Contacts of the helix formed by residues 222 - 236 (chain B) in PDB entry 3BJT
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 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B LYS* 6.0 1.2 - - - +
116B GLY 5.0 4.5 + - - -
117B PRO* 6.4 0.4 - - - -
219B PRO* 4.3 21.2 + - - +
220B ALA 4.1 0.6 - - - -
221B VAL* 1.3 75.4 - - - +
223B GLU* 1.3 55.7 + - - +
224B LYS* 3.4 10.3 + - - +
225B ASP* 2.5 37.4 + - - +
226B ILE* 2.8 34.3 + - - +
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Residues in contact with GLU 223 (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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222B SER* 1.3 73.7 - - - +
224B LYS* 1.3 63.5 + - - +
226B ILE* 3.1 19.6 + - - +
227B GLN* 2.9 54.5 + - + +
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Residues in contact with LYS 224 (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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76B PHE* 4.4 13.5 - - - -
77B SER 6.3 0.7 - - - -
79B GLY 5.2 9.3 + - - -
80B THR* 6.3 0.6 - - - +
81B HIS* 5.8 1.8 + - - -
115B LYS* 4.1 25.6 - - + -
222B SER* 3.2 9.0 + - - +
223B GLU* 1.3 75.5 - - - +
225B ASP* 1.3 68.6 + - - +
227B GLN* 3.3 6.5 + - + +
228B ASP* 2.8 54.5 + - - +
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Residues in contact with ASP 225 (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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114B THR* 4.1 10.2 - - - +
115B LYS* 3.9 11.6 + - - +
116B GLY* 3.0 40.2 + - - -
117B PRO 4.6 0.2 - - - -
219B PRO 4.8 0.2 - - - +
220B ALA 3.8 2.5 - - - +
221B VAL* 3.5 17.8 - - + -
222B SER* 2.5 42.3 + - - +
224B LYS* 1.3 79.5 - - - +
226B ILE* 1.3 55.6 + - - +
228B ASP* 3.8 6.6 - - - +
229B LEU* 2.9 39.4 + - + +
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Residues in contact with ILE 226 (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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221B VAL* 3.9 21.8 - - + +
222B SER 2.8 19.1 + - - +
223B GLU* 3.1 24.7 + - - +
225B ASP* 1.3 73.8 - - - +
227B GLN* 1.3 77.1 + - - +
229B LEU* 3.5 5.7 + - - +
230B LYS* 3.2 39.8 + - - +
253B GLU* 5.9 2.7 - - - +
257B VAL* 4.1 19.4 - - + +
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Residues in contact with GLN 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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81B HIS* 3.8 16.1 - - + +
223B GLU* 2.9 40.3 + - + +
224B LYS* 3.3 8.9 + - + +
226B ILE* 1.3 85.0 - - - +
228B ASP* 1.3 58.8 + - - +
230B LYS* 3.1 19.4 + - - +
231B PHE* 2.8 29.6 + - - +
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Residues in contact with ASP 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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76B PHE* 3.4 32.4 - - + +
81B HIS* 2.6 37.6 + - - -
112B LEU* 3.2 17.8 - - + +
114B THR* 5.7 4.5 - - + -
115B LYS* 5.4 2.3 + - - +
224B LYS* 2.8 53.9 + - - +
225B ASP* 3.8 7.6 + - - +
227B GLN* 1.3 76.8 - - - +
229B LEU* 1.3 58.7 + - + +
231B PHE* 3.3 3.2 + - - +
232B GLY 2.9 21.5 + - - -
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Residues in contact with LEU 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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112B LEU* 4.7 3.4 - - + -
114B THR* 4.1 16.8 - - + -
221B VAL* 3.8 25.1 - - + -
225B ASP* 2.9 22.3 + - + +
228B ASP* 1.3 76.8 - - - +
230B LYS* 1.3 61.8 + - - +
232B GLY* 3.1 9.8 + - - +
233B VAL* 3.3 17.3 + - - +
240B VAL* 3.7 32.3 - - + -
254B VAL* 3.9 30.1 - - + +
257B VAL* 3.7 29.6 - - + -
258B LEU* 4.2 11.9 - - + +
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Residues in contact with LYS 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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226B ILE* 3.2 28.2 + - + +
227B GLN* 3.1 25.7 + - - +
229B LEU* 1.3 73.6 - - - +
231B PHE* 1.3 65.7 + - - +
232B GLY 3.1 0.2 - - - -
233B VAL* 3.3 11.0 + - - +
234B GLU* 3.0 35.4 + - - +
257B VAL* 4.3 20.6 - - + +
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Residues in contact with PHE 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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76B PHE* 3.6 37.5 - + - -
81B HIS* 3.3 59.0 - + + +
84B HIS* 4.3 5.8 - - + -
85B ALA* 4.1 10.8 - - + -
88B ILE* 4.3 4.9 - - + -
112B LEU* 4.7 0.4 - - + -
227B GLN 2.8 14.3 + - - +
228B ASP 3.4 7.4 - - - +
230B LYS* 1.3 75.3 - - - +
232B GLY* 1.3 59.8 + - - +
234B GLU* 3.1 28.1 + - - +
235B GLN* 2.8 66.4 + - + +
237B VAL* 6.4 0.2 - - + -
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Residues in contact with GLY 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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112B LEU* 3.8 21.3 - - - -
228B ASP 2.9 10.9 + - - -
229B LEU 3.1 6.3 + - - -
230B LYS 3.1 0.8 - - - -
231B PHE* 1.3 77.3 - - - +
233B VAL* 1.3 62.1 + - - +
235B GLN* 2.9 12.3 + - - +
236B ASP 3.0 9.5 + - - -
237B VAL* 3.4 27.4 + - - +
258B LEU* 6.1 0.2 - - - -
265B ILE* 5.6 0.2 - - - -
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Residues in contact with VAL 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 LEU 3.3 13.6 + - - +
230B LYS* 3.3 10.0 + - + +
232B GLY* 1.3 74.0 - - - +
234B GLU* 1.3 64.5 + - + +
236B ASP* 3.1 14.0 + - - +
257B VAL 5.4 0.9 - - - +
258B LEU* 4.0 26.5 - - + +
261B LYS* 3.9 49.5 - - + +
262B GLY* 4.0 2.0 - - - +
265B ILE* 3.9 22.2 - - + +
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Residues in contact with GLU 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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230B LYS* 3.0 30.0 + - - +
231B PHE* 3.1 29.8 - - - +
233B VAL* 1.3 78.4 - - + +
235B GLN* 1.3 69.4 + - - +
236B ASP* 3.3 2.8 + - - +
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Residues in contact with GLN 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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85B ALA* 4.0 17.9 - - - +
88B ILE* 3.8 30.8 - - + +
89B LYS* 6.0 1.0 - - - -
92B ARG* 2.5 35.1 + - - +
231B PHE* 2.8 61.4 + - + +
232B GLY 2.9 3.8 + - - +
234B GLU* 1.3 81.8 + - - +
236B ASP* 1.3 64.3 + - - +
237B VAL* 3.4 6.3 - - + +
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Residues in contact with ASP 236 (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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92B ARG* 3.4 18.2 + - - +
232B GLY 3.0 3.4 + - - -
233B VAL* 3.1 14.8 + - - +
234B GLU 3.2 2.8 - - - +
235B GLN* 1.3 81.8 - - - +
237B VAL* 1.3 66.4 + - - +
238B ASP* 4.0 5.4 + - - +
265B ILE* 6.1 0.7 - - - -
458B GLN* 4.5 12.7 + - - -
461B ARG* 4.0 19.1 + - - -
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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