Contacts of the helix formed by residues 220 - 232 (chain C) in PDB entry 2AG1
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 ARG 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B ASP* 5.8 0.2 + - - -
184C ALA 4.6 5.1 + - - -
185C HIS* 4.4 35.0 + - - +
186C GLY 5.2 2.0 - - - +
215C ALA 4.4 0.2 + - - -
218C THR* 2.9 45.7 + - - +
219C ALA* 1.3 71.7 + - - +
221C LYS* 1.3 58.9 + - - +
222C THR 3.5 2.0 - - - -
223C ALA* 4.0 18.9 - - + +
224C LEU* 3.0 27.9 + - - +
244C MSE 3.8 7.7 - - - +
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Residues in contact with LYS 221 (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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219C ALA* 2.7 27.9 + - - +
220C ARG* 1.3 70.0 - - - +
222C THR* 1.3 70.2 + - + +
224C LEU* 3.6 2.9 - - - +
225C SER* 3.0 27.6 + - - -
243C SER 5.6 4.3 - - - -
244C MSE 3.9 31.6 - - + +
247C GLY* 6.4 1.8 - - - -
248C LEU* 5.5 0.2 - - - +
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Residues in contact with THR 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 ARG 3.5 0.4 - - - -
221C LYS* 1.3 81.7 - - + +
223C ALA* 1.3 63.9 + - - +
225C SER* 3.6 7.5 + - - -
226C ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 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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220C ARG* 3.5 21.6 + - + +
221C LYS 3.2 0.4 - - - -
222C THR* 1.3 77.7 + - - +
224C LEU* 1.3 65.7 + - - +
226C ALA* 3.0 8.2 + - - +
227C PHE* 2.9 24.2 + - - +
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Residues in contact with LEU 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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209C ILE* 5.8 3.4 - - + -
211C LEU* 4.0 31.4 - - + -
215C ALA* 6.4 0.2 - - + -
220C ARG* 3.0 19.4 + - - +
221C LYS* 3.6 5.4 - - - +
223C ALA* 1.3 74.4 - - - +
225C SER* 1.3 58.2 + - - +
227C PHE* 3.1 15.6 + - + +
228C VAL* 2.8 50.5 + - + +
235C VAL* 5.2 3.4 - - + -
244C MSE 3.3 39.5 - - + +
248C LEU* 3.9 16.2 - - + -
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Residues in contact with SER 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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221C LYS 3.0 16.4 + - - -
222C THR* 3.6 8.0 + - - -
224C LEU* 1.3 79.0 - - - +
226C ALA* 1.3 58.6 + - - +
228C VAL* 4.1 0.9 - - - +
229C ALA* 2.9 30.9 + - - +
247C GLY 4.5 13.0 - - - -
248C LEU* 3.7 24.5 - - - -
249C PRO* 5.3 5.6 - - - +
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Residues in contact with ALA 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 THR 3.1 13.5 + - - +
223C ALA* 3.0 11.2 + - - +
225C SER* 1.3 74.8 + - - +
227C PHE* 1.3 58.9 + - - +
229C ALA* 3.9 4.9 - - - +
230C ALA* 3.0 30.5 + - - +
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Residues in contact with PHE 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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198C LEU* 4.5 15.7 - - + -
201C LEU* 3.8 24.5 - - + -
209C ILE* 3.7 29.2 - - + -
223C ALA 2.9 12.7 + - - +
224C LEU* 3.5 16.8 - - + +
226C ALA* 1.3 74.5 - - - +
228C VAL* 1.3 64.4 + - + +
230C ALA* 3.4 4.8 + - + +
231C THR* 3.0 48.5 + - + +
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Residues in contact with VAL 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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209C ILE* 4.8 2.5 - - + -
224C LEU* 2.8 43.9 + - + +
225C SER 4.1 2.7 - - - +
227C PHE* 1.3 74.6 - - + +
229C ALA* 1.3 60.5 + - - +
231C THR* 4.0 5.2 - - - -
232C GLY* 2.8 29.8 + - - -
233C VAL 3.9 13.5 - - - +
235C VAL* 3.6 20.0 - - + -
248C LEU* 4.0 18.2 - - + -
249C PRO* 4.8 1.6 - - + -
252C MSE 3.4 34.8 - - + +
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Residues in contact with ALA 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 SER 2.9 20.2 + - - +
226C ALA* 3.9 5.4 - - - +
228C VAL* 1.3 76.5 - - - +
230C ALA* 1.3 62.3 + - - +
232C GLY* 4.2 2.9 + - - -
249C PRO* 5.4 6.3 - - + +
252C MSE 3.8 16.0 - - + +
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Residues in contact with ALA 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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226C ALA 3.0 18.3 + - - +
227C PHE* 3.9 5.6 - - + +
228C VAL 3.3 0.2 - - - -
229C ALA* 1.3 80.0 - - - +
231C THR* 1.3 64.0 + - + +
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Residues in contact with THR 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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198C LEU* 6.0 0.4 - - + -
201C LEU* 4.4 9.4 - - + -
209C ILE* 5.2 0.5 - - - +
227C PHE* 3.0 45.9 + - + +
228C VAL* 3.7 4.0 + - - -
230C ALA* 1.3 81.2 - - + +
232C GLY* 1.3 65.4 + - - +
233C VAL* 3.3 31.2 + - - +
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Residues in contact with GLY 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 VAL 2.8 17.0 + - - -
229C ALA 4.2 2.5 + - - -
230C ALA 3.6 1.4 - - - -
231C THR* 1.3 77.7 - - - +
233C VAL* 1.3 59.5 + - - +
234C PRO* 3.6 7.4 - - - +
252C MSE 4.2 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