Contacts of the strand formed by residues 196 - 214 (chain B) in PDB entry 3Q02
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 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B LEU* 4.8 19.2 - - + +
189B PHE 3.1 10.5 - - - +
190B HIS* 3.4 34.5 - - + +
194B GLY 3.4 12.3 - - - +
195B SER* 1.3 76.6 - - - +
197B VAL* 1.3 72.6 + - - +
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Residues in contact with VAL 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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187B ARG 3.4 0.9 - - - +
188B LEU* 3.4 4.6 - - - -
189B PHE* 2.7 54.1 + - + +
191B LYS* 4.4 17.5 - - + -
195B SER* 5.6 0.9 - - - +
196B THR* 1.3 81.4 - - - +
198B SER* 1.3 61.6 + - - +
199B VAL* 4.0 15.3 - - + -
378B GLU* 4.0 27.6 - - + +
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Residues in contact with SER 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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186B ARG* 3.9 32.0 + - - +
187B ARG 3.4 12.3 + - - -
188B LEU* 4.3 12.5 - - - +
197B VAL* 1.3 73.7 - - - +
199B VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ARG* 4.3 4.3 - - - +
187B ARG 3.0 26.5 + - - +
189B PHE* 4.1 10.5 - - + -
197B VAL* 4.0 20.4 - - + -
198B SER* 1.3 80.6 - - - +
200B PRO* 1.3 76.4 - - + +
201B MET* 3.3 29.8 + - + +
276B PRO* 4.7 1.1 - - + -
379B PRO* 4.2 37.9 - - + +
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Residues in contact with PRO 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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184B THR* 3.9 18.6 - - + -
185B HIS 3.5 10.8 - - - +
186B ARG* 3.7 31.8 - - - +
199B VAL* 1.3 88.5 - - + +
201B MET* 1.3 60.6 + - - +
276B PRO* 3.9 2.8 - - - +
277B LYS* 3.3 36.4 + - + +
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Residues in contact with MET 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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184B THR* 3.5 3.7 - - - +
185B HIS* 2.7 42.8 + - - +
187B ARG* 3.6 34.5 - - + +
188B LEU 4.2 4.7 - - - +
189B PHE* 4.1 14.8 - - + +
199B VAL* 3.6 29.2 - - + +
200B PRO* 1.3 74.6 - - - +
202B MET* 1.3 58.8 + - - +
274B VAL* 3.7 27.6 - - + +
275B LEU 3.7 7.9 - - - +
276B PRO* 3.9 30.3 - - + -
353B ILE* 4.8 4.0 - - - -
354B MET 4.1 10.8 - - - +
355B ASP* 4.3 4.7 - - + -
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Residues in contact with MET 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PHE* 3.5 37.7 - - + -
180B PRO 5.9 0.2 - - - -
184B THR* 4.2 10.5 - - - +
201B MET* 1.3 74.3 - - - +
203B ALA* 1.3 59.9 + - - +
273B LEU 4.0 0.2 - - - +
274B VAL* 3.4 4.2 - - - +
275B LEU* 2.9 57.3 + - + +
276B PRO 4.1 4.9 - - - +
277B LYS* 3.3 21.5 - - + -
328B VAL* 4.0 20.9 - - + +
329B ASN* 3.6 33.2 - - - +
330B GLU* 3.8 15.5 - - - +
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Residues in contact with ALA 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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179B PHE* 3.6 3.1 - - - +
180B PRO* 3.5 19.9 - - - +
183B SER* 3.6 23.9 + - - +
185B HIS* 4.1 21.1 - - + -
201B MET 4.0 0.2 + - - -
202B MET* 1.3 76.7 - - - +
204B GLN* 1.3 66.7 + - - +
272B LEU* 4.7 6.1 - - + -
273B LEU 3.4 8.7 - - - +
274B VAL* 4.4 8.1 - - + -
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Residues in contact with GLN 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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177B THR* 3.2 43.1 + - - +
178B PRO 4.3 4.7 - - - -
179B PHE* 3.5 41.1 - - + +
180B PRO* 4.5 9.0 - - + -
203B ALA* 1.3 77.5 - - - +
205B THR* 1.3 69.9 + - - +
206B ASN* 3.9 11.1 + - - +
208B PHE* 3.9 17.8 - - + -
226B LEU* 6.1 0.2 - - - +
271B ARG 3.7 1.2 - - - +
272B LEU* 3.7 8.8 - - - +
273B LEU* 2.9 31.8 + - - +
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Residues in contact with THR 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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204B GLN* 1.3 75.4 - - - +
206B ASN* 1.3 73.8 + - - +
270B PRO* 5.8 3.1 - - + -
271B ARG 3.3 13.7 - - - +
272B LEU* 3.5 22.9 - - - +
349B PRO* 4.7 16.8 - - + +
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Residues in contact with ASN 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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177B THR* 3.6 32.3 + - - +
204B GLN* 3.9 6.1 + - - +
205B THR* 1.3 84.2 - - - +
207B LYS* 1.3 89.5 + - - +
208B PHE* 3.5 24.4 + - + -
268B ARG* 6.0 0.4 - - - +
270B PRO* 3.3 2.9 - - - +
271B ARG 2.8 30.3 + - - +
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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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206B ASN* 1.3 92.9 + - - +
208B PHE* 1.3 61.4 + - - +
268B ARG* 3.3 46.7 + - + +
269B LEU* 3.5 10.3 - - - +
270B PRO* 4.1 25.5 - - + +
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B THR* 5.5 1.8 - - - -
204B GLN* 3.9 29.8 - - - -
206B ASN* 3.7 34.3 - - + -
207B LYS* 1.3 75.6 - - - +
209B ASN* 1.3 69.7 + - - +
210B TYR* 3.3 6.9 + - + +
224B LEU* 3.9 17.7 - - + -
225B GLU 3.9 7.0 - - - -
226B LEU* 3.4 33.4 - - + -
227B PRO* 5.5 4.0 - - + -
267B THR 3.4 0.2 - - - +
268B ARG* 3.3 3.9 - - - +
269B LEU 3.0 29.7 + - - +
271B ARG* 3.6 31.2 - - + -
273B LEU* 3.9 22.4 - - + -
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Residues in contact with ASN 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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216A PRO* 3.0 25.7 + - - +
217A ASP* 5.0 2.4 - - - +
207B LYS 4.1 1.4 + - - -
208B PHE* 1.3 71.4 - - - +
210B TYR* 1.3 59.3 + - - +
224B LEU* 3.5 5.0 - - - +
225B GLU* 2.9 65.9 + - + +
227B PRO* 5.5 4.8 - - - +
263B LYS* 3.8 3.2 + - - +
266B MET* 3.7 24.7 - - + +
267B THR 3.7 2.8 + - - -
268B ARG* 3.1 37.1 + - - +
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Residues in contact with TYR 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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208B PHE* 3.9 9.4 - - + +
209B ASN* 1.3 76.9 - - - +
211B THR* 1.3 87.2 + - - +
212B GLU* 3.9 12.8 + - + +
222B ASP* 2.6 43.0 + - + -
223B ILE 3.4 17.9 - - - -
224B LEU* 4.5 16.4 - - + -
265B ASN 4.2 0.2 - - - +
266B MET* 3.5 6.5 - - - -
267B THR* 3.0 35.4 + - - +
269B LEU* 4.0 13.7 - - + -
271B ARG* 3.6 37.7 + - + +
352B ILE* 4.2 16.0 - - + +
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Residues in contact with THR 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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210B TYR* 1.3 89.3 - - - +
212B GLU* 1.3 65.4 + - - +
213B PHE* 4.0 18.0 - - + -
222B ASP* 3.9 1.4 - - - -
223B ILE* 2.9 40.0 + - + +
262B TRP 3.5 23.1 - - - +
265B ASN* 3.5 27.6 + - + +
266B MET* 4.0 5.4 - - - -
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Residues in contact with GLU 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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210B TYR* 3.9 19.9 + - + +
211B THR* 1.3 80.6 + - - +
213B PHE* 1.3 65.9 + - - +
220B TYR* 3.0 42.3 - - + +
221B TYR 3.4 10.8 - - - +
222B ASP* 4.2 5.9 - - - +
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Residues in contact with PHE 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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211B THR* 4.0 11.0 - - + -
212B GLU* 1.3 82.1 - - - +
214B THR* 1.3 67.3 + - - +
220B TYR* 3.4 6.7 - - - -
221B TYR* 3.0 63.8 + - + +
223B ILE* 3.7 5.8 - - + +
258B LEU* 4.0 15.0 - - + -
261B HIS* 3.6 30.1 - - + -
262B TRP* 3.6 34.5 - + - -
265B ASN* 4.0 15.9 - - + -
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Residues in contact with THR 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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213B PHE* 1.3 80.2 - - - +
215B THR* 1.3 69.6 + - - +
216B PRO* 4.7 0.5 - - - +
218B GLY* 4.3 11.0 - - - +
219B HIS 3.1 5.8 - - - +
220B TYR* 3.4 44.6 - - + -
221B TYR* 3.7 10.0 + - - -
253B ILE* 5.0 1.9 - - - +
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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