Contacts of the helix formed by residues 183 - 197 (chain B) in PDB entry 2BPI
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 ASN 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B ASP* 3.7 6.9 + - - +
79B SER 2.8 26.7 + - - +
80B MET 3.3 21.9 + - - +
81B GLY* 4.4 1.6 - - - -
84B CYS* 4.0 18.2 - - - -
154B LEU* 3.7 9.9 - - - +
181B LEU 3.3 0.6 + - - -
182B VAL* 1.3 71.7 - - - +
184B TRP* 1.3 61.9 + - - +
185B ASN* 3.0 15.3 + - - +
186B PHE* 2.9 25.8 + - - +
187B ALA 3.2 15.2 + - - -
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Residues in contact with TRP 184 (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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84B CYS* 5.3 2.3 - - - -
85B GLY* 3.2 19.3 + - - -
86B GLY 3.0 27.3 + - - -
87B GLU 3.3 11.0 + - - -
88B PRO* 3.6 15.7 - - + -
89B HIS* 3.6 27.7 - + + +
92B ILE* 3.7 22.4 - - + -
96B ILE* 3.9 23.3 - - + -
103B PHE* 3.8 29.2 - + - -
106B PHE* 4.5 3.6 - + - -
154B LEU* 3.9 18.8 - - + -
179B TRP* 4.5 7.0 - + - -
182B VAL* 3.9 28.1 + - + -
183B ASN* 1.3 72.6 + - - +
185B ASN* 1.3 55.1 + - - +
187B ALA* 3.3 8.0 + - + +
188B ASN* 2.7 41.0 + - - -
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Residues in contact with ASN 185 (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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84B CYS* 5.7 3.5 - - - -
89B HIS* 3.1 30.5 + - - -
183B ASN* 3.0 10.1 + - - +
184B TRP* 1.3 74.7 - - - +
186B PHE* 1.3 60.8 + - - +
188B ASN* 3.8 9.0 - - - +
189B GLU* 2.9 41.9 + - - +
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Residues in contact with PHE 186 (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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8B LYS* 4.7 8.1 - - - -
75B PHE* 3.5 51.6 - + - -
78B ASP* 3.2 54.3 - - + +
79B SER* 3.7 9.6 - - - -
153B ILE 4.0 3.4 - - - -
154B LEU* 4.5 0.4 - - + -
183B ASN* 2.9 17.8 + - - +
185B ASN* 1.3 78.0 - - - +
187B ALA* 1.3 51.7 + - - +
189B GLU* 3.3 24.1 + - - +
190B ASN* 2.8 65.7 + - - -
193B LYS* 6.2 1.1 - - - -
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Residues in contact with ALA 187 (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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92B ILE* 3.9 18.4 - - + -
153B ILE* 3.6 29.4 - - + +
154B LEU* 4.0 16.1 - - + +
183B ASN 3.2 11.2 + - - +
184B TRP* 3.3 14.3 + - + +
186B PHE* 1.3 77.6 - - - +
188B ASN* 1.3 59.3 + - - +
190B ASN* 3.1 4.0 + - - +
191B LEU* 2.8 30.4 + - - +
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Residues in contact with ASN 188 (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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89B HIS* 3.3 33.7 + - - -
90B GLY* 4.0 4.6 - - - -
91B GLU* 3.6 11.6 + - + +
92B ILE* 2.9 36.5 + - - +
184B TRP 2.7 24.9 + - - +
185B ASN* 3.9 8.7 - - - +
187B ALA* 1.3 68.7 - - - +
189B GLU* 1.3 67.2 + - - +
191B LEU* 3.2 5.5 + - - +
192B LYS* 3.1 24.9 + - - +
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Residues in contact with GLU 189 (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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8B LYS* 5.2 4.9 + - - -
185B ASN* 2.9 37.7 + - - +
186B PHE* 3.4 25.9 + - + +
188B ASN* 1.3 71.8 - - - +
190B ASN* 1.3 61.9 + - - +
192B LYS* 3.9 4.1 - - - +
193B LYS* 3.1 43.6 + - - +
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Residues in contact with ASN 190 (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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75B PHE* 3.6 10.7 - - - -
151B ILE* 5.2 0.7 - - - +
152B PRO 3.8 6.0 - - - +
153B ILE* 2.7 42.2 + - + +
186B PHE* 2.8 60.7 + - - +
187B ALA 3.6 3.6 - - - +
189B GLU* 1.3 74.7 - - - +
191B LEU* 1.3 54.4 + - - +
193B LYS* 3.5 18.7 + - - +
194B ALA* 2.8 36.6 + - - +
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Residues in contact with LEU 191 (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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91B GLU* 3.9 38.1 - - + +
92B ILE* 4.0 15.7 - - + +
95B LYS* 3.7 33.0 - - + -
127B LEU* 4.3 15.0 - - + -
133B LEU* 4.0 21.8 - - + -
153B ILE* 3.8 7.1 - - + +
187B ALA 2.8 18.8 + - - +
188B ASN* 3.8 5.6 - - - +
190B ASN* 1.3 70.2 - - - +
192B LYS* 1.3 62.3 + - - +
194B ALA* 3.7 1.0 - - - +
195B MET* 2.8 46.2 + - - +
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Residues in contact with LYS 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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188B ASN 3.1 16.2 + - - +
189B GLU* 3.9 4.7 - - - +
191B LEU* 1.3 75.4 - - - +
193B LYS* 1.3 66.1 + - - +
195B MET* 3.5 6.9 + - - +
196B GLN* 3.3 43.7 + - + +
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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
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151B ILE* 6.4 0.2 - - + -
186B PHE* 6.2 1.0 - - - -
189B GLU* 3.1 33.1 + - - +
190B ASN* 3.5 20.2 + - - +
192B LYS* 1.3 75.3 - - - +
194B ALA* 1.3 62.9 + - + +
196B GLN* 3.2 22.8 + - - +
197B LYS 3.2 16.6 + - - +
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Residues in contact with ALA 194 (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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127B LEU* 3.8 25.6 - - + +
151B ILE* 3.7 35.2 - - + +
153B ILE* 4.1 10.1 - - + -
190B ASN 2.8 22.4 + - - +
191B LEU 3.7 3.8 - - - +
192B LYS 3.3 0.2 - - - -
193B LYS* 1.3 72.2 - - - +
195B MET* 1.3 65.3 + - - +
197B LYS* 3.1 22.2 - - - +
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Residues in contact with MET 195 (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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91B GLU* 6.1 2.0 - - - +
95B LYS* 4.4 12.6 - - - -
127B LEU* 4.4 5.6 - - + -
131B ASN* 3.3 31.9 + - - +
191B LEU* 2.8 37.8 + - + +
192B LYS* 3.9 6.7 - - - +
194B ALA* 1.3 75.5 - - - +
196B GLN* 1.3 66.0 + - - +
197B LYS* 3.1 15.5 + - - +
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Residues in contact with GLN 196 (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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192B LYS* 3.3 35.1 + - + +
193B LYS* 3.2 21.3 + - - +
195B MET* 1.3 75.1 - - - +
197B LYS* 1.3 70.1 + - - +
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Residues in contact with LYS 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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127B LEU* 6.2 2.0 - - + -
129B ASN* 5.9 3.1 - - - +
131B ASN* 6.2 2.7 - - + +
151B ILE* 3.6 25.4 - - + +
193B LYS 3.2 9.4 + - - +
194B ALA* 3.1 17.0 + - - +
195B MET* 3.1 11.3 + - - +
196B GLN* 1.3 84.7 + - - +
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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