Contacts of the helix formed by residues 193 - 207 (chain B) in PDB entry 2B7O
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 SER 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B SER 4.4 1.4 + - - -
190B GLY* 3.3 15.6 + - - -
192B ALA* 1.3 75.9 - - - +
194B LEU* 1.3 62.1 + - - +
195B HIS* 2.6 36.1 + - - -
196B LEU* 3.2 7.1 + - - +
197B VAL* 3.1 21.3 + - - +
235B ASP* 3.3 29.2 - - - -
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Residues in contact with LEU 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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111B VAL* 3.4 27.9 - - + +
192B ALA 3.3 7.7 + - - +
193B SER* 1.3 71.4 - - - +
195B HIS* 1.3 57.0 + - - +
197B VAL* 3.8 6.7 - - + +
198B HIS* 3.0 32.2 + - - +
225B LEU* 3.8 19.8 - - + +
228B MSE 3.9 31.0 - - + -
235B ASP* 4.4 4.9 + - - +
238B LEU* 4.0 19.5 - - + -
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Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLY 5.6 0.4 - - - -
193B SER* 2.6 30.5 + - - -
194B LEU* 1.3 80.4 - - - +
196B LEU* 1.3 83.0 + - + +
198B HIS* 3.5 1.7 + - - +
199B ASP* 3.1 35.3 + - - +
225B LEU* 4.9 11.1 - - + +
235B ASP* 4.1 10.8 + - - +
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLY 3.2 24.7 - - - +
191B LEU* 4.0 3.4 - - + -
193B SER* 3.2 16.5 + - - +
195B HIS* 1.3 89.3 - - + +
197B VAL* 1.3 67.6 + - - +
199B ASP* 2.9 29.1 + - + +
200B TRP* 3.3 51.8 + - + +
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Residues in contact with VAL 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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107B LEU* 3.4 24.0 - - + +
108B GLN* 3.4 40.4 - - + +
111B VAL* 3.9 11.0 - - + -
191B LEU 3.2 25.4 - - - +
192B ALA 4.2 3.8 - - - +
193B SER 3.1 13.2 + - - +
194B LEU* 3.8 11.0 - - + +
196B LEU* 1.3 79.1 - - - +
198B HIS* 1.3 57.1 + - - +
200B TRP* 3.0 38.1 - - + +
201B ASN* 3.6 2.9 + - - -
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Residues in contact with HIS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 4.2 7.4 - - + +
112B VAL* 4.8 0.9 - - + -
194B LEU 3.0 10.7 + - - +
195B HIS 4.3 1.6 - - - +
196B LEU 3.2 0.2 - - - -
197B VAL* 1.3 73.5 - - - +
199B ASP* 1.3 59.9 + - - +
200B TRP 3.2 2.0 - - - -
201B ASN* 3.0 53.5 + - + +
202B ARG* 3.1 25.9 + - + +
218B ALA* 2.9 31.9 + - + -
221B ILE* 3.4 41.4 - - + +
222B ASP* 3.8 12.3 - - - -
225B LEU* 3.5 24.5 - - + -
454B PHE* 4.8 0.4 - + - -
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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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195B HIS* 3.1 27.1 + - - +
196B LEU* 2.9 22.5 + - + +
198B HIS* 1.3 71.8 - - - +
200B TRP* 1.3 68.2 + - + +
202B ARG* 3.0 35.4 + - - +
203B GLU* 3.1 22.7 + - - +
206B ARG* 4.6 3.3 + - - -
222B ASP* 5.1 1.7 - - - +
226B ARG* 5.3 0.5 + - - -
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Residues in contact with TRP 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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104B ARG* 4.3 16.4 - - + -
107B LEU* 5.1 0.2 - - + -
108B GLN* 3.4 34.8 + - + +
191B LEU* 3.3 42.6 - - + -
196B LEU* 3.3 40.4 - - + +
197B VAL* 3.0 48.5 - - + +
199B ASP* 1.3 80.6 - - + +
201B ASN* 1.3 60.6 + - - +
203B GLU* 3.4 9.3 + - + +
204B PHE* 3.1 21.1 + - - +
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Residues in contact with ASN 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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108B GLN* 2.6 62.8 + - - +
111B VAL* 3.3 11.3 - - - +
112B VAL* 3.5 7.7 - - - +
197B VAL 4.0 2.9 - - - -
198B HIS* 3.0 40.3 + - + +
200B TRP* 1.3 76.7 - - - +
202B ARG* 1.3 58.0 + - - +
204B PHE* 3.4 9.7 - - - +
205B VAL* 3.1 30.2 + - - +
218B ALA* 5.3 0.2 - - - -
450B LEU* 3.5 10.8 - - - +
454B PHE* 4.5 8.7 - - + -
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Residues in contact with ARG 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 HIS* 3.1 29.2 + - + +
199B ASP* 3.0 37.0 + - - +
200B TRP 3.2 0.6 - - - -
201B ASN* 1.3 76.6 - - - +
203B GLU* 1.3 62.8 + - - +
205B VAL* 3.2 11.1 + - - +
206B ARG* 3.2 49.1 + - - +
218B ALA* 4.5 10.1 - - + +
219B THR* 5.8 0.9 - - - +
222B ASP* 3.7 25.0 + - - -
226B ARG* 3.7 26.9 - - - +
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Residues in contact with GLU 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 3.1 12.4 + - - +
200B TRP* 3.4 12.8 - - + +
202B ARG* 1.3 72.7 - - - +
204B PHE* 1.3 65.8 + - - +
206B ARG* 3.2 29.2 + - - +
207B THR* 3.1 48.6 + - - +
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Residues in contact with PHE 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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200B TRP 3.1 12.6 + - - +
201B ASN 3.4 13.2 - - - +
202B ARG 3.3 0.2 - - - -
203B GLU* 1.3 76.2 - - - +
205B VAL* 1.3 72.4 + - + +
207B THR* 3.5 8.0 - - - +
208B SER* 2.9 39.0 - - - -
211B GLY* 5.8 0.2 - - - -
214B TYR* 4.2 22.0 - + - -
447B GLN* 3.5 48.0 - - + -
450B LEU* 3.7 29.2 - - + -
451B GLU* 4.2 19.3 - - + -
454B PHE* 3.9 24.2 - + - -
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Residues in contact with VAL 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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201B ASN 3.1 14.9 + - - +
202B ARG* 3.4 11.0 - - - +
203B GLU 3.2 0.4 - - - -
204B PHE* 1.3 85.1 - - + +
206B ARG* 1.3 68.3 + - + +
208B SER 4.2 0.2 + - - -
211B GLY* 3.3 27.0 - - - +
212B ALA 4.6 0.2 + - - -
214B TYR* 4.1 19.3 - - + +
215B GLU* 3.5 36.6 - - + -
218B ALA* 3.7 24.0 - - + -
454B PHE* 4.6 1.8 - - + -
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Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASP 4.6 2.8 + - - -
202B ARG* 3.2 38.2 + - - +
203B GLU* 3.2 40.9 + - - +
205B VAL* 1.3 81.3 - - + +
207B THR* 1.3 65.6 + - + +
208B SER 3.0 11.6 + - - +
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Residues in contact with THR 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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203B GLU* 3.1 40.8 + - - +
204B PHE* 3.5 2.5 + - - +
206B ARG* 1.3 76.2 - - + +
208B SER* 1.3 58.4 + - - +
447B GLN* 3.0 21.8 + - - +
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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