Contacts of the helix formed by residues 218 - 226 (chain B) in PDB entry 2BAP
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 ASN 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B VAL* 4.1 29.8 - - + +
171B VAL* 4.0 16.6 - - - +
214B ALA 4.5 1.8 + - - -
215B PHE 2.7 30.3 + - - -
216B MET 2.5 12.1 + - - +
217B ASN* 1.3 77.4 - - - +
219B LYS* 1.3 64.7 + - - +
220B PHE* 3.1 18.9 + - - +
221B GLY* 2.6 23.5 + - - +
222B ILE* 3.1 24.3 + - - +
1180D GLY 5.6 1.1 - - - +
1181D VAL* 3.5 16.5 - - + +
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Residues in contact with LYS 219 (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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218B ASN* 1.3 75.5 - - - +
220B PHE* 1.3 63.7 + - - +
222B ILE* 3.5 8.8 + - + +
223B LYS* 3.2 30.1 + - + +
1181D VAL* 3.8 16.4 - - + +
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Residues in contact with PHE 220 (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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168B VAL* 5.0 3.5 - - + +
171B VAL* 4.3 4.9 - - + -
172B GLN* 3.5 63.0 - - + +
175B GLY* 4.0 24.0 - - - -
176B ALA 4.9 1.1 - - - -
215B PHE* 4.4 9.2 - + - -
218B ASN* 3.1 11.4 + - - +
219B LYS* 1.3 78.7 - - - +
221B GLY* 1.3 61.3 + - - +
223B LYS* 3.4 13.0 - - + +
224B THR* 2.5 48.0 + - + -
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Residues in contact with GLY 221 (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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215B PHE* 3.3 44.9 - - - -
216B MET* 3.7 7.3 - - - +
218B ASN* 2.6 17.6 + - - -
220B PHE* 1.3 75.3 - - - +
222B ILE* 1.3 66.9 + - - +
224B THR 3.4 0.9 + - - -
225B MET* 3.2 15.8 + - - +
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Residues in contact with ILE 222 (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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216B MET* 3.0 31.3 - - + +
218B ASN 3.1 17.0 + - - +
219B LYS* 4.0 6.7 - - + +
221B GLY* 1.3 73.8 - - - +
223B LYS* 1.3 56.8 + - + +
225B MET* 2.8 26.9 + - - +
226B LEU* 3.0 18.8 + - + +
257B LEU* 4.1 10.5 - - + +
260B LEU* 3.5 33.7 - - + -
1181D VAL* 4.0 23.6 - - + -
1182D MET* 5.0 5.6 - - + -
1185D LEU* 4.9 12.6 - - + -
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Residues in contact with LYS 223 (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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219B LYS* 3.2 22.3 + - + +
220B PHE* 3.4 21.8 - - + +
222B ILE* 1.3 79.5 - - + +
224B THR* 1.3 58.4 + - - +
226B LEU* 3.4 16.1 + - + +
227B GLU* 3.3 50.0 + - - +
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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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175B GLY 4.6 0.7 - - - -
176B ALA* 3.7 30.1 - - + +
179B LEU* 3.1 25.8 - - + +
215B PHE* 4.2 10.3 - - + -
220B PHE* 2.5 40.9 + - + -
221B GLY 3.9 4.3 - - - -
222B ILE 3.0 0.8 + - - -
223B LYS* 1.3 78.2 + - - +
225B MET* 1.3 62.9 + - - +
226B LEU 3.2 0.7 - - - -
227B GLU* 3.7 19.0 + - + +
228B THR* 3.7 8.1 + - - +
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Residues in contact with MET 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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179B LEU* 4.0 21.5 - - + +
183B LEU* 3.9 15.7 - - + -
212B LEU* 4.0 6.7 - - + -
215B PHE* 5.2 0.9 - - + -
216B MET* 3.3 41.1 - - + -
221B GLY 3.2 9.6 + - - +
222B ILE 2.8 11.2 + - - +
224B THR* 1.3 76.2 - - - +
226B LEU* 1.3 63.2 + - + +
227B GLU 3.2 2.0 - - - -
228B THR* 2.8 31.3 + - - +
231B GLY* 3.5 30.3 - - - +
232B ILE* 4.0 10.8 - - + +
234B LEU* 5.7 0.2 - - + -
235B LEU* 3.8 19.1 - - + +
257B LEU* 5.8 2.9 - - + -
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Residues in contact with LEU 226 (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 ILE* 3.0 29.1 + - + +
223B LYS* 3.6 16.8 - - + +
224B THR 3.2 0.6 - - - -
225B MET* 1.3 79.1 - - + +
227B GLU* 1.3 58.2 + - - +
232B ILE* 4.1 20.4 - - + -
257B LEU* 3.6 23.6 - - + -
260B LEU* 4.2 2.9 - - + -
263B PRO* 3.6 37.0 - - + -
266B MET* 4.1 15.7 - - + -
269B ARG* 3.3 30.3 + - - +
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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