Contacts of the helix formed by residues 198 - 211 (chain A) in PDB entry 3EBV
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A TYR* 5.2 0.5 - - - +
195A ALA* 2.8 32.3 + - + +
196A GLN 3.3 3.3 - - - +
197A GLY* 1.3 84.7 - - - +
199A VAL* 1.3 64.4 + - - +
200A ASP* 3.8 8.7 + - - +
201A PHE* 3.2 23.2 + - - +
202A LEU* 3.6 10.7 + - - +
235A VAL* 4.0 1.1 - - - +
239A VAL* 4.2 5.8 - - - -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR* 1.3 72.8 - - - +
200A ASP* 1.3 67.0 + - - +
202A LEU* 3.1 8.6 + - - +
203A THR* 3.0 25.5 + - + -
239A VAL* 3.8 22.5 - - + +
242A ALA* 4.2 11.2 - - + -
243A ALA* 3.8 33.0 - - + +
252A ASN 4.3 7.0 - - - +
253A CYS* 4.8 1.1 - - - -
254A GLY* 3.8 29.8 - - - +
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Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TYR* 3.5 25.0 - - + -
198A THR* 3.2 7.7 + - - +
199A VAL* 1.3 78.7 - - - +
201A PHE* 1.3 62.4 + - - +
203A THR* 3.5 6.1 + - - -
204A ALA* 2.8 35.2 + - - +
254A GLY* 3.4 11.7 + - - -
255A SER* 2.7 34.2 + - - -
256A PHE* 2.9 30.3 + - + +
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Residues in contact with PHE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A THR* 3.9 1.8 - - + -
180A TYR* 3.9 36.0 - - + -
183A SER* 3.5 26.7 - - - -
184A GLY 4.0 3.4 - - - -
186A MSE 3.9 10.8 - - + -
194A TYR* 3.7 29.7 - - + +
195A ALA 3.2 28.7 - - - +
196A GLN* 3.6 28.7 - - + -
197A GLY 4.7 0.9 - - - -
198A THR* 3.2 15.7 + - - +
200A ASP* 1.3 76.0 - - - +
202A LEU* 1.3 64.9 - - + +
205A LEU* 3.2 55.1 + - + +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 3.4 41.6 - - + +
197A GLY 6.3 0.9 - - - +
198A THR 3.8 10.3 - - - +
199A VAL 3.1 5.7 + - - +
201A PHE* 1.3 81.4 - - + +
203A THR* 1.3 58.5 + - - +
206A ALA* 3.0 32.2 + - - +
221A LEU* 4.3 12.0 - - + +
223A LEU* 4.0 29.6 - - + -
235A VAL* 4.6 7.0 - - + -
239A VAL* 4.3 14.6 - - + +
240A VAL* 4.3 14.6 - - - -
243A ALA* 3.7 26.0 - - + -
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Residues in contact with THR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A VAL* 3.0 18.5 + - + +
200A ASP* 3.5 9.7 + - - -
202A LEU* 1.3 76.3 - - - +
204A ALA* 1.3 60.0 + - - +
206A ALA* 3.9 1.6 - - - +
207A CYS* 3.0 28.8 + - - +
243A ALA* 3.8 31.2 - - + +
246A CYS* 3.8 25.8 - - + -
247A LEU* 4.0 18.4 - - + +
253A CYS* 5.8 0.2 - - - -
254A GLY 5.6 0.5 + - - -
256A PHE* 3.4 25.3 + - - +
258A PRO* 4.7 0.2 - - - -
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLY* 3.9 5.4 - - - -
189A CYS 2.9 24.3 + - - -
194A TYR* 3.5 34.8 - - + -
200A ASP 2.8 21.4 + - - +
203A THR* 1.3 76.4 + - - +
205A LEU* 1.3 61.2 + - + +
207A CYS* 3.4 7.6 - - - +
208A ILE* 3.8 1.2 - - - +
256A PHE* 3.6 27.1 - - + -
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A THR* 3.9 17.5 - - + +
155A MSE 5.3 0.7 - - - +
156A GLN* 4.2 6.1 - - - +
178A MSE 3.8 11.0 - - + +
180A TYR* 3.8 10.5 - - + -
186A MSE 3.8 13.7 - - + -
187A LEU 3.6 25.6 - - - +
188A GLY* 4.1 4.9 - - - +
194A TYR* 4.4 6.5 - - + -
201A PHE* 3.2 65.0 + - + +
204A ALA* 1.3 77.1 - - + +
206A ALA* 1.3 65.2 + - - +
207A CYS 3.1 1.6 - - - -
208A ILE* 3.1 24.8 + - + +
209A GLN* 3.8 8.8 + - - +
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 3.4 20.5 + - - +
202A LEU 3.0 21.6 + - - +
203A THR 3.9 0.7 - - - +
205A LEU* 1.3 74.8 - - - +
207A CYS* 1.3 62.6 + - - +
209A GLN* 3.0 18.7 + - - +
210A LEU* 3.0 17.6 + - + +
219A VAL* 4.3 11.6 - - + +
221A LEU* 3.9 6.1 - - + -
247A LEU* 3.9 24.2 - - + -
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Residues in contact with CYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A CYS* 2.1 47.1 - - - -
203A THR 3.0 19.5 + - - +
204A ALA 3.4 4.5 - - - +
206A ALA* 1.3 78.3 - - - +
208A ILE* 1.3 61.1 + - - +
210A LEU* 4.3 10.9 - - - +
211A GLU* 2.8 52.5 + - - +
247A LEU* 5.2 2.7 - - + -
256A PHE* 3.8 11.4 - - + -
258A PRO* 5.3 6.5 - - + -
262A TYR* 5.5 2.9 - - + -
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A MSE 3.6 21.8 - - - +
156A GLN* 3.7 32.5 - - - +
157A SER* 4.5 3.6 - - - -
158A THR* 5.5 1.1 - - + +
163A PHE* 3.8 11.9 - - + -
187A LEU* 3.4 26.0 - - + +
188A GLY 4.1 4.0 - - - +
189A CYS* 3.6 27.1 - - - +
204A ALA 3.8 0.9 - - - +
205A LEU* 3.1 19.8 + - + +
207A CYS* 1.3 76.4 - - - +
209A GLN* 1.3 57.8 + - - +
211A GLU* 3.8 2.2 - - - -
212A GLY* 3.0 26.0 + - - -
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Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A MSE 3.7 32.9 - - + +
163A PHE* 3.8 11.0 - - + -
176A VAL* 4.0 18.7 - - - +
178A MSE 3.5 43.9 - - - +
180A TYR* 3.7 11.8 + - - -
205A LEU 4.3 5.2 + - - +
206A ALA 3.0 8.1 + - - +
208A ILE* 1.3 77.7 - - - +
210A LEU* 1.3 61.5 + - - +
212A GLY* 3.1 9.9 + - - -
213A GLY 3.6 0.3 + - - -
214A LEU* 3.4 28.2 + - + +
219A VAL* 3.6 30.3 - - + +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ALA* 3.0 24.6 + - + +
207A CYS* 3.3 4.9 + - - +
209A GLN* 1.3 76.6 - - - +
211A GLU* 1.3 60.8 + - - +
212A GLY 3.8 0.2 + - - -
213A GLY 4.7 1.6 + - - -
214A LEU 4.0 11.8 - - - +
216A PRO* 3.6 33.8 - - + +
219A VAL* 3.7 19.1 - - + -
247A LEU* 3.8 29.6 - - + -
262A TYR* 3.7 49.1 - - + +
265A LEU* 4.0 15.7 - - + -
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A CYS* 3.8 14.0 - - - +
207A CYS* 2.8 41.7 + - - +
208A ILE* 3.8 2.2 - - - +
210A LEU* 1.3 75.7 - - - +
212A GLY* 1.3 57.5 + - - +
213A GLY 3.5 2.2 - - - -
259A SER* 4.4 22.2 + - - -
260A LYS* 6.1 2.4 - - - -
262A TYR* 3.8 18.7 + - - +
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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