Contacts of the helix formed by residues 191 - 212 (chain B) in PDB entry 2VUU
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 ASP 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ASN* 3.2 25.1 + - - +
155B ASN* 5.5 5.6 - - - +
190B LEU* 1.3 76.6 - - - +
192B ALA* 1.3 55.5 + - - +
193B GLU* 3.9 4.2 + - - +
194B HIS* 3.6 6.7 + - - -
195B ASP* 2.8 53.1 + - - +
196B VAL 3.9 0.2 + - - -
220B PHE* 5.1 0.6 - - - -
329B ARG* 2.5 58.9 + - - +
334B TYR* 4.0 9.0 - - - +
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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
----------------------------------------------------------
16B ARG* 3.9 22.0 - - + -
17B GLN 5.0 0.2 - - - +
20B SER* 3.4 5.8 + - - -
153B TYR* 3.9 38.2 - - + +
155B ASN* 4.5 4.1 + - - +
190B LEU* 3.4 7.3 + - - -
191B ASP* 1.3 71.8 + - - +
193B GLU* 1.3 62.1 + - - +
196B VAL* 3.1 44.5 + - + +
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Residues in contact with GLU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 4.7 11.1 - - + +
20B SER* 3.3 24.4 + - - -
23B ARG* 4.4 17.7 + - - +
155B ASN* 5.6 8.8 + - - +
191B ASP* 3.5 6.5 + - - +
192B ALA* 1.3 78.4 - - - +
194B HIS* 1.3 60.5 + - - +
198B PRO* 5.4 0.3 - - - +
329B ARG* 3.9 15.2 + - - +
338B VAL* 5.1 7.1 - - - +
342B GLU* 5.3 5.9 - - - +
708J ARG* 5.5 0.5 + - - -
711J SER* 3.3 29.6 + - - +
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Residues in contact with HIS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASP* 3.3 9.3 + - - +
193B GLU* 1.3 82.1 - - - +
195B ASP* 1.3 81.6 + - - +
198B PRO* 3.5 19.8 - - - +
325B TRP* 4.1 2.1 + + - -
327B GLY 2.9 28.0 - - - -
328B TRP 4.1 0.4 - - - -
329B ARG* 3.2 57.4 - - + +
333B GLU* 4.8 8.1 + - - -
676J CYS* 5.9 0.6 - - - -
694J CYS* 5.7 0.8 - - - -
696J ALA* 3.6 15.3 - - + +
708J ARG* 3.2 45.0 + - - +
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Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 4.4 0.7 - - + -
191B ASP* 2.8 32.8 + - - +
194B HIS* 1.3 104.3 + - - +
196B VAL* 1.3 63.5 + - - +
197B GLY 3.4 2.0 - - - -
198B PRO* 3.7 1.7 - - - +
199B ALA* 3.3 24.9 + - - +
220B PHE* 3.6 27.2 - - + +
325B TRP* 2.9 19.1 + - + +
328B TRP* 3.1 19.1 - - - +
329B ARG 3.1 16.6 + - - +
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN* 3.7 32.8 - - + +
20B SER* 3.6 3.8 - - - +
78B PHE* 4.6 1.1 - - + -
190B LEU* 4.3 20.6 - - + -
191B ASP 3.9 0.2 + - - -
192B ALA* 3.1 38.4 + - + +
195B ASP* 1.3 75.6 - - - +
197B GLY* 1.3 68.0 + - - +
199B ALA* 3.7 3.6 - - - +
200B LEU* 3.0 45.6 + - + +
218B LEU* 4.4 13.7 - - + -
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Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER* 2.4 27.4 + - - -
21B LEU* 3.6 11.7 - - - +
24B VAL* 3.4 25.2 - - - +
196B VAL* 1.3 70.6 - - - +
198B PRO* 1.3 67.1 - - - +
200B LEU* 3.8 2.1 - - - +
201B LEU* 3.0 23.9 + - - +
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Residues in contact with PRO 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER* 4.3 1.3 - - - +
24B VAL* 4.1 17.7 - - + -
193B GLU 5.4 0.4 - - - +
194B HIS 3.5 25.1 - - - +
195B ASP 3.7 4.0 - - - +
197B GLY* 1.3 88.3 - - - +
199B ALA* 1.3 60.1 + - - +
201B LEU* 3.5 11.1 - - + +
202B GLN* 3.1 22.0 + - - +
324B LEU 4.8 0.2 - - - +
325B TRP* 3.5 47.2 - - + +
700J PHE* 4.4 11.0 - - + -
704J HIS* 5.0 5.4 + - - +
708J ARG* 5.2 4.3 - - + +
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ASP 3.3 17.2 + - - +
196B VAL 3.7 2.0 - - - +
197B GLY 3.3 0.8 - - - -
198B PRO* 1.3 76.0 - - - +
200B LEU* 1.3 67.9 + - - +
202B GLN* 3.0 8.1 + - - +
203B ILE* 3.0 28.2 + - + +
218B LEU* 3.9 26.5 - - + -
220B PHE* 4.2 11.4 - - + -
321B ALA* 6.4 0.2 - - - -
324B LEU* 4.8 9.5 - - + +
325B TRP* 4.2 11.3 - - + +
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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
----------------------------------------------------------
21B LEU* 4.0 20.6 - - + -
78B PHE* 3.4 57.9 - - + -
109B ILE* 3.9 27.0 - - + +
148B VAL* 4.2 15.7 - - + -
196B VAL* 3.0 30.2 + - + +
197B GLY 3.8 2.9 - - - +
199B ALA* 1.3 75.7 - - - +
201B LEU* 1.3 62.2 + - - +
203B ILE* 3.3 8.8 + - + +
204B PHE* 3.0 30.1 + - + -
218B LEU* 4.7 5.4 - - + -
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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
----------------------------------------------------------
8B ILE* 5.5 1.3 - - + -
21B LEU* 4.6 6.0 - - + +
24B VAL* 4.1 24.9 - - + +
25B ALA* 4.7 8.1 - - + -
28B VAL* 4.0 27.4 - - + -
30B HIS* 4.1 28.0 - - + +
197B GLY 3.0 16.6 + - - +
198B PRO* 3.5 7.4 - - + +
200B LEU* 1.3 76.5 - - - +
202B GLN* 1.3 58.0 + - - +
204B PHE* 3.2 14.4 + - + +
205B LYS* 2.8 29.5 + - + +
700J PHE* 4.6 3.4 - - + -
704J HIS* 4.1 27.1 - - + +
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Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO 3.1 7.4 + - - +
199B ALA 3.0 9.3 + - - +
201B LEU* 1.3 80.0 - - - +
203B ILE* 1.3 56.5 + - - +
205B LYS* 3.1 32.3 + - - +
206B ASP* 2.9 46.5 + - - +
323B LYS 5.6 0.2 - - - +
324B LEU* 3.3 45.1 + - + +
703J LEU* 5.0 14.1 - - - +
704J HIS* 4.3 10.5 + - - -
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B HIS* 3.4 9.6 - - + -
109B ILE* 3.9 15.5 - - + -
146B THR* 4.0 15.9 - - + -
148B VAL* 3.9 23.3 - - + -
199B ALA* 3.0 20.8 + - + +
200B LEU* 3.3 16.1 + - + +
202B GLN* 1.3 76.0 - - - +
204B PHE* 1.3 63.8 + - - +
206B ASP* 3.2 11.3 + - - +
207B GLY 3.2 9.5 + - - -
211B TRP* 3.8 22.2 - - + -
216B ILE* 3.7 22.9 - - + -
218B LEU* 5.7 1.1 - - + -
324B LEU* 3.8 22.7 - - + -
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Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.0 21.8 - - + -
21B LEU* 4.4 17.5 - - + -
30B HIS* 6.4 1.3 - - + -
76B LEU* 3.6 35.5 - - + +
77B ALA 3.6 29.4 - - - -
78B PHE* 4.2 2.0 - - + -
107B HIS* 3.5 37.9 + - + -
109B ILE* 3.7 24.2 - - + -
200B LEU* 3.0 23.1 + - + -
201B LEU* 3.4 15.3 - - + +
203B ILE* 1.3 75.2 - - - +
205B LYS* 1.3 64.1 + - - +
207B GLY* 3.1 15.9 + - - -
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Residues in contact with LYS 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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3B GLN 6.1 3.6 - - - +
201B LEU* 2.8 17.7 + - + +
202B GLN* 3.5 27.1 - - - +
204B PHE* 1.3 76.6 - - - +
206B ASP* 1.3 62.0 + - - +
207B GLY* 4.7 0.2 - - - -
209B GLN* 5.3 1.6 + - - -
703J LEU* 4.0 13.4 + - - -
704J HIS* 3.3 37.3 + - + +
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Residues in contact with ASP 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 GLN* 2.9 29.1 + - - +
203B ILE 3.5 2.2 - - - +
204B PHE 3.1 0.2 - - - -
205B LYS* 1.3 81.3 - - - +
207B GLY* 1.3 59.2 + - - +
209B GLN* 3.2 24.5 + - - +
210B LYS* 3.9 24.6 + - + +
211B TRP* 2.8 38.4 + - + +
324B LEU* 3.4 18.0 - - - +
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Residues in contact with GLY 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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107B HIS* 3.4 12.5 - - - -
203B ILE 3.2 3.2 + - - -
204B PHE 3.1 14.6 + - - -
206B ASP* 1.3 79.6 - - - +
208B PRO* 1.3 72.5 - - - +
209B GLN* 2.9 14.6 - - - -
210B LYS* 3.1 11.6 + - - -
211B TRP* 3.2 10.7 + - - -
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Residues in contact with PRO 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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106B GLN* 3.4 28.7 - - + +
107B HIS* 3.5 27.5 - - + +
144B PRO* 4.0 15.5 - - + -
207B GLY* 1.3 78.2 - - - +
209B GLN* 1.3 71.8 + - - +
210B LYS 2.9 6.7 - - - -
212B ASN* 2.8 44.8 + - + +
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Residues in contact with GLN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS 5.3 1.4 + - - -
206B ASP 3.2 28.6 + - - +
207B GLY* 3.7 6.5 - - - -
208B PRO* 1.3 94.1 - - + +
210B LYS* 1.3 57.1 + - + +
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Residues in contact with LYS 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 ASP* 3.9 27.4 + - + +
207B GLY 3.1 8.0 + - - +
208B PRO 2.9 0.2 - - - -
209B GLN* 1.3 83.7 - - + +
211B TRP* 1.3 97.7 + - + +
212B ASN 3.6 1.3 + - - -
214B HIS* 3.2 19.6 + - - -
323B LYS* 5.5 7.9 - - - +
324B LEU* 5.7 0.6 - - - +
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Residues in contact with TRP 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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107B HIS* 4.2 1.3 - - - +
146B THR* 3.2 25.4 + - + +
203B ILE* 3.8 21.1 - - + -
206B ASP* 2.8 41.6 + - + +
207B GLY 3.2 7.3 + - - +
210B LYS* 1.3 101.2 - - + +
212B ASN* 1.3 65.9 + - - +
213B GLY 3.2 0.9 + - - -
214B HIS* 2.9 50.4 + + + +
215B ARG 5.4 0.7 - - - -
216B ILE* 3.5 31.9 - - + -
320B GLU* 3.9 28.3 - - + -
324B LEU* 4.1 23.8 - - + +
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Residues in contact with ASN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU 4.4 1.0 + - - -
144B PRO* 3.7 13.2 - - - +
145B SER* 3.1 31.0 + - - +
208B PRO* 2.8 28.8 + - + +
210B LYS 3.6 1.4 - - - -
211B TRP* 1.3 75.9 - - - +
213B GLY* 1.3 69.8 + - - +
214B HIS* 3.2 15.1 + - - -
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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