Contacts of the helix formed by residues 196 - 207 (chain B) in PDB entry 1WB8
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 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B GLU 3.7 10.4 + - - +
90B ASN* 2.8 30.7 + - - +
91B MET 3.8 7.9 + - - -
92B ALA* 3.7 22.6 - - + +
96B LYS* 4.5 14.4 - - - +
97B GLY* 4.8 1.1 - - - -
194B VAL 3.4 1.0 + - - -
195B VAL* 1.3 74.8 - - - +
197B TRP* 1.3 60.4 + - - +
198B ASP* 3.4 11.8 + - - +
199B ALA* 3.1 28.4 + - - +
200B ALA* 3.1 20.3 + - - +
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Residues in contact with TRP 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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96B LYS 5.7 1.4 + - - -
97B GLY* 5.6 0.2 - - - -
98B GLY* 3.4 25.9 + - - -
99B GLY 3.6 14.8 + - - -
100B LYS 3.8 13.0 - - - +
101B PRO* 3.4 38.5 - - + +
102B GLY 5.2 1.0 + - - +
105B LEU* 3.8 23.9 - - + +
109B ILE* 4.7 4.3 - - + -
116B PHE* 3.5 30.5 - + - -
119B PHE* 4.4 4.7 - + - -
138B LEU* 6.1 0.4 - - + -
167B LEU* 3.7 37.2 - - + -
192B TRP* 3.9 17.5 + + - -
195B VAL* 3.2 26.3 + - + +
196B ASN* 1.3 72.6 - - - +
198B ASP* 1.3 59.0 + - - +
200B ALA* 3.6 2.6 - - + +
201B GLU* 2.9 30.8 + - - +
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Residues in contact with ASP 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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96B LYS* 4.0 24.3 - - - +
196B ASN* 3.2 8.9 + - - +
197B TRP* 1.3 78.0 - - - +
199B ALA* 1.3 63.7 + - - +
201B GLU* 3.2 8.6 + - - +
202B LYS* 3.0 38.5 + - - +
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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
----------------------------------------------------------
89B GLU* 3.7 16.8 - - + +
90B ASN* 5.3 2.7 - - - +
196B ASN* 3.1 32.9 + - - +
198B ASP* 1.3 75.6 - - - +
200B ALA* 1.3 62.4 + - - +
202B LYS* 3.3 11.4 + - - +
203B LYS* 3.0 23.4 + - - +
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Residues in contact with ALA 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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90B ASN* 4.4 4.4 - - - +
105B LEU* 3.8 18.8 - - + -
166B ILE* 3.8 30.5 - - + +
167B LEU* 4.4 11.2 - - + -
196B ASN 3.1 12.8 + - - +
197B TRP* 3.6 10.8 - - - +
199B ALA* 1.3 76.9 - - - +
201B GLU* 1.3 62.8 + - - +
203B LYS* 3.4 5.8 + - - +
204B LEU* 3.1 23.7 + - - +
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Residues in contact with GLU 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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102B GLY 3.4 11.6 - - - +
103B GLY* 3.9 5.5 - - - -
104B ALA* 3.2 17.1 + - - +
105B LEU* 2.9 38.3 + - + +
197B TRP 2.9 18.1 + - - +
198B ASP* 3.2 9.2 + - - +
200B ALA* 1.3 77.2 - - - +
202B LYS* 1.3 64.0 + - + +
204B LEU* 3.3 5.2 + - - +
205B GLN* 3.1 51.7 + - + +
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Residues in contact with LYS 202 (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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198B ASP* 3.0 27.5 + - - +
199B ALA* 3.3 10.3 + - - +
201B GLU* 1.3 80.0 - - + +
203B LYS* 1.3 63.3 + - - +
205B GLN* 3.3 17.0 + - - +
206B LYS* 3.4 15.4 + - - +
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Residues in contact with LYS 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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86B LEU* 3.5 29.5 - - + +
164B PRO* 4.2 15.0 - - - +
165B ILE* 2.8 37.3 + - - +
166B ILE* 4.1 10.5 - - + +
199B ALA 3.0 16.2 + - - +
200B ALA* 3.8 7.0 - - - +
202B LYS* 1.3 76.5 - - - +
204B LEU* 1.3 64.6 + - - +
206B LYS* 3.2 19.9 + - + +
207B TYR* 3.2 35.3 - - + -
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Residues in contact with LEU 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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104B ALA* 4.1 8.5 - - + -
105B LEU* 3.6 46.2 - - + +
108B LEU* 4.1 15.3 - - + -
140B TYR* 3.6 47.3 - - + -
147B LEU* 5.0 1.6 - - + -
166B ILE* 4.0 14.1 - - + +
200B ALA 3.1 17.4 + - - +
201B GLU* 3.6 7.0 - - - +
203B LYS* 1.3 77.6 - - - +
205B GLN* 1.3 63.5 + - - +
207B TYR* 2.9 15.5 + - - +
208B LEU 3.2 15.1 + - - -
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Residues in contact with GLN 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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104B ALA* 3.5 20.8 - - - +
201B GLU* 3.1 40.8 + - + +
202B LYS* 3.5 12.3 - - - +
203B LYS 3.3 0.4 - - - -
204B LEU* 1.3 76.5 - - - +
206B LYS* 1.3 62.7 + - - +
208B LEU* 2.9 26.6 + - - +
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Residues in contact with LYS 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 LYS 3.4 12.5 + - - +
203B LYS* 3.2 19.6 + - + +
204B LEU 3.1 0.6 + - - -
205B GLN* 1.3 77.6 - - - +
207B TYR* 1.3 84.9 + - + +
208B LEU* 4.1 7.3 - - - +
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Residues in contact with TYR 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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140B TYR* 3.9 24.4 + + + -
142B THR* 3.9 22.0 - - + +
164B PRO* 3.6 38.7 - - + +
166B ILE* 5.4 0.7 - - + -
203B LYS* 3.2 36.3 - - + -
204B LEU* 2.9 9.2 + - - +
206B LYS* 1.3 101.9 + - + +
208B LEU* 1.3 77.0 + - - +
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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