Contacts of the helix formed by residues 191 - 212 (chain B) in PDB entry 3RAW
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 VAL 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B GLU 3.6 24.5 - - - +
142B GLY* 4.5 2.5 - - - -
189B ARG* 2.9 22.1 + - + +
190B ASN* 1.3 80.4 - - - +
192B GLY* 1.3 63.2 + - - +
193B LYS* 4.2 7.6 - - + +
194B TYR* 3.4 27.7 + - + -
195B ARG* 2.9 33.5 + - - +
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Residues in contact with GLY 192 (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 VAL* 1.3 74.6 - - - +
193B LYS* 1.3 63.7 + - - +
194B TYR 3.2 0.2 + - - -
195B ARG* 3.3 17.8 + - - +
196B GLU* 3.0 27.5 + - - +
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 4.2 5.0 - - + +
192B GLY* 1.3 73.3 - - - +
194B TYR* 1.3 75.8 + - + +
196B GLU* 3.7 5.8 - - - +
197B ALA* 3.3 24.4 + - - +
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Residues in contact with TYR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 3.3 30.5 + - - -
167B PHE* 3.6 22.2 - - + +
188B ILE* 3.4 27.9 - - + +
189B ARG* 3.4 35.8 + - + +
191B VAL* 3.4 29.5 + - + +
192B GLY 3.2 0.4 - - - -
193B LYS* 1.3 84.5 - - + +
195B ARG* 1.3 66.6 + - - +
196B GLU 3.2 1.1 - - - -
197B ALA* 3.9 8.0 - - + +
198B ALA* 3.0 17.8 + - - +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 4.1 5.3 - - - +
189B ARG 4.7 2.7 - - - +
190B ASN* 2.5 43.9 + - - -
191B VAL* 2.9 18.7 + - - +
192B GLY* 3.7 21.8 - - - +
194B TYR* 1.3 74.4 - - - +
196B GLU* 1.3 58.3 + - - +
198B ALA* 3.2 4.5 + - - +
199B ARG* 2.9 57.6 + - - +
227B ASN* 5.2 2.9 - - - +
230B GLY* 3.1 20.4 + - - +
232B MET* 3.5 30.8 - - + +
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Residues in contact with GLU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B GLY 3.0 17.6 + - - +
193B LYS* 3.7 7.2 - - - +
195B ARG* 1.3 77.6 - - - +
197B ALA* 1.3 62.3 + - - +
199B ARG* 3.2 23.0 + - - +
200B LEU* 3.0 35.0 + - + +
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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
----------------------------------------------------------
193B LYS 3.3 14.9 + - - +
194B TYR* 3.9 10.3 - - + +
195B ARG 3.4 0.2 - - - -
196B GLU* 1.3 78.7 - - - +
198B ALA* 1.3 57.4 + - - +
200B LEU* 3.3 9.5 + - - +
201B GLU* 2.8 28.2 + - - +
322B GLY* 3.6 27.1 - - - +
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Residues in contact with ALA 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 3.7 28.7 - - + -
194B TYR 3.0 18.1 + - - +
195B ARG 3.6 4.0 - - - +
197B ALA* 1.3 73.7 - - - +
199B ARG* 1.3 60.5 + - - +
201B GLU* 3.4 12.9 - - - +
202B ILE* 2.8 35.7 + - - +
232B MET* 3.9 15.0 - - + -
234B ILE* 4.8 5.8 - - + -
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Residues in contact with ARG 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 ARG* 2.9 45.5 + - - +
196B GLU* 3.2 22.5 + - - +
198B ALA* 1.3 75.8 - - - +
200B LEU* 1.3 64.8 + - + +
202B ILE* 3.3 9.2 + - + +
203B ASN* 3.1 21.3 + - - +
227B ASN* 4.3 15.4 - - - +
232B MET* 4.2 22.7 - - + +
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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 GLU* 3.0 29.0 + - + +
197B ALA* 3.5 10.5 - - - +
199B ARG* 1.3 77.5 - - + +
201B GLU* 1.3 57.8 + - - +
203B ASN* 3.3 10.0 + - + +
204B VAL* 3.0 35.7 + - + +
321B PHE 4.8 1.3 - - - +
322B GLY 4.6 11.2 - - - +
323B SER 6.5 0.4 - - - -
324B ALA 5.6 7.4 - - - +
329B GLU* 5.0 15.0 - - - +
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Residues in contact with GLU 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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2B 3RA 3.7 2.6 - - - +
186B LYS* 2.6 36.1 + - - -
188B ILE* 5.2 0.2 - - - +
197B ALA 2.8 17.6 + - - +
198B ALA* 3.1 14.4 + - - +
200B LEU* 1.3 71.8 - - - +
202B ILE* 1.3 61.7 + - - +
204B VAL* 3.2 2.1 + - - +
205B LEU* 2.9 47.6 + - + +
234B ILE* 3.6 17.5 - - + +
236B PHE* 4.4 2.6 - - - -
320B ASP* 3.4 5.5 + - - -
321B PHE* 3.0 34.8 + - + +
322B GLY* 3.8 15.1 + - - +
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Residues in contact with ILE 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 ALA 2.8 24.7 + - - +
199B ARG* 3.7 7.9 - - + +
201B GLU* 1.3 72.7 - - - +
203B ASN* 1.3 63.8 + - - +
205B LEU* 3.8 5.5 - - - +
206B LYS* 3.0 26.3 + - + +
222B MET* 4.1 8.2 - - + +
225B TRP* 3.5 57.4 - - + +
232B MET* 3.6 29.8 - - + -
233B CYS 5.0 0.4 - - - +
234B ILE* 3.7 23.8 - - + -
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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
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199B ARG 3.1 13.3 + - - +
200B LEU* 3.6 14.5 + - + +
201B GLU 3.3 0.2 - - - -
202B ILE* 1.3 78.9 - - - +
204B VAL* 1.3 63.6 + - - +
206B LYS* 3.4 13.2 + - - +
207B LYS* 3.0 28.4 + - - +
326B PHE* 4.3 20.2 - - - -
329B GLU* 5.9 0.8 + - - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.0 24.0 + - + +
201B GLU 3.2 4.0 + - - +
203B ASN* 1.3 77.5 - - - +
205B LEU* 1.3 52.6 + - - +
207B LYS* 3.1 7.3 + - - +
208B ILE* 2.8 53.3 + - + +
279B LEU* 4.1 12.3 - - + -
321B PHE* 3.9 23.1 - - + +
324B ALA* 4.1 30.3 - - + +
326B PHE* 4.2 18.6 - - + -
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Residues in contact with LEU 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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201B GLU* 2.9 41.1 + - + +
202B ILE 3.8 3.1 - - - +
204B VAL* 1.3 76.6 - - - +
206B LYS* 1.3 61.8 + - - +
208B ILE* 3.3 10.1 + - + +
209B LYS* 3.1 25.3 + - - +
219B CYS* 5.8 0.4 - - + -
220B VAL* 4.0 26.5 - - + +
222B MET* 4.1 31.7 - - + +
234B ILE* 4.3 3.1 - - + -
236B PHE* 3.7 26.7 - - + -
321B PHE* 3.7 28.0 - - + -
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Residues in contact with LYS 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 ILE* 3.0 21.7 + - + +
203B ASN* 3.6 12.6 - - - +
205B LEU* 1.3 77.4 - - - +
207B LYS* 1.3 62.1 + - - +
209B LYS* 3.4 19.7 + - - +
210B GLU* 2.8 63.2 + - + +
222B MET* 4.1 8.0 - - + +
225B TRP* 6.2 1.8 - - - +
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Residues in contact with LYS 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 ASN* 3.0 19.7 + - - +
204B VAL* 3.5 10.1 - - - +
206B LYS* 1.3 75.9 - - - +
208B ILE* 1.3 59.2 + - + +
210B GLU* 3.4 12.9 + - + +
211B LYS* 3.0 44.5 + - + +
279B LEU* 6.1 0.9 - - + -
326B PHE* 3.8 32.3 - - + -
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Residues in contact with ILE 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 VAL* 2.8 39.6 + - + +
205B LEU* 3.6 10.8 - - + +
206B LYS 3.2 0.4 - - - -
207B LYS* 1.3 77.6 - - - +
209B LYS* 1.3 60.6 + - - +
211B LYS* 3.2 5.2 + - - +
212B ASP* 2.9 34.0 + - + +
219B CYS* 4.2 20.0 - - + -
220B VAL 5.7 2.2 - - - +
273B PHE* 4.2 15.9 - - + -
274B LEU* 4.1 20.2 - - + -
279B LEU* 4.5 7.6 - - + -
321B PHE* 3.8 32.1 - - + -
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Residues in contact with LYS 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 LEU 3.1 14.1 + - - +
206B LYS* 3.6 26.0 - - - +
208B ILE* 1.3 78.6 - - + +
210B GLU* 1.3 69.0 + - + +
212B ASP 4.3 7.6 - - - +
213B LYS* 3.3 26.1 + - - +
221B LEU* 4.9 16.2 - - + -
222B MET* 3.7 43.5 + - + +
223B SER 5.4 4.4 - - - -
224B ASP* 6.1 0.4 - - - +
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Residues in contact with GLU 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 LYS* 2.8 59.6 + - + +
207B LYS* 3.7 13.5 - - + +
209B LYS* 1.3 86.8 - - + +
211B LYS* 1.3 60.1 + - + +
213B LYS* 4.4 6.5 + - - +
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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
----------------------------------------------------------
207B LYS* 3.0 33.5 + - + +
208B ILE* 3.9 3.1 - - - +
210B GLU* 1.3 77.7 - - + +
212B ASP* 1.3 58.1 + - - +
213B LYS 3.8 1.6 + - - -
217B PHE* 5.5 1.2 - - - -
273B PHE* 4.1 21.3 - - + -
277B ASN* 4.3 19.3 - - + +
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Residues in contact with ASP 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 ILE* 2.9 18.7 + - + +
209B LYS* 3.5 10.5 - - - +
211B LYS* 1.3 77.3 - - - +
213B LYS* 1.3 64.7 + - - +
214B GLU* 4.2 2.6 + - - +
215B ASN* 3.0 29.6 + - - +
216B LYS* 3.0 20.0 + - - +
217B PHE* 3.2 39.0 + - + +
219B CYS* 5.5 1.0 + - - +
273B PHE* 3.6 18.0 - - + -
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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
------------------------------------------------------------
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