Contacts of the helix formed by residues 218 - 227 (chain B) in PDB entry 2IOY
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 THR 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ASN* 4.9 2.7 - - - +
14B PRO* 4.4 16.6 - - + -
15B PHE* 4.1 25.6 - - + +
192B ASP* 3.0 19.5 + - + +
193B GLU* 5.0 3.8 + - + +
196B LEU* 4.7 1.7 - - - +
216B ASP* 3.7 25.4 - - + +
217B GLY* 1.3 80.6 - - - +
219B GLU* 1.3 64.5 + - - +
220B ASP* 3.9 6.7 + - - +
221B ALA* 3.1 14.4 + - - +
222B LEU* 3.0 20.3 + - - +
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Residues in contact with GLU 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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14B PRO* 5.9 0.8 - - - +
218B THR* 1.3 72.5 - - - +
220B ASP* 1.3 66.4 + - - +
222B LEU* 3.1 12.9 + - + +
223B LYS* 2.9 25.4 + - - +
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Residues in contact with ASP 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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14B PRO* 4.7 10.1 - - + +
167B ARG* 2.8 27.0 + - - +
193B GLU* 4.5 1.7 - - - +
196B LEU* 3.6 25.0 - - + +
218B THR* 3.3 5.4 + - - +
219B GLU* 1.3 80.3 - - - +
221B ALA* 1.3 57.6 + - - +
223B LYS* 3.5 12.5 + - - +
224B ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 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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192B ASP* 3.1 42.8 - - + +
196B LEU* 4.2 2.2 - - - +
217B GLY 4.6 1.3 - - - -
218B THR* 3.1 13.0 + - - +
220B ASP* 1.3 78.6 - - - +
222B LEU* 1.3 57.6 + - - +
224B ALA* 3.0 6.1 + - - +
225B ILE* 2.9 32.9 + - - +
230B MET* 4.0 19.8 - - + +
233B THR* 4.6 5.6 - - + -
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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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217B GLY* 3.9 26.9 - - - +
218B THR 3.0 17.1 + - - +
219B GLU* 3.1 14.8 + - + +
221B ALA* 1.3 76.9 - - - +
223B LYS* 1.3 56.9 + - - +
225B ILE* 3.2 5.8 + - + +
226B LYS* 3.0 38.9 + - - +
233B THR* 4.3 6.7 - - + -
235B ALA* 5.9 0.4 - - + -
269B ILE* 4.1 19.1 - - + -
274B VAL* 3.8 24.9 - - + +
275B GLN* 5.2 13.9 - - + +
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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 GLU 2.9 17.0 + - - +
220B ASP* 3.6 13.0 - - - +
222B LEU* 1.3 77.0 - - - +
224B ALA* 1.3 56.2 + - - +
226B LYS* 3.4 13.0 + - + +
227B GLU* 3.0 58.8 + - + +
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Residues in contact with ALA 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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196B LEU* 4.0 19.7 - - + -
199B ILE* 4.6 1.3 - - + -
220B ASP 3.0 14.9 + - - +
221B ALA 3.0 11.6 + - - +
223B LYS* 1.3 76.3 - - - +
225B ILE* 1.3 54.9 + - - +
227B GLU* 3.4 10.9 + - - +
228B GLY 3.1 6.6 + - - -
229B LYS* 2.9 38.7 + - + +
230B MET* 3.7 20.4 - - + +
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Residues in contact with ILE 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 ALA 2.9 16.4 + - - +
222B LEU* 3.2 12.3 + - - +
224B ALA* 1.3 74.4 - - - +
226B LYS* 1.3 64.8 + - - +
228B GLY* 3.1 12.8 + - - -
230B MET* 3.3 30.6 - - + +
231B ALA 4.5 2.0 - - - +
232B ALA 3.9 2.7 - - - +
233B THR* 3.7 36.1 - - + +
269B ILE* 3.7 24.7 - - + +
270B THR* 3.7 5.2 - - - -
271B LYS* 3.6 42.8 - - + +
274B VAL* 4.1 8.3 - - + -
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Residues in contact with LYS 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* 3.0 22.9 + - - +
223B LYS* 3.6 12.1 - - + +
225B ILE* 1.3 77.3 - - - +
227B GLU* 1.3 61.5 + - + +
228B GLY 3.5 0.3 + - - -
271B LYS* 3.5 18.9 - - - +
274B VAL* 3.7 27.1 - - + -
275B GLN* 3.3 47.7 + - - +
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Residues in contact with GLU 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 LYS* 3.0 52.7 + - + +
224B ALA* 3.7 9.1 - - - +
225B ILE 3.2 0.2 - - - -
226B LYS* 1.3 78.8 - - + +
228B GLY* 1.3 59.0 + - - +
229B LYS* 3.5 34.6 + - + +
271B LYS* 5.2 0.7 - - - -
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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