Contacts of the helix formed by residues 221 - 232 (chain C) in PDB entry 6UML
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 TYR 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C SER* 1.3 80.7 - - - +
222C LYS* 1.3 55.8 + - - +
223C TRP 3.0 2.2 - - - +
224C TRP* 2.7 42.1 + - + +
225C GLN* 3.4 4.0 + - - +
259C LYS* 6.0 5.6 - - - +
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Residues in contact with LYS 222 (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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220C SER 4.3 14.8 - - - +
221C TYR* 1.3 72.4 - - - +
223C TRP* 1.3 67.0 + - - +
225C GLN* 2.9 25.5 + - + +
226C LYS* 2.9 28.4 + - - +
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Residues in contact with TRP 223 (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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208C PHE* 5.1 19.4 - + + +
220C SER* 4.9 10.3 - - - +
221C TYR* 4.0 3.3 - - - +
222C LYS* 1.3 88.6 - - + +
224C TRP* 1.3 94.2 + + + +
226C LYS* 3.4 9.0 + - + +
227C TYR* 2.8 52.6 + + + +
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Residues in contact with TRP 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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220C SER 4.4 5.7 + - - -
221C TYR* 2.7 37.7 + - + +
223C TRP* 1.3 96.6 - + + +
225C GLN* 1.3 58.1 + - - +
227C TYR* 3.6 28.4 - + - +
228C GLN* 2.9 29.3 + - - +
251C GLU* 3.5 23.8 - - + -
252C THR* 3.5 37.5 - - + -
255C ASP* 3.3 39.8 + - + -
259C LYS* 5.5 4.5 - - - +
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Residues in contact with GLN 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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838A PRO* 3.6 35.8 - - + +
221C TYR 3.4 3.6 + - - +
222C LYS* 2.9 25.8 + - + +
224C TRP* 1.3 74.4 - - - +
226C LYS* 1.3 64.6 + - - +
228C GLN* 3.4 11.0 + - - +
229C LYS* 3.0 24.6 + - - +
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Residues in contact with LYS 226 (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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222C LYS 2.9 11.6 + - - +
223C TRP* 3.5 14.4 - - + +
225C GLN* 1.3 73.4 - - - +
227C TYR* 1.3 66.4 + - - +
229C LYS* 2.9 8.5 + - - +
230C ARG* 2.9 26.9 + - - +
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Residues in contact with TYR 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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208C PHE* 3.7 31.2 - + - -
223C TRP* 2.8 46.8 + + + +
224C TRP* 3.6 24.0 - + - +
226C LYS* 1.3 73.1 - - - +
228C GLN* 1.3 62.1 + - + +
230C ARG* 5.1 0.2 - - - -
231C LYS* 2.9 61.4 + - + +
232C PHE* 4.1 11.9 - + - -
246C SER* 5.6 1.1 - - - -
249C ASP* 2.5 38.1 + - - -
251C GLU* 3.6 17.8 - - + +
252C THR* 3.4 10.3 - - + -
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Residues in contact with GLN 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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224C TRP 2.9 21.9 + - - +
225C GLN* 3.7 9.5 + - - +
227C TYR* 1.3 78.9 - - + +
229C LYS* 1.3 62.6 - - - +
232C PHE* 3.4 25.9 + - + +
242C ARG* 3.3 47.0 - - + +
243C TRP* 3.6 30.5 - - - +
246C SER* 3.8 25.9 + - - +
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Residues in contact with LYS 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 GLN 3.0 16.1 + - - +
226C LYS* 2.9 7.9 + - - +
228C GLN* 1.3 78.2 - - - +
230C ARG* 1.3 60.7 + - - +
233C HIS* 3.5 27.7 - - - +
242C ARG* 3.7 22.6 + - - +
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Residues in contact with ARG 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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198C GLN* 5.7 0.3 + - - -
205C CYS* 5.4 4.2 - - + +
206C GLN* 4.2 6.2 - - - +
208C PHE* 3.5 27.7 - - + -
226C LYS 2.9 14.9 + - - +
227C TYR* 5.1 0.2 - - - -
229C LYS* 1.3 77.3 - - + +
231C LYS* 1.3 65.6 + - - +
232C PHE 3.6 0.2 + - - -
233C HIS* 3.7 13.8 + - - +
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Residues in contact with LYS 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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192C SER* 4.5 22.0 - - - -
194C MET* 3.7 14.6 - - + +
198C GLN* 4.2 1.9 - - - +
206C GLN* 3.5 31.6 + - - +
208C PHE* 3.3 20.9 - - + -
227C TYR* 2.9 50.6 + - + +
230C ARG* 1.3 78.9 - - - +
232C PHE* 1.3 76.6 + - + +
233C HIS* 3.3 2.9 + - - +
234C CYS 4.9 0.3 + - - -
249C ASP* 3.5 17.8 + - - +
251C GLU* 5.2 5.9 - - - +
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Residues in contact with PHE 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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192C SER* 5.7 0.9 - - - -
193C THR* 3.5 20.4 - - - -
194C MET* 3.7 21.5 - - + -
227C TYR* 4.1 9.6 - + - -
228C GLN* 3.4 31.1 + - + +
231C LYS* 1.3 98.1 - - + +
233C HIS* 1.3 64.3 + - - +
234C CYS 3.2 2.9 - - - -
235C ALA* 3.0 12.7 + - + +
242C ARG* 3.1 34.4 - - + +
245C TYR* 3.5 26.5 - - + -
246C SER* 4.0 11.0 - - - -
249C ASP* 3.4 41.1 - - + -
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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