Contacts of the helix formed by residues 196 - 212 (chain B) in PDB entry 3L49
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 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B VAL* 5.4 0.7 - - + -
195B PRO* 1.3 92.3 + - - +
197B THR* 1.3 62.7 + - - +
199B GLN* 3.2 39.4 + - + +
200B SER* 3.1 28.1 + - - -
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Residues in contact with THR 197 (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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42B ASP* 5.3 2.3 + - - -
192B ASP* 5.2 0.2 - - + -
193B VAL* 2.6 31.1 + - - +
194B ILE* 3.6 16.8 - - - +
195B PRO* 3.3 1.6 - - - +
196B ASN* 1.3 74.7 + - - +
198B ILE* 1.3 66.1 + - - +
199B GLN* 4.0 0.4 + - - -
200B SER* 3.8 1.4 - - - -
201B ALA* 3.0 24.3 + - - +
225B TRP* 3.7 24.5 - - + -
227B VAL* 3.8 17.9 - - + -
228B PRO* 3.7 21.8 - - + -
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Residues in contact with ILE 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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196B ASN 3.6 0.4 - - - -
197B THR* 1.3 79.6 - - - +
199B GLN* 1.3 69.1 + - - +
201B ALA* 3.7 0.8 - - - +
202B TYR* 3.0 20.1 + - + +
227B VAL* 3.7 31.0 - - + +
230B ILE* 3.9 28.0 - - + -
231B GLY* 3.5 14.8 - - - +
234B GLN* 3.5 27.8 - - - +
254B GLU* 4.3 9.6 - - - +
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Residues in contact with GLN 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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196B ASN* 3.2 49.9 + - + +
198B ILE* 1.3 82.7 + - - +
200B SER* 1.3 60.4 + - - +
202B TYR* 3.4 8.7 + - - +
203B SER* 3.0 33.5 + - - +
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ARG 4.8 2.9 + - - -
192B ASP* 5.9 0.4 - - - -
193B VAL* 3.6 26.7 + - - +
196B ASN* 3.1 22.5 + - - -
197B THR 3.8 1.6 - - - -
199B GLN* 1.3 77.2 - - - +
201B ALA* 1.3 58.6 + - - +
203B SER* 3.4 5.8 + - - -
204B ASN* 3.0 41.6 + - - -
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Residues in contact with ALA 201 (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 PHE* 4.1 19.3 - - + -
192B ASP* 6.0 0.9 - - + -
197B THR 3.0 18.1 + - - +
198B ILE 3.7 3.4 - - - +
200B SER* 1.3 74.3 - - - +
202B TYR* 1.3 64.0 + - - +
204B ASN* 3.5 1.0 + - - +
205B VAL* 3.1 32.1 + - - +
228B PRO* 3.2 41.1 - - + +
231B GLY 4.3 1.8 - - - -
232B ALA 4.3 0.2 - - - +
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Residues in contact with TYR 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 ILE* 3.0 13.7 + - + +
199B GLN* 3.4 12.8 - - - +
201B ALA* 1.3 75.8 - - - +
203B SER* 1.3 65.1 + - - +
206B THR* 2.9 47.3 + - + -
231B GLY* 3.4 25.9 - - - +
234B GLN* 3.7 23.3 - - + +
235B ALA* 3.4 25.1 - - + +
238B ALA* 3.5 19.3 - - + +
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Residues in contact with SER 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 GLN* 3.0 16.9 + - - +
200B SER* 3.4 6.3 + - - -
201B ALA 3.3 0.2 - - - -
202B TYR* 1.3 80.8 - - - +
204B ASN* 1.3 64.9 + - - +
206B THR* 3.5 5.4 + - - -
207B ASP* 3.1 24.6 + - - +
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Residues in contact with ASN 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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157B PHE* 4.1 11.3 - - + -
190B LEU* 3.8 28.1 - - + +
191B ARG 4.1 9.5 + - - -
200B SER* 3.0 31.3 + - - +
201B ALA 3.8 4.7 - - - +
202B TYR 3.4 0.2 - - - -
203B SER* 1.3 74.1 - - - +
205B VAL* 1.3 64.8 + - - +
207B ASP* 3.4 10.9 + - - +
208B MET* 3.0 27.7 + - - +
187D GLU* 3.2 32.8 + - - +
188D PRO* 5.4 4.3 - - - +
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Residues in contact with VAL 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 LEU* 4.4 6.1 - - + -
157B PHE* 4.0 15.3 - - + -
201B ALA 3.1 18.4 + - - +
202B TYR 3.8 3.8 - - - +
204B ASN* 1.3 75.1 - - - +
206B THR* 1.3 53.3 + - - +
208B MET* 3.0 8.5 + - - +
209B LEU* 2.8 53.3 + - + +
221B ILE* 4.0 14.6 - - + -
232B ALA* 3.6 25.4 - - + +
235B ALA* 3.8 13.7 - - + -
236B LEU* 4.0 16.4 - - + -
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Residues in contact with THR 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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202B TYR* 2.9 32.4 + - + -
203B SER* 3.6 8.1 - - - +
205B VAL* 1.3 75.1 - - - +
207B ASP* 1.3 56.4 + - - +
209B LEU* 3.2 13.2 + - - +
210B THR* 2.8 35.9 + - - +
235B ALA* 3.6 14.2 + - - +
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Residues in contact with ASP 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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203B SER 3.1 17.3 + - - +
204B ASN* 3.4 9.4 - - - +
206B THR* 1.3 75.7 - - - +
208B MET* 1.3 75.8 + - - +
210B THR* 3.4 9.7 + - - -
211B LYS* 3.1 46.8 + - - +
188D PRO* 3.6 28.0 - - - +
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Residues in contact with MET 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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155B LEU* 3.7 35.7 - - + -
186B ILE* 4.9 3.4 - - + -
188B PRO* 4.8 17.0 - - + -
190B LEU* 3.6 28.5 - - + -
204B ASN* 3.0 16.4 + - - +
205B VAL 3.0 6.1 + - - +
207B ASP* 1.3 97.6 - - - +
209B LEU* 1.3 60.8 + - - +
211B LYS* 4.4 10.8 - - + -
212B TYR* 2.8 63.0 + - + +
218B VAL* 5.4 2.9 - - + +
188D PRO* 5.6 3.1 - - + -
189D GLU 6.3 0.4 - - - +
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Residues in contact with LEU 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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205B VAL* 2.8 40.9 + - + +
206B THR* 3.2 10.3 + - - +
208B MET* 1.3 70.5 - - - +
210B THR* 1.3 62.5 + - - +
212B TYR 3.8 3.6 - - - -
213B PRO* 3.3 26.5 - - - +
218B VAL* 4.4 10.1 - - + -
235B ALA 4.1 6.3 - - - +
236B LEU* 3.9 22.7 - - + -
239B ALA* 3.8 27.8 - - + -
241B ARG* 3.5 32.9 + - + +
244B ILE* 4.3 7.6 - - + -
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Residues in contact with THR 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 THR* 2.8 22.6 + - - +
207B ASP* 3.5 9.6 - - - -
208B MET 3.3 0.2 - - - -
209B LEU* 1.3 77.2 - - - +
211B LYS* 1.3 64.4 + - - +
213B PRO* 3.9 13.8 - - - +
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Residues in contact with LYS 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 ASP* 3.1 43.8 + - - +
208B MET* 3.4 17.7 + - + +
210B THR* 1.3 79.8 - - - +
212B TYR* 1.3 81.6 + - + +
213B PRO* 3.5 7.4 - - - +
188D PRO* 4.8 2.0 - - - +
189D GLU* 3.2 31.1 + - - +
190D LEU* 5.0 2.4 - - - +
191D ARG* 4.1 38.2 + - - +
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Residues in contact with TYR 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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186B ILE* 4.3 19.7 - - + +
187B GLU 3.7 16.1 + - - -
188B PRO* 5.3 1.0 - - - +
208B MET* 2.8 55.5 + - + +
209B LEU* 3.4 7.5 - - - +
211B LYS* 1.3 95.8 - - + +
213B PRO* 1.4 63.2 - - - +
214B ASN 3.5 2.5 + - - -
217B ASP* 3.7 29.1 - - + +
218B VAL* 3.9 15.5 - - + +
241B ARG* 3.9 12.0 + - - -
158D ASN* 5.7 1.7 + - - -
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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