Contacts of the helix formed by residues 221 - 233 (chain B) in PDB entry 4BOS
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 GLY 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B LEU* 4.3 0.9 - - - -
219B TRP 3.9 0.8 + - - -
220B GLY* 1.3 74.3 - - - -
222B ALA* 1.3 67.2 + - - -
223B ILE 3.3 2.7 - - - -
224B GLU* 2.8 14.8 + - - +
225B ILE* 2.9 29.5 + - - +
268B TYR* 4.3 11.7 - - - -
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Residues in contact with ALA 222 (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 GLY* 1.3 71.4 - - - -
223B ILE* 1.3 64.5 + - + +
225B ILE* 3.3 4.6 + - - +
226B SER* 2.9 25.6 + - - -
249B PHE* 4.0 28.2 - - + -
268B TYR* 5.2 0.2 + - - -
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Residues in contact with ILE 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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190B VAL* 4.8 0.9 - - + -
197B TYR* 4.8 5.4 - - + -
201B ILE* 3.6 50.0 - - + +
202B LEU* 4.2 13.2 - - + +
209B TYR* 3.7 26.9 - - + +
221B GLY 3.3 0.2 - - - -
222B ALA* 1.3 78.0 - - + +
224B GLU* 1.3 71.8 + - - +
226B SER* 2.9 23.5 + - - +
227B ILE* 3.1 27.0 + - + +
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Residues in contact with GLU 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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161B LEU* 4.0 14.6 - - + -
162B PHE* 4.0 8.3 - - + -
186B ILE* 4.0 31.7 - - + +
209B TYR* 2.3 43.8 + - - -
213B ILE* 3.5 24.7 - - + +
219B TRP 4.8 0.2 - - - +
220B GLY* 3.6 1.5 - - - -
221B GLY* 2.8 28.7 + - - +
223B ILE* 1.3 77.1 - - - +
225B ILE* 1.3 58.5 - - - +
227B ILE* 3.4 3.9 + - - +
228B LEU* 2.8 37.8 + - + +
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Residues in contact with ILE 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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161B LEU* 3.7 26.9 - - + -
165B VAL* 5.3 2.0 - - + -
221B GLY 2.9 21.9 + - - +
222B ALA* 3.9 5.6 - - - +
224B GLU* 1.3 78.4 - - - +
226B SER* 1.3 56.5 + - - +
228B LEU* 4.5 5.2 - - - +
229B SER* 2.9 26.9 + - - -
236B ILE* 3.8 22.8 - - + +
238B VAL* 4.3 12.8 - - + -
249B PHE* 3.5 39.9 - - + -
261B LEU* 5.1 2.7 - - + -
268B TYR* 3.7 27.4 - - + +
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Residues in contact with SER 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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197B TYR* 4.7 5.2 + - - -
222B ALA 2.9 15.2 + - - -
223B ILE* 2.9 14.4 + - - +
225B ILE* 1.3 76.7 - - - +
227B ILE* 1.3 75.0 + - - +
229B SER* 3.3 8.1 + - - -
230B LYS* 3.2 40.5 + - - +
249B PHE* 4.4 15.3 - - - -
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Residues in contact with ILE 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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185B LEU* 6.0 0.7 - - + -
186B ILE* 4.0 24.5 - - + +
189B ILE* 3.6 34.3 - - + +
190B VAL* 3.8 27.1 - - + -
197B TYR* 3.1 42.0 - - + +
223B ILE* 3.1 21.3 + - + +
224B GLU* 3.8 4.0 - - - +
226B SER* 1.3 82.7 + - - +
228B LEU* 1.3 60.7 + - + +
229B SER 3.3 0.2 + - - -
230B LYS* 3.3 10.4 + - - +
231B PHE* 2.9 26.1 + - + +
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Residues in contact with LEU 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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161B LEU* 5.2 3.1 - - + -
162B PHE* 4.4 8.5 - - + -
165B VAL* 4.2 16.8 - - + -
182B MET* 3.7 34.3 - - + -
185B LEU* 4.5 15.3 - - + -
186B ILE* 3.7 29.6 - - + -
224B GLU* 2.8 30.0 + - + +
225B ILE* 4.2 3.1 - - - +
227B ILE* 1.3 75.2 - - + +
229B SER* 1.3 58.1 + - - +
231B PHE* 4.2 3.6 - - + -
232B TYR* 2.9 50.9 + - + +
236B ILE* 4.1 10.8 - - + +
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Residues in contact with SER 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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225B ILE 2.9 19.5 + - - -
226B SER* 3.4 9.2 - - - -
228B LEU* 1.3 77.8 - - - +
230B LYS* 1.3 55.5 + - - +
233B GLN* 3.0 22.9 + - - -
234B CYS* 2.8 35.2 + - - +
236B ILE* 3.8 13.6 - - - +
249B PHE* 3.5 20.4 + - - -
250B GLY* 3.8 4.6 - - - -
255B TYR* 3.8 12.5 - - - -
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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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189B ILE* 6.5 0.2 - - - -
196B PHE* 5.6 8.3 - - - -
197B TYR* 3.7 23.5 + - - -
226B SER* 3.2 28.9 + - - +
227B ILE* 3.6 7.6 - - - +
229B SER* 1.3 76.5 - - - +
231B PHE* 1.3 63.8 + - - +
233B GLN* 2.7 30.4 + - - +
255B TYR* 3.4 20.2 + - - +
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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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185B LEU* 3.7 46.7 - - + -
189B ILE* 4.6 13.9 - - + -
227B ILE* 2.9 17.3 + - + +
228B LEU* 3.3 8.3 + - - +
230B LYS* 1.3 78.7 - - - +
232B TYR* 1.3 91.7 + + - +
233B GLN* 3.5 6.6 + - - +
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Residues in contact with TYR 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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165B VAL* 4.1 13.9 - - + -
166B TYR* 4.4 10.6 - - - -
169B VAL* 3.7 49.6 - - + -
170B GLU* 3.9 12.9 + - - -
182B MET* 4.0 20.6 - - + +
185B LEU* 5.1 2.8 - - + +
228B LEU* 2.9 44.0 + - + +
231B PHE* 1.3 105.0 - + - +
233B GLN* 1.3 72.2 + - - +
234B CYS* 3.4 8.3 + - - -
236B ILE* 6.0 0.2 - - + -
257B LYS* 3.8 14.4 + - - -
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Residues in contact with GLN 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 SER 3.0 9.7 + - - -
230B LYS* 2.7 24.5 + - - +
231B PHE 3.2 7.5 - - - +
232B TYR* 1.3 82.4 - - - +
234B CYS* 1.3 61.3 + - - +
255B TYR* 3.7 35.3 + - + +
256B THR* 5.0 1.0 + - - +
257B LYS* 3.3 22.4 + - - +
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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