Contacts of the helix formed by residues 217 - 229 (chain A) in PDB entry 4A4C
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ILE* 3.4 10.8 + - - +
216A SER* 1.3 81.4 - - - +
218A GLY* 1.3 62.8 + - - +
219A LEU* 3.4 13.1 + - - +
220A GLU* 3.5 19.7 + - - +
221A ALA* 3.2 17.8 + - - +
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Residues in contact with GLY 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 1.3 73.0 - - - +
219A LEU* 1.3 64.3 + - - +
221A ALA* 3.1 9.4 + - - +
222A MET* 3.0 28.2 + - - +
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 3.4 9.3 + - - +
218A GLY* 1.3 75.1 - - - +
220A GLU* 1.3 58.6 + - - +
222A MET* 2.9 24.5 + - + +
223A ALA* 3.0 14.2 + - - +
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A PRO 4.4 1.0 - - - +
215A ILE* 3.9 13.0 - - + +
216A SER* 3.1 38.0 + - - -
217A SER* 3.5 16.3 + - - +
218A GLY 3.4 0.6 - - - -
219A LEU* 1.3 77.4 - - - +
221A ALA* 1.3 56.4 + - - +
223A ALA* 4.2 6.5 - - - -
224A LEU* 2.9 26.4 + - + +
255A LEU* 4.2 11.6 - - - +
258A TRP* 3.4 17.7 - - + -
259A ASN* 3.7 27.3 + - - +
263A VAL* 5.9 1.6 - - + -
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A TRP* 3.4 11.6 - - + -
206A ARG* 4.3 25.8 - - + -
215A ILE* 3.8 13.7 - - + +
217A SER 3.2 13.8 + - - +
218A GLY* 3.1 12.7 + - - +
219A LEU 3.1 0.6 - - - -
220A GLU* 1.3 75.4 - - - +
222A MET* 1.3 71.2 + - + +
224A LEU* 3.4 4.7 + - - -
225A LYS* 2.7 23.9 + - - +
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Residues in contact with MET 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A TRP* 4.4 17.0 - - + +
203A LYS* 4.4 10.3 - - - +
218A GLY* 3.0 20.5 + - - +
219A LEU* 2.9 13.0 + - + +
221A ALA* 1.3 90.2 - - + +
223A ALA* 1.3 58.6 + - - +
225A LYS* 3.1 13.6 + - - +
226A SER* 2.8 31.5 + - - -
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU 3.0 11.1 + - - +
220A GLU* 3.6 11.7 - - - +
222A MET* 1.3 74.8 - - - +
224A LEU* 1.3 61.5 + - - +
226A SER* 2.7 21.9 + - - -
227A THR* 2.8 17.3 + - - -
258A TRP* 3.5 14.4 - - + -
263A VAL* 5.1 7.0 - - + -
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A TRP* 4.2 11.7 - - + -
205A PHE* 5.4 2.9 - - + -
209A LEU* 3.8 29.4 - - + -
215A ILE* 4.0 20.9 - - + -
220A GLU 2.9 18.9 + - - +
221A ALA* 3.7 5.8 - - - +
223A ALA* 1.3 73.7 - - - +
225A LYS* 1.3 69.9 + - - +
227A THR* 3.2 2.1 + - - -
228A ILE* 3.1 26.3 + - + +
244A PHE* 3.4 37.5 - - + -
255A LEU* 4.0 14.6 - - + -
258A TRP* 3.3 20.8 - - + -
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Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A TRP* 3.4 53.5 - - + +
221A ALA 2.7 21.4 + - - +
222A MET* 3.1 17.4 + - - +
224A LEU* 1.3 73.3 - - - +
226A SER* 1.3 65.4 + - - +
227A THR 2.9 0.7 + - - -
229A ASP* 2.8 45.1 + - + +
234A ASP* 2.6 43.7 + - - +
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A MET 2.8 17.3 + - - -
223A ALA* 2.7 26.0 + - - -
225A LYS* 1.3 75.1 - - - +
227A THR* 1.3 60.9 + - - +
229A ASP* 3.8 7.5 - - - +
232A CYS* 5.7 0.5 - - - -
271A PHE* 3.6 28.6 - - - -
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Residues in contact with THR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA 2.8 20.3 + - - -
224A LEU 3.2 4.4 + - - -
225A LYS 3.1 0.6 - - - -
226A SER* 1.3 85.3 + - - +
228A ILE* 1.3 61.3 - - - +
230A LEU* 3.7 18.9 - - - +
244A PHE* 3.8 17.1 - - + -
248A PHE* 4.0 14.1 - - + -
258A TRP* 3.2 29.8 + - + +
262A ALA* 5.4 0.3 - - - +
268A TYR* 4.4 21.2 + - + +
271A PHE* 5.2 2.2 - - - -
295A LEU* 5.5 4.0 - - + +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A TRP* 3.9 12.1 - - + -
205A PHE* 4.0 26.7 - - + -
224A LEU* 3.1 21.8 + - + +
225A LYS 3.7 2.5 - - - +
227A THR* 1.3 76.3 - - - +
229A ASP* 1.3 63.1 + - - +
230A LEU* 3.1 11.3 + - - +
236A ILE* 3.7 32.1 - - + +
240A GLU* 3.8 20.9 - - - +
241A PHE* 4.3 7.9 - - + -
244A PHE* 3.3 50.3 - - + -
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Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LYS* 2.8 36.2 + - + +
226A SER* 3.8 12.8 - - - +
227A THR 3.5 0.2 - - - -
228A ILE* 1.3 76.3 - - - +
230A LEU* 1.3 57.4 + - - +
232A CYS* 2.3 51.8 + - - -
233A ASN 3.4 0.7 + - - -
234A ASP* 3.0 31.4 + - - +
235A TYR 4.1 3.6 - - - +
236A ILE* 4.6 6.7 - - + +
240A GLU* 3.8 3.8 - - - -
271A PHE* 4.2 0.7 - - - -
1438A CA 2.9 15.9 - - - -
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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