Contacts of the helix formed by residues 197 - 206 (chain B) in PDB entry 2B8W
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 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B LEU* 4.1 1.6 - - - -
196B LEU* 1.3 78.2 - - - +
198B PRO* 1.3 76.6 - - + +
199B ASP* 3.5 8.6 + - - +
200B GLU* 3.1 41.0 + - - +
201B TYR* 3.0 19.4 + - - +
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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
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189B LEU* 3.8 23.8 - - + -
197B THR* 1.3 88.2 - - + +
199B ASP* 1.3 61.3 + - - +
201B TYR* 3.2 15.9 + - + +
202B LEU 3.2 9.9 + - - -
235B CYS* 3.4 42.3 - - - +
236B PHE* 4.4 0.9 - - - -
237B VAL* 4.2 24.7 - - + +
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Residues in contact with ASP 199 (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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197B THR* 3.1 8.4 + - - +
198B PRO* 1.3 81.7 - - - +
200B GLU* 1.3 53.4 + - + +
202B LEU* 3.2 6.3 + - - +
203B THR* 2.7 39.6 + - + +
233B LYS 4.5 2.4 - - - +
234B LYS* 2.7 41.4 + - - +
235B CYS* 2.9 32.2 + - - +
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Residues in contact with GLU 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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195B PRO 4.1 5.2 - - - +
196B LEU* 3.7 23.4 - - + +
197B THR* 3.1 40.2 + - - +
199B ASP* 1.3 75.8 - - + +
201B TYR* 1.3 53.6 + - - +
203B THR* 3.9 9.2 + - + -
204B TYR* 2.7 36.2 + - - +
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Residues in contact with TYR 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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47A TYR* 4.1 3.5 + - - -
71A VAL* 3.6 42.0 + - + +
104A VAL* 5.3 5.4 - - + -
133B THR* 3.6 12.8 - - - -
134B ILE* 2.9 53.5 + - + -
182B LEU* 3.8 24.9 - - + -
185B PHE* 4.8 2.5 - + - -
189B LEU* 3.7 22.7 - - + -
196B LEU* 4.0 10.5 - - + +
197B THR 3.0 12.0 + - - +
198B PRO* 3.2 10.1 + - + +
200B GLU* 1.3 75.4 - - - +
202B LEU* 1.3 61.7 + - - +
204B TYR* 3.3 21.5 - + - +
205B SER* 3.0 19.6 + - - -
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Residues in contact with LEU 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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134B ILE* 3.9 10.9 - - + +
139B MET* 4.6 1.3 - - + -
178B PHE* 4.3 12.8 - - + -
180B TRP* 3.9 29.8 - - + -
198B PRO 3.2 5.5 + - - -
199B ASP* 3.2 8.5 + - - +
201B TYR* 1.3 78.9 - - - +
203B THR* 1.3 59.1 + - + +
205B SER* 2.7 34.8 + - - +
206B LEU* 3.3 23.4 + - + +
233B LYS* 4.1 23.8 - - + -
234B LYS 3.6 27.6 - - - +
235B CYS* 3.9 14.6 - - + -
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Residues in contact with THR 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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199B ASP* 2.7 24.5 - - + +
200B GLU* 3.9 9.2 + - + +
202B LEU* 1.3 73.4 - - + +
204B TYR* 1.3 65.5 + - - +
206B LEU* 3.1 18.9 + - - +
207B LYS* 3.1 14.3 + - - +
227B ARG* 5.3 1.2 + - - -
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Residues in contact with TYR 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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71A VAL* 5.5 1.1 - - + -
72A GLN* 3.2 27.8 + - + +
104A VAL* 4.6 17.3 - - + +
105A GLU* 3.4 30.4 + - + +
191B ALA* 4.1 20.2 - - + -
192B ASP* 4.3 11.4 - - - -
196B LEU* 4.8 11.0 - - + -
200B GLU 2.7 24.0 + - - +
201B TYR* 3.3 28.0 - + - +
203B THR* 1.3 76.0 + - - +
205B SER* 1.3 64.8 + - - +
206B LEU 3.3 0.7 + - - -
207B LYS* 3.4 44.0 + - - +
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Residues in contact with SER 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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104A VAL* 4.1 21.4 - - - +
134B ILE* 4.0 21.7 - - - +
139B MET* 3.1 25.8 - - - +
201B TYR* 3.0 14.0 + - - -
202B LEU* 2.7 24.2 + - - +
204B TYR* 1.3 81.3 - - - +
206B LEU* 1.3 57.2 + - - +
207B LYS 3.4 0.4 - - - -
223B ARG* 3.4 25.6 + - - -
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Residues in contact with LEU 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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139B MET* 3.1 39.3 - - + -
178B PHE* 6.1 1.6 - - + -
202B LEU* 3.3 28.7 + - + +
203B THR* 3.1 10.1 + - - +
205B SER* 1.3 76.5 + - - +
207B LYS* 1.3 64.9 + - - +
208B LEU* 3.6 0.5 + - - +
223B ARG* 3.7 26.3 - - + +
226B ILE* 4.0 27.4 - - + -
227B ARG* 3.1 40.9 + - + +
233B LYS* 4.3 16.2 - - + -
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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