Contacts of the helix formed by residues 215 - 225 (chain E) in PDB entry 5ID3
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 ALA 215 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211E THR 2.9 16.7 + - - +
212E ASP* 3.7 14.8 - - - +
213E ARG 3.4 0.4 - - - -
214E VAL* 1.4 72.3 - - - +
216E TRP* 1.4 50.6 + - - +
217E ALA* 3.0 6.3 - - - -
218E GLY* 2.8 28.2 + - - +
219E PHE* 3.9 18.4 + - + -
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Residues in contact with TRP 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E ASP 3.8 6.3 + - - +
213E ARG* 3.3 26.0 - - - +
214E VAL* 3.1 8.0 - - - -
215E ALA* 1.4 76.0 - - - +
217E ALA* 1.3 71.2 + - - +
218E GLY 3.5 0.3 + - - -
219E PHE* 3.7 19.0 + - - +
220E ALA* 3.8 22.6 + - + +
251E TYR* 3.7 48.2 - + + -
254E VAL* 5.5 2.2 - - + -
255E ALA* 3.5 24.9 - - + +
258E PHE* 6.4 0.2 - - - +
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Residues in contact with ALA 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E VAL 3.4 16.2 - - - +
215E ALA* 4.5 0.4 - - - -
216E TRP* 1.3 88.6 - - - +
218E GLY* 1.4 59.9 + - - +
219E PHE 3.7 0.2 - - - -
220E ALA* 4.0 5.7 + - - +
221E ALA* 3.9 18.0 + - - +
252E SER* 4.3 23.1 - - - +
255E ALA* 3.9 24.2 - - + -
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Residues in contact with GLY 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E ALA* 2.8 18.9 + - - +
217E ALA* 1.4 72.1 - - - +
219E PHE* 1.4 62.9 + - - +
221E ALA* 3.7 4.0 + - - +
222E SER* 3.2 26.4 + - - -
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Residues in contact with PHE 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E ASP 5.7 2.2 - - - -
215E ALA* 3.9 24.7 - - + -
216E TRP* 3.7 10.0 + - - +
217E ALA 3.7 0.2 - - - -
218E GLY* 1.4 73.1 - - - +
220E ALA* 1.4 63.7 + - - +
222E SER* 4.0 6.0 - - - -
223E GLY* 3.3 20.8 + - - -
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Residues in contact with ALA 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E TRP* 3.8 26.5 + - + +
217E ALA* 4.0 11.0 - - - +
218E GLY 3.3 0.8 - - - -
219E PHE* 1.4 80.8 - - - +
221E ALA* 1.3 61.0 + - - +
223E GLY* 4.0 4.2 + - - -
224E VAL* 4.1 18.5 + - - +
248E PHE* 4.3 22.3 - - + +
251E TYR* 6.1 3.1 - - + -
252E SER* 6.4 0.4 - - - -
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Residues in contact with ALA 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E ALA 3.9 10.5 + - - +
218E GLY* 3.7 4.3 + - - +
220E ALA* 1.3 78.2 - - - +
222E SER* 1.4 62.4 + - - +
224E VAL* 3.5 19.7 - - - +
225E GLN* 3.6 14.1 - - - +
245E VAL* 4.5 9.6 - - + +
248E PHE* 4.7 6.7 - - - +
249E ALA* 5.0 19.5 - - + +
252E SER* 5.5 3.6 - - - -
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Residues in contact with SER 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E GLY 3.2 20.6 + - - -
219E PHE* 4.1 7.2 - - - -
220E ALA 3.5 0.2 - - - -
221E ALA* 1.4 77.3 - - - +
223E GLY* 1.4 62.9 + - - +
224E VAL 3.6 0.2 + - - -
225E GLN* 3.7 28.5 + - - +
226E THR* 5.1 2.3 + - - -
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Residues in contact with GLY 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E PHE 3.3 14.5 + - - -
220E ALA 4.0 1.5 + - - -
221E ALA 3.5 0.6 - - - -
222E SER* 1.4 79.1 - - - +
224E VAL* 1.4 61.4 + - - +
225E GLN 3.7 0.3 + - - -
226E THR* 4.1 15.8 + - - -
227E GLY 5.0 0.2 + - - -
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Residues in contact with VAL 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E ALA 4.1 12.8 - - - +
221E ALA* 3.5 20.4 - - - +
223E GLY* 1.4 73.8 - - - +
225E GLN* 1.4 52.1 + - - +
226E THR 3.0 6.3 - - - -
227E GLY* 2.7 31.5 + - - +
228E LEU* 3.4 9.7 - - + +
244E PRO* 5.0 2.0 - - + +
245E VAL* 4.5 21.8 - - + +
248E PHE* 3.8 37.7 - - + -
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Residues in contact with GLN 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E ALA 3.6 14.9 - - - +
222E SER* 3.7 27.1 + - - +
223E GLY 3.5 1.4 - - - -
224E VAL* 1.4 76.3 - - - +
226E THR* 1.4 59.3 + - - +
227E GLY 3.6 0.2 + - - -
228E LEU* 3.8 25.0 + - - +
229E PHE* 4.3 2.8 + - - +
245E VAL* 4.4 15.3 - - + -
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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