Contacts of the strand formed by residues 226 - 231 (chain B) in PDB entry 1BJW
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 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B ALA* 5.5 0.7 - - - +
200B LEU* 3.3 31.1 - - + +
202B SER* 4.3 7.0 - - - -
218B PRO* 4.0 6.5 + - + +
219B GLY* 3.9 26.9 - - - +
222B ALA* 2.8 23.9 + - - +
223B PRO* 3.6 5.3 + - - +
224B GLU 3.6 0.6 - - - -
225B HIS* 1.3 80.1 - - - +
227B LEU* 1.3 68.5 + - - +
228B THR* 3.9 15.8 + - - +
248B GLY* 3.6 7.8 - - - -
249B PRO* 3.5 16.3 - - - +
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Residues in contact with LEU 227 (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* 4.2 32.5 - - + -
111B ILE* 5.0 0.7 - - + -
199B TYR* 4.3 29.4 - - + -
200B LEU 3.0 8.6 + - - +
201B VAL* 3.5 7.7 - - + +
202B SER 3.0 23.0 + - - -
226B THR* 1.3 73.1 - - - +
228B THR* 1.3 62.4 - - - +
229B VAL* 3.7 3.1 + - + +
246B ALA* 5.8 2.2 - - + -
247B CYS 3.6 11.0 - - - +
248B GLY* 4.0 2.7 - - - -
249B PRO* 4.0 15.0 - - + -
252B VAL* 3.7 37.0 - - + -
253B ILE* 4.5 5.6 - - + -
256B MET* 4.4 13.7 - - - -
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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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81B PHE* 4.2 14.7 - - + -
85B ASN* 5.6 0.4 - - - +
87B LEU* 3.8 24.4 - - + +
202B SER* 3.7 4.3 - - - -
204B GLU* 3.8 35.4 + - + +
219B GLY* 4.9 3.8 + - - -
226B THR* 3.9 15.4 + - - +
227B LEU* 1.3 70.4 - - - +
229B VAL* 1.3 65.5 + - - +
230B ASN* 5.3 1.1 - - + +
246B ALA* 3.0 27.0 - - - +
247B CYS* 2.9 29.8 + - - -
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Residues in contact with VAL 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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100B GLY* 3.8 24.9 - - - +
103B ALA* 4.0 12.6 - - + -
104B LEU* 4.0 18.8 - - + -
107B LEU* 3.9 28.5 - - + -
201B VAL* 4.5 2.2 - - + -
202B SER 2.8 12.5 + - - +
203B ASP* 3.8 13.6 - - - +
204B GLU* 2.9 29.3 + - - +
205B ILE* 3.8 0.6 + - + -
227B LEU 4.3 6.1 - - - +
228B THR* 1.3 76.5 - - - +
230B ASN* 1.3 72.8 + - - +
234B LLP 5.8 0.7 - - + -
245B TYR 3.8 2.0 - - - -
246B ALA* 4.3 9.0 - - + -
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Residues in contact with ASN 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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80B LYS* 4.1 6.4 - - - +
81B PHE* 4.3 14.4 - - + -
85B ASN* 4.7 2.4 + - - -
100B GLY* 3.8 12.5 - - - -
204B GLU* 3.5 25.9 + - - +
205B ILE* 3.6 24.5 - - - +
207B GLU* 3.0 30.3 + - - +
228B THR* 5.3 1.0 - - + +
229B VAL* 1.3 73.2 - - - +
231B GLY* 1.3 78.6 + - - +
244B GLY* 3.7 4.0 - - - -
245B TYR* 2.8 43.5 + - + +
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Residues in contact with GLY 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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205B ILE* 3.4 15.6 - - - +
230B ASN* 1.3 91.0 + - - +
232B ALA* 1.3 63.0 + - - -
233B ALA 3.5 2.6 + - - -
234B LLP 4.9 2.3 + - - -
235B ALA* 5.0 6.9 - - - +
236B PHE* 5.2 0.7 - - - -
243B ILE 3.8 0.2 - - - -
244B GLY* 3.8 14.4 - - - -
245B TYR* 3.4 21.3 + - - -
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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