEU* 1.3 62.6 + - - +
209B GLY 3.5 0.2 + - - -
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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
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158B GLN 4.5 6.7 - - - +
163B PHE* 6.0 2.8 - - + +
168B ARG* 3.3 50.6 + - - +
171B LEU* 3.8 31.9 - - + +
172B GLN* 3.9 16.2 - - - +
175B VAL* 3.5 31.6 - - + -
204B THR 3.0 16.5 + - - +
205B HIS* 2.7 16.4 + - - +
207B LEU* 1.3 73.4 - - - +
209B GLY* 1.3 55.3 + - - -
210B ASN* 3.4 18.2 - - - +
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Residues in contact with GLY 209 (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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157B PRO 6.0 0.2 - - - -
158B GLN 4.8 9.9 - - - -
205B HIS 2.8 7.7 + - - -
206B TYR 3.3 8.9 + - - -
207B LEU 3.4 0.6 - - - -
208B LEU* 1.3 75.0 - - - +
210B ASN* 1.3 63.1 + - - +
211B PHE* 3.2 31.1 + - - -
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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
------------------------------------------------------------
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