Contacts of the helix formed by residues 213 - 223 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A ILE* 3.5 7.0 - - - +
212A GLU* 1.3 81.7 - - + +
214A ASN* 1.3 67.3 + - - +
215A PHE* 3.5 29.2 - - + -
216A GLN* 3.0 19.2 + - - +
217A LEU* 3.3 9.7 + - - +
232A TYR* 3.9 11.6 - - - +
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Residues in contact with ASN 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ALA* 1.3 71.9 - - - +
215A PHE* 1.3 63.7 + - - +
217A LEU* 2.8 21.9 + - - +
218A GLN* 2.9 13.7 + - - +
232A TYR* 2.5 39.9 + - + +
253A GLU* 2.8 24.2 + - - +
257A PHE* 4.1 19.1 - - - -
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Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.6 33.9 - - + -
213A ALA* 3.7 22.4 - - + -
214A ASN* 1.3 79.2 - - - +
216A GLN* 1.3 82.2 + - + +
218A GLN* 3.3 12.2 + - - +
219A TYR* 2.9 32.2 + + - +
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Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 2.7 45.3 + - + +
177A GLN* 4.3 4.0 - - - +
179A LEU* 4.1 15.0 - - + -
210A ASP 4.3 6.1 + - - -
211A ILE* 4.2 9.6 - - + -
212A GLU* 2.6 40.9 + - - +
213A ALA* 3.0 16.0 + - - +
214A ASN 3.1 0.8 - - - -
215A PHE* 1.3 101.8 - - + +
217A LEU* 1.3 59.5 + - - +
219A TYR* 3.4 7.7 + - - +
220A ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 4.0 18.7 - - + +
213A ALA 3.3 7.6 + - - +
214A ASN* 2.8 10.9 + - - +
216A GLN* 1.3 78.2 - - - +
218A GLN* 1.3 58.7 + - - +
220A ALA* 3.2 5.8 + - - +
221A TRP* 2.8 27.5 + - - +
228A PHE* 3.9 34.1 - - + -
232A TYR* 4.1 14.6 - - + -
233A LEU* 4.4 11.0 - - + -
250A LEU* 4.3 7.2 - - + -
253A GLU* 4.0 21.8 - - - +
254A PHE* 4.1 20.6 - - + -
257A PHE* 4.0 15.9 - - + -
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Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ASN* 2.9 12.4 + - - +
215A PHE* 3.6 13.4 - - - +
217A LEU* 1.3 73.8 - - - +
219A TYR* 1.3 67.0 + - - +
221A TRP* 3.2 1.4 + - - +
222A ARG* 2.9 59.8 + - + +
257A PHE* 3.7 45.8 + - + +
260A HIS* 4.3 24.0 + - - +
261A GLU* 6.0 2.0 - - - +
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Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 4.7 9.0 - - + -
179A LEU* 2.6 44.6 - - + -
189A GLU* 3.3 48.8 + - + +
192A LEU* 3.3 33.2 - - + +
208A TYR* 4.9 4.5 - + - -
215A PHE* 2.9 18.0 + + - +
216A GLN 3.5 8.3 - - - +
217A LEU 3.4 0.2 - - - -
218A GLN* 1.3 75.3 - - - +
220A ALA* 1.3 65.0 - - - +
222A ARG* 4.2 9.4 - - + +
223A ASN* 2.7 59.9 + - + +
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 4.0 1.8 - - + -
208A TYR* 3.3 47.7 - - + -
211A ILE* 4.3 2.0 - - + -
216A GLN 2.9 15.1 + - - +
217A LEU* 3.3 11.7 - - - +
218A GLN 3.1 0.2 - - - -
219A TYR* 1.3 78.9 - - - +
221A TRP* 1.3 63.4 + - - +
223A ASN 3.3 3.5 + - - -
225A GLY 3.0 20.4 + - - -
228A PHE* 3.6 16.8 - - + -
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Residues in contact with TRP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA* 4.8 0.7 - - + -
217A LEU 2.8 16.3 + - - +
218A GLN* 3.2 4.7 + - + +
220A ALA* 1.3 78.0 - - - +
222A ARG* 1.3 82.8 + - + +
223A ASN 3.3 0.7 + - - -
224A GLY 3.4 7.8 + - - -
225A GLY 3.8 3.1 + - - +
228A PHE* 3.9 14.1 - + + -
254A PHE* 4.0 39.5 - + + +
257A PHE* 3.6 40.8 - + + -
258A ILE* 3.6 26.2 - - + -
261A GLU* 4.2 16.6 - - + -
343B ASN* 4.8 2.7 + - - -
345B SER* 3.3 46.7 - - - -
346B TRP* 3.4 39.4 - - + +
351B LEU* 4.0 4.9 - - + -
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Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLU* 5.5 4.9 + - - -
218A GLN* 2.9 53.5 + - + +
219A TYR* 3.8 7.8 - - - +
221A TRP* 1.3 94.1 - - + +
223A ASN* 1.3 76.3 + - - +
224A GLY 3.4 3.1 + - - -
260A HIS* 4.5 13.7 + - - -
261A GLU* 3.7 29.4 + - + +
264A LYS* 4.0 22.4 - - - +
345B SER 6.0 0.2 - - - -
346B TRP* 5.0 2.4 - - - +
348B PRO* 6.1 1.2 - - - +
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Residues in contact with ASN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLU* 5.0 7.7 + - - +
192A LEU* 6.2 2.0 - - + -
193A TYR* 5.8 7.1 + - - +
196A SER* 4.0 10.9 + - - +
206A LEU* 3.5 7.3 - - - +
208A TYR* 2.6 34.5 + - - +
219A TYR* 2.7 57.9 + - + +
220A ALA 3.5 0.9 - - - -
221A TRP 3.2 0.2 - - - -
222A ARG* 1.3 94.8 - - - +
224A GLY* 1.3 58.3 + - - +
225A GLY 3.3 2.2 - - - -
348B PRO* 5.7 0.4 - - - -
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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