Contacts of the helix formed by residues 223 - 239 (chain C) in PDB entry 5BOU
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 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C ALA 3.8 1.6 + - - -
222C LEU* 1.3 73.2 - - - +
224C SER* 1.3 65.6 + - - +
225C GLU* 3.8 13.0 + - - +
226C GLU* 2.9 38.8 + - - +
227C ILE* 3.2 28.2 + - - +
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Residues in contact with SER 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ALA 5.4 10.0 - - - +
206C LYS* 5.0 14.3 - - - +
223C SER* 1.3 75.1 - - - +
225C GLU* 1.3 61.8 + - - +
227C ILE* 3.4 7.4 + - - +
228C ASN* 2.8 35.1 + - - +
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Residues in contact with GLU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C SER* 3.8 11.1 + - - +
224C SER* 1.3 86.1 + - - +
226C GLU* 1.3 67.2 + - + +
228C ASN* 3.2 9.5 + - - +
229C GLN* 3.0 38.7 + - - +
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Residues in contact with GLU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ALA 5.2 0.7 - - - +
222C LEU* 3.6 28.2 - - + +
223C SER* 2.9 35.7 + - - +
225C GLU* 1.3 76.0 - - + +
227C ILE* 1.3 62.9 + - - +
229C GLN* 3.4 22.0 + - - +
230C TYR* 3.2 23.8 + - + -
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Residues in contact with ILE 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C VAL* 4.6 9.4 - - + -
204C GLY 5.0 3.6 - - - +
205C ALA 5.3 2.9 - - - +
208C ILE* 3.5 44.6 - - + +
209C GLU* 4.3 0.9 - - - -
210C ILE* 3.9 25.1 - - + +
222C LEU* 3.8 29.6 - - + +
223C SER 3.2 19.6 + - - +
224C SER* 3.8 6.3 - - - +
226C GLU* 1.3 73.8 - - - +
228C ASN* 1.3 67.0 + - - +
230C TYR* 3.0 12.6 + - + +
231C VAL* 3.0 30.6 + - + +
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Residues in contact with ASN 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C GLY 4.4 10.0 + - - +
205C ALA* 5.5 2.4 - - - -
224C SER 2.8 19.6 + - - +
225C GLU* 3.2 12.3 + - - +
227C ILE* 1.3 76.9 - - - +
229C GLN* 1.3 52.9 + - + +
231C VAL* 3.4 15.3 + - - +
232C THR* 2.7 43.2 + - - -
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Residues in contact with GLN 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C GLU* 3.0 31.2 + - - +
226C GLU* 3.6 16.5 - - - +
227C ILE 3.2 0.2 - - - -
228C ASN* 1.3 74.8 - - - +
230C TYR* 1.3 64.3 + - + +
232C THR* 3.6 7.0 + - - -
233C GLN* 3.1 25.3 + - - +
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Residues in contact with TYR 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C VAL* 4.8 1.6 - - - +
187C GLU* 3.5 55.7 - - + +
190C VAL* 3.6 27.2 - - + +
191C LYS* 3.8 29.2 - - + -
194C VAL* 4.3 15.9 - - + -
222C LEU* 4.2 10.9 - - + +
226C GLU* 3.2 25.1 - - + -
227C ILE* 3.0 10.8 + - - +
229C GLN* 1.3 77.6 - - + +
231C VAL* 1.3 64.1 + - - +
233C GLN* 3.4 7.8 + - - +
234C ILE* 3.0 33.2 + - + +
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C VAL* 4.1 17.0 - - + -
198C LEU* 4.5 13.4 - - + +
204C GLY* 3.6 39.5 - - - +
208C ILE* 4.8 2.0 - - + -
227C ILE* 3.0 25.3 + - + +
228C ASN* 3.6 14.6 - - - +
229C GLN 3.4 0.2 - - - -
230C TYR* 1.3 76.6 - - - +
232C THR* 1.3 62.9 + - - +
234C ILE* 3.7 8.3 + - - +
235C GLU* 3.2 35.7 + - - +
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Residues in contact with THR 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ASN* 2.7 30.0 + - - -
229C GLN* 3.7 7.9 - - - -
230C TYR 3.2 0.2 - - - -
231C VAL* 1.3 79.2 - - - +
233C GLN* 1.3 61.8 + - - +
234C ILE 3.4 0.2 + - - -
235C GLU* 3.5 4.4 + - - +
236C GLN* 3.3 48.2 + - + +
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Residues in contact with GLN 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLU* 5.6 4.2 + - - -
191C LYS* 3.9 17.7 + - - +
229C GLN 3.1 17.1 + - - +
230C TYR* 4.0 7.8 - - - +
232C THR* 1.3 79.3 - - - +
234C ILE* 1.3 62.9 + - + +
236C GLN* 3.6 9.1 + - + +
237C GLU* 3.3 44.2 + - + +
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Residues in contact with ILE 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LYS* 4.0 26.0 - - + +
194C VAL* 3.7 28.7 - - + -
195C ARG* 3.7 35.2 - - + +
198C LEU* 3.9 18.6 - - + -
230C TYR* 3.0 24.0 + - + +
231C VAL 3.9 4.5 - - - +
232C THR 3.3 0.2 - - - -
233C GLN* 1.3 79.3 - - + +
235C GLU* 1.3 61.5 + - + +
237C GLU* 3.5 8.5 + - - +
238C LYS* 3.1 28.5 + - + +
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Residues in contact with GLU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C LEU* 5.4 9.6 - - + +
231C VAL* 3.2 32.1 + - - +
232C THR* 3.5 6.1 + - - +
233C GLN 3.4 0.2 - - - -
234C ILE* 1.3 82.6 - - + +
236C GLN* 1.3 61.1 + - + +
238C LYS* 3.2 16.8 + - + +
239C GLN* 3.0 40.4 + - - +
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C THR* 3.3 40.0 + - + +
233C GLN* 4.0 8.6 - - - +
234C ILE 3.4 0.2 - - - -
235C GLU* 1.3 77.0 - - + +
237C GLU* 1.3 59.8 + - + +
238C LYS 3.7 0.2 + - - -
239C GLN* 3.8 23.4 + - - +
240C GLU* 3.3 13.3 - - - +
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Residues in contact with GLU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LYS* 3.3 25.8 + - - -
233C GLN* 3.3 41.9 + - + +
234C ILE* 3.7 8.1 - - - +
235C GLU 3.3 0.4 - - - -
236C GLN* 1.3 76.7 - - + +
238C LYS* 1.3 62.0 + - - +
239C GLN 3.3 0.2 - - - -
240C GLU* 3.2 23.9 - - - +
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Residues in contact with LYS 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C GLU* 5.9 2.6 + - - -
234C ILE* 3.1 19.8 + - + +
235C GLU* 3.2 23.3 + - + +
237C GLU* 1.3 74.6 - - - +
239C GLN* 1.3 50.7 + - + +
240C GLU* 2.8 22.5 + - - +
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Residues in contact with GLN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C GLU* 3.0 28.2 + - - +
236C GLN* 4.0 18.0 - - - +
237C GLU 3.3 0.8 - - - -
238C LYS* 1.3 72.2 - - + +
240C GLU* 1.3 73.8 + - - +
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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