Contacts of the helix formed by residues 213 - 223 (chain B) in PDB entry 2W27
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 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B ILE* 3.6 6.8 - - - +
212B GLU* 1.3 80.6 - - + +
214B ASN* 1.3 67.2 + - - +
215B PHE* 3.5 27.8 - - + -
216B GLN* 3.0 13.7 + - - +
217B LEU 3.3 14.4 + - - -
232B TYR* 3.9 13.0 - - - +
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Residues in contact with ASN 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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213B ALA* 1.3 70.3 - - - +
215B PHE* 1.3 63.8 + - - +
216B GLN 3.0 1.6 - - - -
217B LEU* 2.8 22.1 + - - +
218B GLN* 3.0 13.2 + - - +
232B TYR* 2.6 37.6 + - + +
253B GLU* 3.3 24.7 + - - +
257B PHE* 4.0 21.0 - - - -
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Residues in contact with PHE 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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179B LEU* 4.1 20.4 - - + -
180B LYS 3.8 22.7 - - - -
213B ALA* 3.8 22.7 - - + -
214B ASN* 1.3 79.4 + - - +
216B GLN* 1.3 78.7 + - + +
218B GLN* 3.3 11.7 + - - +
219B TYR* 2.9 51.6 + + + -
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Residues in contact with GLN 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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176B LEU* 2.8 44.7 + - + +
177B GLN* 4.4 2.4 - - - +
179B LEU* 4.3 4.4 - - + +
180B LYS 3.3 24.2 + - - -
210B ASP 4.3 6.2 + - - -
211B ILE* 4.1 9.6 - - + -
212B GLU* 2.6 39.8 + - - +
213B ALA* 3.0 15.5 + - - +
214B ASN 3.0 0.8 - - - -
215B PHE* 1.3 102.0 - - + +
217B LEU* 1.3 60.5 + - - +
219B TYR* 3.3 8.3 + - - +
220B ALA* 2.9 27.0 + - - +
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Residues in contact with LEU 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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211B ILE* 3.9 18.5 - - + +
213B ALA 3.3 7.6 + - - +
214B ASN* 2.8 15.7 + - - +
216B GLN* 1.3 75.7 - - - +
218B GLN* 1.3 57.9 + - - +
220B ALA* 3.2 5.0 + - - +
221B TRP* 2.9 26.9 + - - +
228B PHE* 3.8 36.8 - - + -
232B TYR* 4.0 12.3 - - + -
233B LEU* 4.5 9.9 - - + -
250B LEU* 4.2 9.9 - - + -
253B GLU* 3.1 27.6 - - - +
254B PHE* 4.1 19.3 - - + -
257B PHE* 4.0 11.4 - - + -
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Residues in contact with GLN 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 ASN* 3.0 12.0 + - - +
215B PHE* 3.6 13.8 - - - +
217B LEU* 1.3 74.5 - - - +
219B TYR* 1.3 67.3 + - + +
221B TRP* 3.2 1.4 + - - +
222B ARG* 3.0 58.3 + - + +
257B PHE* 3.6 47.8 + - + +
260B HIS* 4.3 28.3 + - - +
261B GLU* 5.9 3.2 + - - +
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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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176B LEU* 5.1 1.3 - - + -
179B LEU* 3.5 33.9 - - + -
186B PRO 5.5 2.8 + - - -
188B TYR* 6.1 1.6 - - + -
189B GLU* 3.6 43.1 + - + +
192B LEU* 3.8 19.3 - - + -
215B PHE* 2.9 39.7 + + + +
216B GLN 3.5 8.7 - - - +
218B GLN* 1.3 77.1 - - + +
220B ALA* 1.3 60.8 + - - +
222B ARG* 4.3 17.8 + - - +
223B ASN* 2.7 33.0 + - - +
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Residues in contact with ALA 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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176B LEU* 4.3 2.2 - - + +
208B TYR* 3.3 47.6 - - + -
211B ILE* 4.4 1.6 - - + -
216B GLN 2.9 13.8 + - - +
217B LEU* 3.4 11.0 - - - +
218B GLN 3.1 0.2 - - - -
219B TYR* 1.3 78.0 - - - +
221B TRP* 1.3 63.6 + - - +
223B ASN 3.3 3.6 + - - -
225B GLY 3.0 20.8 + - - -
228B PHE* 3.6 16.4 - - + -
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Residues in contact with TRP 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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343A ASN* 5.0 4.0 + - - -
345A SER* 3.6 28.3 - - - -
346A TRP* 3.7 36.9 - - + +
351A LEU* 4.0 9.6 - - + -
24B ALA* 4.7 1.8 + - + +
217B LEU 2.9 16.6 + - - +
218B GLN* 3.6 4.3 - - + +
220B ALA* 1.3 78.6 - - - +
222B ARG* 1.3 80.7 + - + +
223B ASN 3.2 0.7 + - - -
224B GLY 3.5 7.8 + - - -
225B GLY 3.9 3.1 + - - +
228B PHE* 3.9 14.1 - + + -
254B PHE* 4.0 40.1 - + + +
257B PHE* 3.6 42.2 - + + -
258B ILE* 3.5 39.3 - - + -
261B GLU* 4.3 15.9 - - + -
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Residues in contact with ARG 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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346A TRP 5.4 0.9 - - - -
189B GLU* 3.2 31.3 + - - +
218B GLN* 3.0 54.8 + - + +
219B TYR* 3.8 16.6 + - - +
221B TRP* 1.3 94.2 - - + +
223B ASN* 1.3 71.0 + - - +
224B GLY 3.5 2.4 + - - -
260B HIS* 5.7 4.3 - - - -
261B GLU* 4.0 23.5 + - + +
264B LYS* 3.5 23.5 - - - +
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Residues in contact with ASN 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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189B GLU* 2.8 42.8 + - - +
192B LEU* 3.8 24.5 - - + +
193B TYR* 3.5 20.1 + - - +
196B SER* 3.7 9.1 - - - -
206B LEU* 3.4 8.5 - - - +
208B TYR* 2.7 25.8 + - - +
219B TYR* 2.7 29.5 + - - +
220B ALA 3.5 0.7 - - - -
221B TRP 3.2 0.2 - - - -
222B ARG* 1.3 82.9 - - - +
224B GLY* 1.3 60.3 + - - +
225B GLY 3.3 2.2 - - - -
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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