Contacts of the helix formed by residues 195 - 210 (chain A) in PDB entry 2B6V
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 PHE 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ILE* 5.4 2.2 - - - -
191A PHE* 3.2 42.1 + + - +
193A ALA 3.6 1.6 + - - -
194A ILE* 1.3 78.2 - - - +
196A TRP* 1.3 69.8 - + - +
197A ILE 3.6 0.4 - - - -
198A VAL* 3.7 5.3 + - - +
199A PHE* 2.9 74.8 + + - -
246A PHE* 3.5 24.2 - + - -
247A VAL* 4.3 5.6 - - + -
250A HIS* 3.5 38.1 - + + +
251A ILE* 4.3 21.8 - - + -
254A ILE* 6.4 0.4 - - + -
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Residues in contact with TRP 196 (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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191A PHE* 2.9 49.9 + + + +
192A VAL* 3.8 10.5 - - + +
195A PHE* 1.3 83.7 - + - +
197A ILE* 1.4 76.0 + - + +
199A PHE* 3.3 6.1 + + + +
200A LEU* 2.9 66.5 + - + +
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Residues in contact with ILE 197 (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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192A VAL* 3.2 37.3 + - + +
193A ALA* 3.8 10.5 - - - +
196A TRP* 1.4 88.5 - - + +
198A VAL* 1.4 68.4 + - + +
200A LEU* 3.1 18.2 + - + +
201A LEU* 3.2 27.2 + - + +
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Residues in contact with VAL 198 (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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109A ILE* 3.7 38.6 - - + +
110A VAL* 4.3 10.5 - - + +
113A GLY* 4.5 13.1 - - - -
148A LEU* 5.6 1.3 - - + -
193A ALA 3.7 17.2 + - - +
194A ILE* 3.7 28.3 - - + -
195A PHE 3.7 5.6 + - - +
196A TRP 3.3 0.4 - - - -
197A ILE* 1.4 78.6 - - + +
199A PHE* 1.4 51.9 - - + +
201A LEU* 3.5 5.5 + - - +
202A LEU* 2.8 41.5 + - + +
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Residues in contact with PHE 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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109A ILE* 4.1 26.5 - - + -
195A PHE* 2.9 74.9 + + - +
196A TRP* 3.4 9.0 - + + +
197A ILE 3.3 0.2 - - - -
198A VAL* 1.4 77.0 - - + +
200A LEU* 1.4 65.3 + - + +
202A LEU* 3.5 9.0 - - + +
203A ILE* 3.0 39.4 + - + +
243A PHE* 4.6 26.9 - + - -
246A PHE* 4.1 11.7 - + + -
247A VAL* 4.0 20.0 - - + -
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Residues in contact with LEU 200 (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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196A TRP* 2.9 70.3 + - + +
197A ILE* 3.1 13.6 + - + +
199A PHE* 1.4 78.3 - - + +
201A LEU* 1.3 65.3 + - + +
203A ILE* 3.1 7.6 + - + +
204A VAL* 2.9 31.5 + - + +
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Residues in contact with LEU 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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113A GLY* 6.3 1.8 - - - -
116A SER* 5.3 0.7 - - - +
117A PHE* 6.3 2.2 - - + -
197A ILE* 3.2 22.9 + - + +
198A VAL* 4.0 7.2 - - - +
200A LEU* 1.3 80.4 - - + +
202A LEU* 1.3 56.0 + - - +
204A VAL* 3.0 13.1 + - + +
205A PHE* 2.9 64.1 + - + -
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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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109A ILE* 6.4 1.1 - - + -
112A PHE* 3.6 21.8 - - + +
113A GLY* 4.9 1.7 - - - +
116A SER* 3.5 34.3 - - - +
198A VAL* 2.8 27.7 + - + +
199A PHE* 3.5 7.9 - - + +
201A LEU* 1.3 78.2 - - - +
203A ILE* 1.4 61.7 + - + +
205A PHE 4.1 0.2 + - - -
206A TYR* 3.3 28.3 + - + -
239A VAL* 3.4 50.0 - - + -
243A PHE* 3.9 19.1 - - + -
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Residues in contact with ILE 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 PHE* 3.0 28.0 + - + +
200A LEU* 3.7 4.3 - - + +
202A LEU* 1.4 85.8 - - + +
204A VAL* 1.3 68.5 + - + +
205A PHE 3.2 1.8 - - - -
206A TYR* 3.1 27.3 - - + +
207A THR* 3.2 13.1 + - - +
243A PHE* 4.1 23.3 - - + -
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Residues in contact with VAL 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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200A LEU* 2.9 23.3 + - + +
201A LEU* 3.0 18.6 + - + +
203A ILE* 1.3 76.9 - - + +
205A PHE* 1.3 65.7 + - + +
207A THR* 3.2 9.7 + - - -
208A ALA* 3.0 26.6 + - + +
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Residues in contact with PHE 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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113A GLY 5.2 0.2 - - - -
116A SER* 3.3 41.2 - - - +
117A PHE* 3.9 24.9 - + + -
119A ARG* 5.4 0.2 - - - +
120A TYR* 3.7 47.2 - + + +
201A LEU* 2.9 54.5 + - + +
202A LEU 4.3 0.2 - - - +
204A VAL* 1.3 78.8 - - + +
206A TYR* 1.4 67.1 + - - +
208A ALA* 3.7 5.8 - - + +
209A ILE* 3.2 23.8 + - - +
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Residues in contact with TYR 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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116A SER* 5.8 1.3 - - - -
202A LEU* 3.3 23.9 + - + -
203A ILE* 3.1 20.3 + - + +
205A PHE* 1.4 80.6 - - - +
207A THR* 1.4 64.4 + - - +
209A ILE* 3.1 3.6 + - - +
210A THR* 3.1 28.2 + - + +
235A ILE* 4.8 3.8 - - + -
236A PHE* 2.6 79.0 + + - -
239A VAL* 3.2 38.5 - - + +
240A PHE* 4.2 5.4 + - - +
243A PHE* 6.1 0.7 - + - -
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Residues in contact with THR 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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203A ILE* 3.2 16.3 + - - +
204A VAL* 3.2 9.2 + - - -
206A TYR* 1.4 78.1 - - - +
208A ALA* 1.3 63.2 + - - +
210A THR* 2.7 25.5 + - - +
211A LYS* 4.3 5.2 + - - +
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Residues in contact with ALA 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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120A TYR* 4.2 14.6 - - + -
124A VAL* 3.8 22.9 - - + +
204A VAL* 3.0 15.1 + - + +
205A PHE* 3.7 15.0 - - + +
206A TYR 3.2 0.6 - - - -
207A THR* 1.3 79.4 - - - +
209A ILE* 1.4 59.6 + - - +
210A THR 3.4 0.2 + - - -
211A LYS* 3.5 30.5 + - - +
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Residues in contact with ILE 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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119A ARG* 3.6 37.7 - - + +
120A TYR 5.3 0.9 - - - +
123A ILE* 3.5 27.6 - - + -
124A VAL* 3.4 24.2 - - + -
205A PHE 3.2 11.6 + - - +
206A TYR 3.1 14.7 + - - +
208A ALA* 1.4 74.0 - - - +
210A THR* 1.4 56.2 + - - +
211A LYS 3.1 5.6 - - - -
212A LYS* 3.1 18.6 + - + +
213A ILE* 3.1 33.7 + - + +
232A SER* 4.7 1.1 - - - -
236A PHE* 3.7 23.8 - - + -
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Residues in contact with THR 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 TYR* 3.1 21.0 + - + +
207A THR* 2.7 29.8 + - - +
208A ALA 3.2 0.4 - - - -
209A ILE* 1.4 74.3 - - - +
211A LYS* 1.4 58.5 + - - +
212A LYS 3.1 5.3 + - - -
213A ILE 3.5 19.3 - - - +
214A PHE* 3.0 50.4 - - + +
236A PHE* 3.8 15.3 - - + -
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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