Contacts of the helix formed by residues 191 - 208 (chain B) in PDB entry 3M0V
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 ASN 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B SER* 1.3 73.1 - - - +
192B PHE* 1.3 66.7 + - - +
193B THR* 3.1 10.4 + - - -
194B ARG* 3.0 57.0 + - + +
195B ALA* 3.0 22.4 + - - +
198B ARG* 5.0 3.6 + - - +
308D GLU* 5.7 1.2 - - - +
311D ASP* 3.0 33.0 + - - +
315D ARG* 4.2 1.2 - - - +
365D GLN* 3.7 26.2 + - + +
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B SER* 4.7 1.8 - - - -
188B GLY 6.1 0.7 - - - -
190B SER* 3.5 14.0 + - - -
191B ASN* 1.3 71.4 + - - +
193B THR* 1.3 64.0 + - - +
195B ALA* 3.6 4.9 + - - +
196B PHE 3.2 16.5 + - - -
228B TYR* 3.6 31.2 - + - -
229B SER* 3.4 26.2 - - - -
231B VAL* 6.0 0.2 - - - +
263D ASN* 4.1 6.1 - - - -
265D GLU* 3.7 22.0 - - + -
266D MET* 3.7 35.6 - - + +
269D ALA* 3.8 13.0 - - + -
270D ARG* 3.3 22.0 + - - +
308D GLU* 3.4 34.6 + - - +
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Residues in contact with THR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASN* 3.2 8.5 + - - -
192B PHE* 1.3 73.9 - - - +
194B ARG* 1.3 62.5 + - - +
196B PHE* 3.2 4.2 + - - +
197B GLU* 2.9 45.7 + - - +
269D ALA* 3.8 24.8 + - - +
270D ARG* 4.5 2.0 - - - +
273D GLN* 3.6 32.2 + - + +
308D GLU* 5.1 0.9 + - - -
315D ARG* 3.7 37.9 + - - +
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Residues in contact with ARG 194 (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 ASN* 3.0 48.0 + - + +
193B THR* 1.3 75.4 - - - +
195B ALA* 1.3 63.0 + - - +
197B GLU* 3.1 20.0 + - - +
198B ARG* 2.9 45.1 + - - +
311D ASP* 4.5 2.4 + - - -
314D ALA 5.8 0.2 - - - -
315D ARG* 3.9 37.1 + - - +
362D SER* 5.6 7.2 + - - -
365D GLN* 4.8 4.6 + - - -
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B SER* 3.4 17.1 - - - +
190B SER* 4.8 11.0 - - - -
191B ASN 3.0 18.8 + - - +
192B PHE* 3.9 5.8 - - - +
194B ARG* 1.3 76.8 - - - +
196B PHE* 1.3 58.5 + - - +
198B ARG* 3.3 25.3 + - - +
199B TYR* 3.0 22.3 + - - +
231B VAL* 4.3 19.1 - - + -
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Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE 3.2 14.5 + - - +
193B THR 3.2 5.5 + - - +
195B ALA* 1.3 76.4 - - - +
197B GLU* 1.3 61.5 + - - +
199B TYR* 3.3 5.1 + + - -
200B LEU* 2.9 52.6 + - + +
231B VAL* 3.9 19.9 - - + +
237B THR* 3.5 29.8 - - + -
240B LEU* 4.3 7.2 - - + -
241B ILE* 3.5 28.5 - - + -
270D ARG* 3.6 29.8 - - - +
273D GLN* 3.3 24.2 - - - +
274D PHE* 3.8 23.3 - + - -
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B THR* 2.9 31.2 + - - +
194B ARG* 3.1 25.3 + - - +
196B PHE* 1.3 77.4 - - - +
198B ARG* 1.3 62.5 + - + +
200B LEU* 3.3 9.2 + - - +
201B SER* 3.0 24.1 + - - -
273D GLN* 3.9 19.4 + - - +
315D ARG* 6.1 0.3 - - - -
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Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU 3.5 8.4 - - - +
147B SER* 2.9 25.6 + - - -
148B HIS 3.4 17.5 + - - -
149B THR* 3.6 28.6 - - - +
154B ARG* 3.7 30.3 + - - +
190B SER* 5.7 2.8 - - - +
191B ASN* 5.0 5.3 + - - +
194B ARG* 2.9 42.2 + - - +
195B ALA* 3.4 31.0 - - - +
196B PHE 3.2 0.2 - - - -
197B GLU* 1.3 75.5 - - + +
199B TYR* 1.3 62.0 + - - +
201B SER* 3.3 7.5 + - - -
202B ALA* 3.0 19.6 + - - +
366D GLU* 5.6 2.2 + - - -
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Residues in contact with TYR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.8 17.9 - - + -
147B SER* 3.9 7.8 - - - -
178B VAL* 4.9 5.7 + - + +
180B ILE* 3.6 29.4 - - + -
195B ALA 3.0 13.7 + - - +
196B PHE* 3.5 19.5 - + - +
198B ARG* 1.3 77.2 - - - +
200B LEU* 1.3 62.7 + - + +
202B ALA* 3.2 2.4 + - - +
203B MET* 2.8 68.9 + - + +
218B SER* 3.6 17.2 - - - -
231B VAL* 4.1 11.0 - - + -
232B VAL* 3.6 23.6 - - + +
241B ILE* 3.3 29.0 - - + +
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Residues in contact with LEU 200 (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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196B PHE* 2.9 56.4 + - + +
197B GLU* 3.7 6.7 - - + +
199B TYR* 1.3 78.9 - - + +
201B SER* 1.3 57.8 + - - +
203B MET* 3.5 3.9 + - - +
204B ALA* 3.1 27.5 + - - +
240B LEU 4.9 0.4 - - - +
241B ILE* 4.1 26.7 - - + +
244B THR* 4.4 25.3 - - + +
245B LEU* 4.1 8.1 - - + +
273D GLN* 4.1 15.5 - - - +
274D PHE* 4.6 8.1 - - + -
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Residues in contact with SER 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ARG* 6.2 1.1 - - - -
197B GLU 3.0 16.1 + - - -
198B ARG* 3.7 7.0 - - - -
199B TYR 3.2 0.2 - - - -
200B LEU* 1.3 73.3 - - - +
202B ALA* 1.3 65.6 + - - +
204B ALA* 3.3 14.0 + - - +
205B GLU* 3.4 21.8 + - - +
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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
----------------------------------------------------------
146B LEU* 3.4 37.0 - - + +
154B ARG* 4.9 8.1 - - + -
158B VAL* 3.7 25.4 - - + +
198B ARG 3.0 9.4 + - - +
199B TYR 3.6 2.9 - - - +
201B SER* 1.3 75.2 - - - +
203B MET* 1.3 66.6 + - - +
205B GLU* 3.0 21.8 + - - +
206B ILE* 3.2 10.9 + - - +
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Residues in contact with MET 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.9 22.9 - - + -
178B VAL* 4.1 19.3 - - + -
199B TYR* 2.8 57.6 + - + +
200B LEU* 3.9 4.7 - - - +
202B ALA* 1.3 78.1 - - - +
204B ALA* 1.3 57.2 + - - +
206B ILE* 3.2 16.2 + - - +
207B TYR* 2.9 28.6 + - - +
216B LEU* 3.9 30.2 - - + +
218B SER* 4.3 11.9 - - - -
241B ILE* 4.7 0.4 - - + -
245B LEU* 3.9 23.6 - - + +
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Residues in contact with ALA 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 LEU 3.1 15.0 + - - +
201B SER* 3.5 12.8 - - - +
202B ALA 3.1 0.4 - - - -
203B MET* 1.3 76.5 - - - +
205B GLU* 1.3 63.6 + - + +
207B TYR* 3.3 6.3 + - - +
208B LYS* 3.2 30.2 + - + +
245B LEU* 3.8 13.2 - - + +
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Residues in contact with GLU 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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155B ALA* 5.8 3.4 - - - +
158B VAL* 4.0 29.3 - - + +
162B LEU* 4.3 6.8 - - - +
201B SER* 3.7 18.3 + - - +
202B ALA* 3.0 12.8 + - - +
204B ALA* 1.3 76.7 - - + +
206B ILE* 1.3 64.9 + - - +
208B LYS* 3.3 35.1 + - - +
209B GLY 3.8 3.3 + - - -
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Residues in contact with ILE 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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146B LEU* 4.0 19.5 - - + -
158B VAL* 4.2 13.9 - - + +
161B ASN* 3.5 39.3 - - + +
162B LEU* 4.2 8.0 - - + +
165B ILE* 4.1 10.5 - - + +
176B LEU* 4.0 24.2 - - + -
178B VAL* 5.0 0.7 - - + -
202B ALA 3.7 7.6 - - - +
203B MET* 3.2 26.6 + - - +
205B GLU* 1.3 73.6 - - - +
207B TYR* 1.3 67.2 + - - +
209B GLY* 2.9 16.6 + - - -
210B LEU* 3.7 5.8 + - + +
216B LEU* 4.1 15.3 - - + -
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Residues in contact with TYR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B MET 2.9 13.9 + - - +
204B ALA* 3.4 14.4 - - - +
205B GLU 3.3 0.2 - - - -
206B ILE* 1.3 78.3 - - - +
208B LYS* 1.3 65.3 + - + +
210B LEU* 3.3 33.8 + - + +
216B LEU* 4.2 6.3 - - + +
245B LEU* 3.5 41.1 - - + -
246B GLY* 3.4 0.6 - - - -
247B PRO* 3.3 15.6 - - - +
248B LYS* 3.0 46.6 + - + +
249B ALA* 3.6 27.1 - - + -
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Residues in contact with LYS 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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204B ALA* 3.2 11.1 + - + +
205B GLU* 3.6 36.7 - - - +
206B ILE 3.1 1.0 - - - -
207B TYR* 1.3 82.6 - - + +
209B GLY* 1.3 57.4 + - - +
210B LEU 3.3 4.1 + - - +
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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
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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