Contacts of the helix formed by residues 219 - 227 (chain B) in PDB entry 3OPY
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 GLU 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A SER* 6.0 1.4 - - - -
394A HIS* 5.5 9.2 + - - +
218B HIS* 1.3 78.2 + - + +
220B GLY* 1.3 65.1 + - - +
221B TYR 3.4 0.3 + - - -
222B GLU* 3.1 44.6 + - + +
223B GLY 3.2 0.7 + - - -
231B TYR* 4.0 17.9 - - + -
251B ILE 3.4 18.3 + - - +
252B GLY* 3.4 17.9 + - - -
253B THR 3.6 16.8 + - - +
254B ALA* 3.3 16.6 - - + +
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Residues in contact with GLY 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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187B MET* 3.8 15.9 - - - -
188B THR 3.4 21.5 + - - -
189B SER* 5.2 0.7 - - - -
217B ILE* 3.4 18.5 + - - +
218B HIS 3.4 2.2 - - - -
219B GLU* 1.3 73.8 - - - +
221B TYR* 1.3 57.4 + - - -
223B GLY 3.2 2.1 + - - -
224B LEU* 3.0 22.9 + - - +
252B GLY 3.4 8.3 + - - -
254B ALA 4.7 2.7 - - - -
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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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187B MET* 3.7 23.1 - - + +
189B SER* 3.6 24.4 + - - -
219B GLU 3.4 0.6 + - - -
220B GLY* 1.3 67.5 - - - -
222B GLU* 1.4 55.1 + - - +
224B LEU* 3.1 18.6 + - + +
225B VAL* 2.8 38.1 + - - +
254B ALA 4.3 7.7 + - - +
256B CYS* 3.7 19.3 - - + -
259B PHE* 3.5 49.1 - + + -
280B LEU* 5.2 2.2 - - + -
282B VAL* 3.8 8.1 - - + +
288B SER* 2.7 33.0 + - - -
291B GLY* 5.3 2.0 - - - -
292B ALA* 3.1 24.4 + - - +
295B PHE* 5.9 0.4 - + - -
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Residues in contact with GLU 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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219B GLU* 3.1 34.5 + - + +
221B TYR* 1.4 74.9 - - - +
223B GLY* 1.3 58.0 + - - +
225B VAL* 3.9 0.5 - - - +
226B ARG* 2.9 78.1 + - - +
231B TYR* 4.3 6.5 - - + -
254B ALA* 3.6 19.1 + - + +
255B ARG 5.2 2.9 - - - +
256B CYS* 3.5 23.3 - - + +
257B LYS* 4.6 6.9 + - - +
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Residues in contact with GLY 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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217B ILE* 3.8 5.8 - - - -
218B HIS 3.1 23.1 + - - -
219B GLU 3.2 4.4 + - - -
220B GLY 3.2 4.3 + - - -
222B GLU* 1.3 78.6 - - - +
224B LEU* 1.3 55.0 + - - +
227B GLY* 2.8 30.7 + - - -
231B TYR* 3.5 24.3 - - - +
232B ILE* 4.1 2.8 - - - +
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Residues in contact with LEU 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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187B MET* 4.2 4.7 - - - -
217B ILE* 3.5 19.0 - - + +
220B GLY 3.0 12.4 + - - +
221B TYR* 3.4 36.1 - - + +
223B GLY* 1.3 77.1 - - - +
225B VAL* 1.4 59.7 + - - +
232B ILE* 5.0 7.2 - - + -
259B PHE* 4.4 4.3 - - + -
268B ALA* 3.4 27.1 - - + +
271B ASN* 3.3 22.7 + - - +
272B MET* 3.8 30.5 - - + +
277B ILE* 6.1 0.7 - - + -
280B LEU* 4.1 29.8 - - + -
295B PHE* 5.0 2.5 - - + -
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Residues in contact with VAL 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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221B TYR 2.8 23.5 + - - +
222B GLU 4.0 1.3 - - - +
224B LEU* 1.4 71.0 - - - +
226B ARG* 1.4 61.4 + - + +
256B CYS* 3.7 18.8 - - - -
258B GLU* 3.4 37.9 - - + +
259B PHE* 3.6 31.2 - - + -
264B GLY* 3.7 15.0 - - - +
267B LYS* 3.4 22.0 - - + +
268B ALA* 3.9 7.4 - - + +
271B ASN* 2.8 17.5 + - - -
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Residues in contact with ARG 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 GLU* 2.9 53.6 + - - +
225B VAL* 1.4 74.9 - - + +
227B GLY* 1.3 64.1 + - - +
230B LYS* 4.6 7.2 - - - +
231B TYR* 3.3 43.4 + - + -
257B LYS* 4.1 17.7 - - - +
267B LYS* 4.3 18.0 + - - +
271B ASN* 3.7 5.6 + - - +
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Residues in contact with GLY 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 GLY 2.8 20.2 + - - -
225B VAL 3.4 2.0 - - - -
226B ARG* 1.3 81.5 - - - +
228B GLY* 1.3 63.7 + - - -
230B LYS* 4.6 2.3 - - - +
231B TYR* 3.4 20.0 - - - -
232B ILE* 3.7 10.1 - - - -
271B ASN* 3.4 21.1 - - - -
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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