Contacts of the helix formed by residues 210 - 222 (chain B) in PDB entry 1B8I
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 LYS 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B PHE 4.0 0.6 + - - -
209B SER* 1.3 71.5 - - - +
211B GLN* 1.3 55.9 + - - +
213B SER* 3.0 16.4 + - - -
214B GLU* 2.6 77.4 + - - +
217B ASN* 5.6 0.4 - - - -
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Residues in contact with GLN 211 (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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209B SER* 3.3 14.6 + - - +
210B LYS* 1.3 78.8 - - - +
212B ALA* 1.3 61.5 + - - +
214B GLU* 2.8 42.1 + - - +
215B ILE* 2.9 27.3 + - + +
240B LYS 4.6 8.3 + - - -
241B CYS 4.5 10.1 + - - +
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Residues in contact with ALA 212 (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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208B PHE* 4.9 3.4 - - + -
209B SER* 2.9 30.3 + - - +
211B GLN* 1.3 73.8 - - - +
213B SER* 1.3 58.2 + - - +
214B GLU 3.0 4.3 - - - -
215B ILE* 3.2 0.7 + - - -
216B LEU* 3.0 30.1 + - + +
241B CYS* 3.1 45.7 - - + +
243B ILE* 4.3 10.8 - - + -
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Residues in contact with SER 213 (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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207B ASN 4.3 2.1 + - - -
208B PHE* 3.4 23.9 - - - +
209B SER 3.1 13.4 + - - -
210B LYS* 3.0 23.4 + - - -
212B ALA* 1.3 73.4 - - - +
214B GLU* 1.3 63.1 + - - +
216B LEU* 4.1 9.9 - - - -
217B ASN* 2.5 35.7 + - - +
251B TRP* 5.3 3.9 + - - +
20D G 4.5 2.9 + - - -
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Residues in contact with GLU 214 (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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210B LYS* 2.6 37.5 + - - +
211B GLN* 2.8 37.3 + - - +
213B SER* 1.3 77.1 - - - +
215B ILE* 1.3 62.0 + - + +
217B ASN* 3.9 2.4 - - - +
218B GLU* 3.1 23.5 + - - +
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Residues in contact with ILE 215 (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 GLN* 2.9 26.3 + - + +
212B ALA 3.2 0.2 + - - -
214B GLU* 1.3 80.0 - - + +
216B LEU* 1.3 64.7 + - - +
218B GLU* 3.0 15.5 + - + +
219B TYR* 3.0 21.1 + - - +
237B LEU* 3.1 29.2 - - + -
240B LYS* 3.7 21.5 - - + +
241B CYS* 3.2 44.6 - - - +
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Residues in contact with LEU 216 (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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208B PHE* 4.0 16.8 - - + -
212B ALA* 3.0 24.3 + - + +
213B SER* 4.4 4.0 - - - -
215B ILE* 1.3 74.5 - - - +
217B ASN* 1.3 63.1 + - - +
219B TYR* 3.5 2.5 + - - +
220B PHE 3.1 18.9 + - - -
237B LEU* 4.6 7.6 - - + -
241B CYS* 3.8 11.0 - - - -
243B ILE* 4.2 15.7 - - + -
248B VAL* 3.8 29.8 - - + -
251B TRP* 3.6 57.6 - - + +
252B PHE* 4.1 8.2 - - + -
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Residues in contact with ASN 217 (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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210B LYS* 5.6 0.5 - - - -
213B SER* 2.5 30.4 + - - +
214B GLU* 3.9 3.4 - - - +
215B ILE 3.3 0.4 - - - -
216B LEU* 1.3 75.7 - - - +
218B GLU* 1.3 67.4 + - - +
220B PHE 3.3 0.9 + - - -
221B TYR* 2.6 63.1 + - + -
251B TRP* 3.9 11.8 - - - -
255B LYS* 3.0 17.6 - - - +
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Residues in contact with GLU 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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214B GLU 3.1 11.8 + - - +
215B ILE* 3.0 20.1 + - + +
217B ASN* 1.3 80.6 - - - +
219B TYR* 1.3 71.8 + - + +
221B TYR* 3.6 3.1 + - - +
222B SER* 2.5 41.2 + - - -
223B HIS* 5.0 2.9 - - - -
237B LEU* 5.8 0.4 - - + -
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Residues in contact with TYR 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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215B ILE 3.0 7.5 + - - +
216B LEU 3.7 7.2 - - - +
218B GLU* 1.3 87.7 - - + +
220B PHE* 1.3 63.8 + - - +
222B SER* 2.9 6.9 + - - -
223B HIS* 2.6 74.4 + + + -
226B ASN 5.8 0.2 - - - -
227B PRO 5.5 1.3 - - - -
228B TYR 4.8 0.4 - - - -
229B PRO* 3.4 36.1 - - + +
230B SER 4.5 1.0 + - - -
233B ALA* 4.3 12.7 - - + +
237B LEU* 3.4 37.0 - - + -
252B PHE* 3.3 25.4 - + + -
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A TRP* 4.5 7.4 - + - -
216B LEU 3.1 13.2 + - - +
217B ASN 3.8 2.7 - - - +
219B TYR* 1.3 81.4 - - - +
221B TYR* 1.3 78.0 + + - +
223B HIS 3.2 20.1 - - - +
224B LEU* 3.8 13.0 + - + -
227B PRO* 3.6 28.0 - - + -
251B TRP* 3.7 8.5 - - + -
252B PHE* 3.5 31.1 - + + -
255B LYS* 3.3 34.5 - - + -
256B ARG* 4.3 12.3 - - + -
259B TYR* 3.6 43.3 - + + -
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Residues in contact with TYR 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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217B ASN* 2.6 57.7 + - + +
218B GLU* 4.1 3.4 - - - +
220B PHE* 1.3 87.9 - + - +
222B SER* 1.3 68.0 + - - +
224B LEU* 3.1 29.3 - - + +
255B LYS* 2.9 25.1 + - - +
259B TYR* 4.9 10.5 - + - -
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Residues in contact with SER 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 GLU* 2.5 39.7 + - - -
219B TYR 2.9 2.7 + - - -
221B TYR* 1.3 80.6 - - - +
223B HIS* 1.3 75.2 + - - -
224B LEU* 3.0 6.4 + - - +
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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