Contacts of the helix formed by residues 227 - 235 (chain B) in PDB entry 3BSQ
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 PHE 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B HIS* 3.9 21.3 - + - -
97B ASN* 3.4 36.6 - - - -
99B LEU* 3.6 41.1 - - + -
173B SER* 3.8 27.4 - - - -
222B THR* 3.9 18.6 - - + -
223B GLN 3.2 29.2 - - - -
224B VAL* 2.8 6.1 + - - +
226B LYS* 1.3 84.5 - - + +
228B THR* 1.3 62.1 + - - +
229B LYS* 3.0 4.9 + - - -
230B TRP* 3.0 11.1 + + + +
231B ILE* 2.8 29.4 + - + +
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Residues in contact with THR 228 (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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119B LEU* 4.8 9.6 - - + -
120B PRO* 3.8 33.7 + - + +
224B VAL* 3.7 18.2 - - + +
225B CYS 4.4 10.7 + - - +
226B LYS 3.7 0.8 - - - -
227B PHE* 1.3 78.1 - - - +
229B LYS* 1.3 54.9 + - - +
231B ILE* 3.6 10.4 - - + +
232B ASN* 2.5 42.3 + - - -
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Residues in contact with LYS 229 (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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226B LYS 6.0 0.7 - - - +
227B PHE* 3.1 1.5 - - - -
228B THR* 1.3 81.1 + - - +
230B TRP* 1.3 68.7 + - - +
232B ASN* 3.5 5.5 + - - +
233B ASP* 3.0 53.1 + - - +
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Residues in contact with TRP 230 (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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52B LEU* 5.1 0.2 - - + -
85B PHE* 4.0 12.8 - - + -
86B ARG 4.1 4.0 - - - -
87B HIS* 3.5 58.1 - + + +
88B PRO* 3.4 21.6 - - + +
99B LEU* 3.7 30.5 - - + -
101B LEU* 3.9 26.7 - - + -
227B PHE* 3.0 12.3 + - + +
229B LYS* 1.3 79.7 - - - +
231B ILE* 1.3 74.2 + - + +
233B ASP* 3.2 5.7 + - + +
234B THR* 2.5 70.6 + - + +
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Residues in contact with ILE 231 (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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46B VAL* 5.2 5.6 - - + -
52B LEU* 4.7 11.0 - - + -
99B LEU* 4.3 9.9 - - + -
101B LEU* 3.7 14.5 - - + +
119B LEU* 4.4 22.9 - - + -
224B VAL* 4.2 22.9 - - + -
227B PHE* 2.8 33.8 + - + +
228B THR* 3.6 10.8 - - - +
229B LYS 3.2 0.2 - - - -
230B TRP* 1.3 98.0 - - + +
232B ASN* 1.3 60.5 + - - +
234B THR* 3.0 13.7 + - - -
235B MET* 3.4 32.6 + - + +
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Residues in contact with ASN 232 (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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119B LEU* 4.6 15.9 - - - +
228B THR* 2.5 31.0 + - - +
229B LYS* 3.5 9.7 + - - +
231B ILE* 1.3 72.0 - - - +
233B ASP* 1.3 61.4 + - - +
235B MET* 2.4 46.0 - - + +
236B LYS* 4.5 1.0 - - - -
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Residues in contact with ASP 233 (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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229B LYS* 3.0 53.2 + - - +
230B TRP* 3.6 7.6 - - + +
232B ASN* 1.3 81.8 + - - +
234B THR* 1.3 56.3 + - - +
235B MET 3.0 0.2 + - - -
236B LYS* 2.3 39.0 + - - +
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Residues in contact with THR 234 (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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50B TRP* 4.3 2.7 - - + -
85B PHE* 4.3 21.1 - - + -
101B LEU* 3.6 20.2 - - + -
230B TRP* 2.5 63.6 + - + +
231B ILE 3.0 5.8 + - - -
233B ASP* 1.3 73.4 - - - +
235B MET* 1.3 56.8 + - - +
236B LYS 3.6 3.1 - - - -
237B HIS* 3.2 38.0 - - + +
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Residues in contact with MET 235 (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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46B VAL* 4.1 16.4 - - + -
47B ASN* 3.7 7.9 - - - +
50B TRP* 3.5 59.0 - - + +
101B LEU* 4.7 5.8 - - + -
119B LEU* 5.4 3.1 - - + -
231B ILE* 3.4 35.2 - - + +
232B ASN* 2.4 40.3 - - + +
234B THR* 1.3 73.2 - - - +
236B LYS* 1.3 59.1 + - - +
237B HIS 4.6 0.9 - - - +
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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