Contacts of the helix formed by residues 196 - 205 (chain B) in PDB entry 1BMO
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 VAL 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B GLU* 3.7 43.7 + - + +
148B LEU* 3.5 30.9 - - + +
149B ARG* 4.0 10.1 - - - +
194B HIS 3.4 2.8 + - - -
195B PRO* 1.3 69.7 - - + +
197B GLU* 1.3 60.4 + - + +
199B LEU* 3.4 6.4 + - - +
200B ALA* 2.9 28.2 + - + +
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Residues in contact with GLU 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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195B PRO* 2.8 29.6 + - + +
196B VAL* 1.3 80.8 - - + +
198B LEU* 1.3 72.8 + - - +
200B ALA* 3.0 9.0 + - - +
201B ARG* 3.0 22.6 + - - +
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Residues in contact with LEU 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* 4.1 27.4 - - + -
194B HIS* 3.5 35.2 - - + +
195B PRO* 2.8 29.0 + - + +
197B GLU* 1.3 76.4 - - + +
199B LEU* 1.3 63.9 + - - +
200B ALA 2.9 1.9 + - - -
201B ARG* 3.0 8.6 + - + -
202B ASP* 2.9 24.4 + - + +
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Residues in contact with LEU 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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148B LEU* 3.8 34.0 - - + +
149B ARG* 4.0 29.6 - - - +
151B ARG* 4.6 2.4 + - - -
152B ASP* 4.0 24.2 - - + +
189B LEU* 4.4 4.9 - - + -
194B HIS* 3.4 54.7 - - + +
195B PRO 3.1 3.0 + - - +
196B VAL* 3.7 8.3 - - - +
198B LEU* 1.3 78.1 - - - +
200B ALA* 1.3 58.6 + - - +
202B ASP* 4.0 6.6 - - - +
203B PHE* 3.4 19.8 + - - +
210B TYR* 4.7 5.4 + - - +
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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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148B LEU* 3.4 18.4 - - + -
151B ARG* 5.2 0.2 - - - +
196B VAL* 2.9 14.5 + - + +
197B GLU* 3.0 11.6 + - - +
198B LEU 2.9 1.0 + - - -
199B LEU* 1.3 74.5 - - - +
201B ARG* 1.3 65.6 + - - +
202B ASP 3.1 0.9 - - - -
203B PHE* 2.9 17.7 + - - +
204B GLU* 3.3 18.5 + - - +
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Residues in contact with ARG 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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197B GLU 3.0 10.7 + - - +
198B LEU* 3.0 12.1 + - + +
200B ALA* 1.3 75.7 - - - +
202B ASP* 1.3 57.9 + - - +
204B GLU* 2.9 47.6 + - - +
205B LYS* 3.0 48.5 + - + +
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Residues in contact with ASP 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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155B LYS* 5.1 1.7 - - - +
187B LYS 4.5 0.5 - - - +
189B LEU* 3.0 41.8 + - + +
198B LEU* 2.9 18.1 + - + +
199B LEU* 4.0 5.2 - - - +
201B ARG* 1.3 75.6 - - - +
203B PHE* 1.3 56.6 + - - +
205B LYS* 3.0 5.1 + - - +
206B ASN* 2.5 58.0 + - - +
209B MET* 5.6 0.9 - - - +
210B TYR* 2.8 29.0 + - - +
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Residues in contact with PHE 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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151B ARG* 3.3 62.8 - - - +
199B LEU 3.4 8.6 + - - +
200B ALA* 2.9 11.0 + - - +
202B ASP* 1.3 78.1 - - - +
204B GLU* 1.3 63.6 + - + +
207B TYR* 2.9 58.9 + + - +
210B TYR* 3.4 39.5 - + + -
273B PHE 3.6 7.9 - - - -
274B GLY* 3.9 17.9 - - - -
275B ILE* 4.0 2.7 - - + -
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Residues in contact with GLU 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 ALA* 3.3 13.6 + - - +
201B ARG* 2.9 45.2 + - - +
202B ASP 3.2 0.6 - - - -
203B PHE* 1.3 84.6 - - + +
205B LYS* 1.3 65.9 + - - +
206B ASN 3.1 1.6 + - - -
207B TYR* 3.6 12.1 + - - +
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Residues in contact with LYS 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 ARG* 3.0 47.7 + - + +
202B ASP* 3.9 4.5 - - - +
204B GLU* 1.3 78.3 + - - +
206B ASN* 1.3 71.9 + - + +
207B TYR 3.8 0.2 - - - -
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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