Contacts of the helix formed by residues 223 - 234 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B MET* 5.6 1.8 - - - -
222B ALA* 1.3 86.2 - - + +
224B THR* 1.3 67.3 + - - +
225B SER* 4.6 5.2 - - - +
226B PHE* 3.0 23.8 + - + +
227B ILE 3.1 8.1 + - - -
292B VAL 3.6 9.1 - - - +
293B ASP* 3.8 6.3 - - - +
295B ASP 4.4 7.0 - - - +
296B LYS* 3.9 30.3 - - - +
297B ASN 4.4 0.2 - - - +
298B THR 3.6 10.5 - - - +
299B PHE* 3.0 30.7 - - + -
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Residues in contact with THR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ALA 3.3 2.2 + - - -
223B PRO* 1.3 67.3 - - - +
225B SER* 1.3 73.2 + - - +
227B ILE* 2.7 14.3 + - - +
228B ASN* 2.8 29.3 + - - +
291B PRO* 3.7 27.6 - - - +
292B VAL 4.3 0.6 + - - -
293B ASP* 2.9 35.1 + - - +
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PRO* 4.8 5.6 - - - -
224B THR* 1.3 85.2 + - - +
226B PHE* 1.3 64.9 + - - -
227B ILE 3.0 0.3 + - - -
228B ASN* 3.3 19.7 + - - +
229B LYS* 3.5 31.2 + - - +
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.6 13.2 - - + -
201B PHE* 3.5 42.4 - + + -
204B THR* 3.3 31.8 + - + -
205B SER* 3.6 18.6 - - - -
206B MET* 4.0 14.6 - - + -
222B ALA* 3.6 12.3 - - + -
223B PRO* 3.0 21.0 + - + +
225B SER* 1.3 79.7 + - - +
227B ILE* 1.3 65.6 + - + +
229B LYS* 3.9 15.5 - - - +
230B PHE* 3.7 13.0 + - - +
299B PHE* 3.2 35.0 - + + -
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PHE* 5.8 2.5 - - + -
222B ALA* 3.6 15.3 - - + +
223B PRO 3.1 8.0 + - - +
224B THR* 2.7 15.7 + - - +
226B PHE* 1.3 70.1 - - + +
228B ASN* 1.3 59.2 + - - +
229B LYS 3.0 2.0 - - - -
230B PHE* 2.4 39.2 + - + -
231B PHE* 3.0 47.8 + - + -
289B ILE* 4.1 18.4 - - + -
290B LEU 3.4 9.0 - - - +
291B PRO* 3.2 44.0 - - + -
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B THR* 2.8 35.4 + - - +
225B SER* 3.6 13.8 - - - +
227B ILE* 1.3 79.0 - - - +
229B LYS* 1.3 64.2 + - + +
231B PHE* 4.6 4.2 - - - +
232B LYS* 3.1 29.1 + - - +
291B PRO* 6.0 0.7 - - - +
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Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER* 6.0 1.8 - - - -
151A GLN* 5.8 2.6 + - - -
173A ILE* 5.2 18.9 + - + +
175A GLU* 3.6 14.4 - - + +
204B THR* 3.5 22.8 + - - +
205B SER 5.0 8.5 + - - -
225B SER* 3.6 29.5 + - - +
226B PHE* 3.9 10.1 - - - +
227B ILE 2.6 3.6 + - - -
228B ASN* 1.3 78.2 - - + +
230B PHE* 1.3 58.0 + - - +
232B LYS* 2.7 38.7 + - - +
233B ASP* 3.4 2.4 + - - +
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Residues in contact with PHE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PHE* 3.4 58.6 - + + -
202B GLY* 4.4 0.4 - - - -
203B LYS 5.2 1.1 - - - -
204B THR* 3.4 17.2 - - + +
226B PHE 3.7 5.3 + - - +
227B ILE* 2.4 25.6 + - + +
229B LYS* 1.3 67.8 - - - +
231B PHE* 1.3 86.6 + + - +
233B ASP* 2.8 22.5 + - + +
234B LEU* 2.9 30.2 - - + +
255B PRO* 4.2 26.2 - - + -
257B LEU* 4.4 9.4 - - + -
273B TYR* 4.6 6.7 - + - -
287B LEU* 5.9 1.1 - - + -
289B ILE* 4.3 18.4 - - + -
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ILE* 3.0 37.8 + - + -
228B ASN* 4.3 5.4 - - - +
230B PHE* 1.3 99.5 - + - +
232B LYS* 1.3 65.2 + - - +
234B LEU* 3.0 9.4 + - + +
235B ASN* 3.0 18.0 + - - -
236B VAL* 3.5 26.9 - - + +
245B TYR* 3.2 47.1 - + - -
287B LEU* 4.1 18.2 - - + -
289B ILE* 3.9 35.7 - - + -
291B PRO* 4.6 1.8 - - + -
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Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLU* 3.7 13.5 + - - +
228B ASN 3.1 16.9 + - - +
229B LYS* 2.7 21.6 + - - +
231B PHE* 1.3 77.4 - - - +
233B ASP* 1.3 107.3 + - - +
235B ASN* 3.2 18.7 + - - +
236B VAL 5.4 0.2 - - - +
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Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLU* 2.9 30.8 - - - +
203B LYS* 3.8 19.9 + - - +
204B THR* 4.4 1.7 + - - +
229B LYS 3.4 2.7 + - - +
230B PHE* 2.8 29.9 + - + +
232B LYS* 1.3 101.0 + - - +
234B LEU* 1.3 57.8 + - + +
235B ASN* 3.3 11.3 + - - +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B PHE* 2.9 49.4 - - + +
231B PHE* 3.1 14.8 - - - +
233B ASP* 1.3 73.2 - - + +
235B ASN* 1.3 77.2 + - - +
236B VAL* 3.3 13.3 + - + +
247B THR* 4.1 14.5 + - + +
251B ASN* 4.1 27.8 + - - +
254B MET* 5.9 2.9 - - + -
255B PRO* 4.6 13.2 - - + -
273B TYR* 5.3 4.5 - - + +
287B LEU* 5.4 11.4 - - + -
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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