Contacts of the helix formed by residues 217 - 228 (chain B) in PDB entry 5B2R
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B LEU* 1.3 75.7 - - - +
218B LYS* 1.3 57.0 + - - +
219B SER* 4.0 12.2 + - - -
220B ARG* 2.7 40.7 + - - +
221B ARG* 3.1 11.2 + - - +
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Residues in contact with LYS 218 (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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217B SER* 1.3 72.4 - - - +
219B SER* 1.3 63.1 + - - +
220B ARG 3.2 0.7 + - - -
221B ARG* 3.2 42.0 + - - +
222B LEU* 3.2 22.2 + - - +
246B LEU* 3.4 61.3 - - + +
247B GLY* 4.2 5.6 - - - +
248B LEU* 4.7 13.2 - - + +
304B ASP* 4.0 17.6 + - - -
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Residues in contact with SER 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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217B SER* 4.2 10.9 + - - -
218B LYS* 1.3 77.5 + - - +
220B ARG* 1.3 60.4 + - - +
222B LEU* 3.8 8.4 - - - +
223B GLU* 3.7 23.0 + - - +
234B LYS* 4.1 12.4 + - - +
248B LEU* 5.8 8.8 - - - +
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Residues in contact with ARG 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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216B LEU* 4.1 29.7 - - + +
217B SER* 2.7 29.6 + - - +
219B SER* 1.3 70.4 - - - +
221B ARG* 1.3 64.4 + - - +
222B LEU 3.1 2.0 - - - -
223B GLU* 3.0 36.9 + - - +
224B ASN* 3.0 35.7 + - - +
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Residues in contact with ARG 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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211B ILE* 3.3 24.8 - - - +
212B LEU* 2.8 32.7 + - - +
213B SER* 4.6 2.6 - - - +
214B ALA* 3.3 23.3 + - + +
215B ARG 4.9 0.4 + - - -
216B LEU* 2.8 36.8 + - + -
217B SER* 3.1 13.4 + - - +
218B LYS* 3.2 53.5 + - - +
220B ARG* 1.3 75.0 - - - +
222B LEU* 1.3 55.9 + - - +
224B ASN* 3.7 9.7 - - - +
225B LEU* 2.9 32.1 + - - +
246B LEU* 4.5 10.4 - - + +
303B SER* 5.5 1.6 + - - -
304B ASP* 4.3 12.9 + - - -
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Residues in contact with LEU 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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218B LYS 3.2 15.0 + - - +
219B SER* 3.8 9.0 - - - +
220B ARG 3.1 0.4 - - - -
221B ARG* 1.3 77.9 - - - +
223B GLU* 1.3 63.6 + - - +
225B LEU* 3.7 2.7 - - - +
226B ILE* 2.9 42.7 + - + +
234B LYS* 3.5 38.8 - - + +
239B GLY 3.5 26.2 - - - +
240B ASN* 6.0 0.4 - - - -
242B ILE* 4.0 22.9 - - + -
243B ALA* 5.0 12.6 - - + +
246B LEU* 5.3 6.1 - - + +
248B LEU* 5.7 7.0 - - + -
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Residues in contact with GLU 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 SER 3.7 14.9 - - - +
220B ARG* 3.0 32.2 + - - +
222B LEU* 1.3 78.5 - - - +
224B ASN* 1.3 60.3 + - - +
226B ILE* 3.2 4.6 + - - +
227B ALA* 2.8 31.2 + - - +
234B LYS* 4.5 21.7 + - + +
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Residues in contact with ASN 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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211B ILE* 3.7 18.5 + - + +
214B ALA* 5.6 0.4 - - - +
216B LEU* 3.6 29.1 - - - +
220B ARG* 3.0 36.6 + - - +
221B ARG* 3.7 10.3 - - - +
222B LEU 3.3 0.2 - - - -
223B GLU* 1.3 76.9 - - - +
225B LEU* 1.3 63.9 + - - +
227B ALA* 3.2 20.4 + - - +
228B GLN* 3.5 13.2 + - - +
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Residues in contact with LEU 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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185B PHE* 4.0 12.6 - - + -
206B VAL* 4.0 26.5 - - + -
208B ALA* 5.0 2.5 - - - -
211B ILE* 3.5 21.4 - - + +
212B LEU* 4.0 20.9 - - + -
221B ARG 2.9 17.7 + - - +
222B LEU* 3.7 4.7 - - - +
224B ASN* 1.3 77.0 - - - +
226B ILE* 1.3 60.7 + - + +
228B GLN* 3.0 24.3 + - - +
229B LEU* 3.6 27.4 - - + +
238B PHE* 4.1 2.0 - - + -
242B ILE* 3.8 31.6 - - + -
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Residues in contact with ILE 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 LEU* 2.9 31.4 + - + +
223B GLU* 3.8 4.7 - - - +
225B LEU* 1.3 90.2 - - + +
227B ALA* 1.3 63.2 + - - +
229B LEU* 3.1 29.1 + - + +
232B GLU* 3.3 27.4 - - + +
233B LYS* 3.8 2.5 - - - +
234B LYS* 3.6 27.8 - - + +
238B PHE* 4.8 2.9 - - + -
239B GLY* 3.8 26.5 - - - +
242B ILE* 5.0 0.4 - - + -
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Residues in contact with ALA 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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223B GLU 2.8 13.9 + - - +
224B ASN* 3.3 15.9 - - - +
225B LEU 3.1 0.8 - - - -
226B ILE* 1.3 77.6 - - - +
228B GLN* 1.3 64.8 + - + +
229B LEU 3.3 2.6 + - - -
230B PRO* 4.9 2.4 - - - +
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Residues in contact with GLN 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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202B ASN 4.9 1.2 - - - +
205B GLY 5.8 0.3 - - - +
206B VAL* 4.0 29.0 - - + +
211B ILE* 3.7 21.5 - - + +
224B ASN 3.6 14.2 + - - +
225B LEU 3.0 9.4 + - - +
227B ALA* 1.3 81.0 + - - +
229B LEU* 1.3 66.1 - - - +
230B PRO* 3.5 10.9 - - - +
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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