Contacts of the helix formed by residues 223 - 234 (chain A) in PDB entry 2ANL
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 PRO 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A MET* 5.6 2.0 - - - -
222A ALA* 1.3 87.3 - - + +
224A THR* 1.3 67.6 + - + +
225A SER* 4.6 5.6 - - - +
226A PHE* 3.0 22.8 + - + +
227A ILE 3.1 8.3 + - - -
292A VAL 3.6 9.8 - - - +
293A ASP* 3.8 6.3 - - - +
295A ASP 4.4 6.7 - - - +
296A LYS* 3.9 29.4 - - - +
298A THR 3.6 10.8 - - - +
299A PHE* 3.0 31.0 - - + -
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Residues in contact with THR 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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222A ALA 3.3 1.6 + - - -
223A PRO* 1.3 67.1 - - + +
225A SER* 1.3 72.9 + - - +
227A ILE* 2.7 14.4 + - - +
228A ASN* 2.8 30.4 + - - +
291A PRO* 3.7 26.8 - - - +
292A VAL 4.3 0.8 + - - -
293A ASP* 2.9 34.3 + - - +
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Residues in contact with SER 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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223A PRO* 4.8 5.4 - - - -
224A THR* 1.3 84.3 + - - +
226A PHE* 1.3 65.2 + - - +
227A ILE 3.0 0.5 + - - -
228A ASN* 3.3 20.1 + - - +
229A LYS* 3.5 30.5 + - - +
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Residues in contact with PHE 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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199A VAL* 3.6 13.2 - - + -
201A PHE* 3.5 44.0 - + + -
204A THR* 3.3 29.9 + - + -
205A SER* 3.6 17.9 - - - -
206A MET* 4.0 15.3 - - + -
222A ALA* 3.6 12.3 - - + -
223A PRO* 3.0 21.0 + - + +
225A SER* 1.3 81.2 + - - +
227A ILE* 1.3 65.0 + - + +
229A LYS* 3.9 15.2 - - - +
230A PHE* 3.7 13.7 + - + +
299A PHE* 3.2 36.1 - + + -
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Residues in contact with ILE 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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201A PHE* 5.8 2.5 - - + -
222A ALA* 3.6 14.8 - - + +
223A PRO 3.1 8.4 + - - +
224A THR* 2.7 15.5 + - - +
226A PHE* 1.3 69.9 - - + +
228A ASN* 1.3 60.0 + - - +
229A LYS 3.0 1.8 - - - -
230A PHE* 2.4 39.5 + - + -
231A PHE* 3.0 48.4 + - + -
289A ILE* 4.1 18.2 - - + -
290A LEU 3.4 8.7 - - - +
291A PRO* 3.2 45.5 - - + -
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Residues in contact with ASN 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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224A THR* 2.8 36.0 + - - +
225A SER* 3.6 13.8 - - - +
227A ILE* 1.3 78.9 - - - +
229A LYS* 1.3 64.9 + - + +
231A PHE* 4.6 4.0 - - - +
232A LYS* 3.1 28.8 + - - +
291A PRO* 6.0 0.9 - - - +
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Residues in contact with LYS 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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204A THR* 3.5 26.1 + - - +
205A SER 5.0 8.3 + - - -
225A SER* 3.6 30.7 + - - +
226A PHE* 3.9 10.3 - - - +
227A ILE 2.5 3.8 + - - -
228A ASN* 1.3 79.7 - - + +
230A PHE* 1.3 57.2 + - - +
232A LYS* 2.7 41.2 + - - +
233A ASP* 3.4 5.0 + - - +
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Residues in contact with PHE 230 (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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201A PHE* 3.4 58.8 - + + -
202A GLY* 4.7 0.7 - - - -
203A LYS 5.2 1.1 - - - -
204A THR* 3.4 16.7 - - + +
226A PHE 3.7 4.7 + - - +
227A ILE* 2.4 25.6 + - + +
229A LYS* 1.3 68.1 - - - +
231A PHE* 1.3 86.5 + + - +
233A ASP* 2.8 23.4 + - + +
234A LEU* 2.9 30.5 - - + +
255A PRO* 4.2 26.5 - - + -
257A LEU* 4.4 9.6 - - + -
273A TYR* 4.6 7.0 - + - -
287A LEU* 5.9 1.1 - - + -
289A ILE* 4.3 18.6 - - + -
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Residues in contact with PHE 231 (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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227A ILE* 3.0 38.7 + - + -
228A ASN* 4.3 5.4 - - - +
230A PHE* 1.3 98.6 - + - +
232A LYS* 1.3 66.0 + - - +
233A ASP 3.0 0.2 + - - -
234A LEU* 3.0 8.2 + - + +
235A ASN* 3.0 18.4 + - - -
236A VAL* 3.5 27.1 - - + +
245A TYR* 3.2 48.9 - + - -
287A LEU* 4.1 18.4 - - + -
289A ILE* 3.9 35.0 - - + -
291A PRO* 4.6 1.1 - - + -
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Residues in contact with LYS 232 (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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203A LYS* 6.0 0.2 - - - +
228A ASN 3.1 17.1 + - - +
229A LYS* 2.7 24.0 + - - +
231A PHE* 1.3 77.6 - - - +
233A ASP* 1.3 109.0 + - - +
235A ASN* 3.2 17.7 + - - +
236A VAL 5.4 0.2 - - - +
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Residues in contact with ASP 233 (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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203A LYS* 3.8 35.6 + - - +
204A THR* 4.4 6.8 + - - +
229A LYS 3.4 8.2 + - - +
230A PHE* 2.8 29.4 + - + +
232A LYS* 1.3 102.0 + - - +
234A LEU* 1.3 57.4 + - + +
235A ASN* 3.3 11.6 + - - +
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Residues in contact with LEU 234 (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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230A PHE* 2.9 47.3 - - + +
231A PHE* 3.1 14.8 - - - +
233A ASP* 1.3 73.1 - - + +
235A ASN* 1.3 77.4 + - - +
236A VAL* 3.3 13.8 + - + +
247A THR* 4.1 15.4 + - + +
251A ASN* 4.1 27.0 + - - +
254A MET* 5.9 2.7 - - + -
255A PRO* 4.6 13.2 - - + -
273A TYR* 5.3 4.7 - - + +
287A LEU* 5.4 11.7 - - + -
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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