Contacts of the helix formed by residues 227 - 239 (chain A) in PDB entry 2W93
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 VAL 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A CYS* 3.1 28.0 + - - +
225A HIS 3.5 13.7 - - - +
226A ASP* 1.3 78.7 - - - +
228A LYS* 1.3 55.7 + - - +
229A ALA 3.3 2.2 - - - -
230A GLU* 3.3 10.2 + - + +
231A THR* 2.7 38.8 + - + +
285A VAL* 3.8 20.2 - - + -
326A MET* 3.9 16.2 - - + -
327A LYS* 3.9 24.9 - - + -
330A LEU* 3.7 22.7 - - + -
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Residues in contact with LYS 228 (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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222A CYS* 3.6 18.1 + - - +
223A SER* 5.1 8.1 - - - -
226A ASP* 3.6 4.0 - - - +
227A VAL* 1.3 78.1 - - - +
229A ALA* 1.3 59.7 + - - +
231A THR* 3.3 1.7 + - - -
232A LYS* 3.0 32.4 + - + +
250A GLY 3.8 16.6 + - - +
251A SER* 3.4 30.2 - - - +
253A ASP* 2.8 35.9 + - - +
403A ASN* 3.8 23.6 + - - +
404A THR 4.9 0.6 + - - -
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Residues in contact with ALA 229 (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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226A ASP* 5.3 5.1 + - - +
227A VAL 3.3 0.2 - - - -
228A LYS* 1.3 80.8 - - - +
230A GLU* 1.3 71.5 + - - +
232A LYS* 3.5 7.6 + - - +
233A LYS* 3.3 39.5 + - - +
327A LYS* 6.0 0.2 - - - +
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Residues in contact with GLU 230 (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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226A ASP 3.5 5.3 - - - +
227A VAL* 3.5 21.5 - - + +
229A ALA* 1.3 82.8 - - - +
231A THR* 1.3 61.1 + - - +
233A LYS* 3.4 6.6 + - - +
234A LEU* 3.0 25.6 + - - +
327A LYS* 2.4 35.4 + - - +
330A LEU* 3.9 32.4 - - + +
331A GLN* 3.9 20.1 - - + +
334A LEU* 3.5 28.3 - - + +
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Residues in contact with THR 231 (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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216A ILE* 4.6 11.1 - - - +
218A ALA* 4.8 0.9 - - - +
222A CYS* 3.6 27.0 - - - -
227A VAL* 2.7 25.9 + - + +
228A LYS 3.6 4.5 - - - -
230A GLU* 1.3 74.8 - - - +
232A LYS* 1.3 64.1 + - - +
234A LEU* 3.1 9.6 + - - +
235A ILE* 3.0 33.9 + - - +
251A SER 5.2 2.2 - - - -
252A ILE* 4.4 8.0 - - - +
285A VAL* 3.8 25.1 - - + +
330A LEU* 4.8 5.6 - - + -
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Residues in contact with LYS 232 (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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228A LYS* 3.0 21.1 + - + +
229A ALA* 3.5 9.0 - - - +
231A THR* 1.3 75.4 - - - +
233A LYS* 1.3 63.0 + - + +
235A ILE* 3.2 16.0 + - + +
236A ASP* 3.1 39.6 + - - +
253A ASP* 4.2 27.1 - - + +
256A HIS* 4.3 21.7 - - + -
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Residues in contact with LYS 233 (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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229A ALA* 3.3 27.5 + - - +
230A GLU* 3.5 9.6 - - - +
232A LYS* 1.3 75.1 - - + +
234A LEU* 1.3 66.7 + - - +
236A ASP* 3.4 9.7 + - - +
237A LEU* 3.0 36.2 + - + +
334A LEU* 3.7 27.7 - - + +
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Residues in contact with LEU 234 (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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216A ILE* 3.8 28.5 - - + -
230A GLU 3.0 14.0 + - - +
231A THR* 3.2 11.4 - - - +
233A LYS* 1.3 76.8 - - - +
235A ILE* 1.3 60.5 + - - +
237A LEU* 4.2 2.0 - - - +
238A THR* 2.9 33.6 + - + +
283A LEU* 4.1 23.3 - - + -
285A VAL* 4.7 10.3 - - + -
309A PHE* 5.2 2.5 - - + -
330A LEU* 4.3 22.7 - - + -
333A LEU* 4.8 11.2 - - + -
334A LEU* 3.4 18.1 - - + +
337A ILE* 4.4 22.9 - - + -
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Residues in contact with ILE 235 (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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216A ILE* 3.7 17.7 - - + -
231A THR* 3.0 20.9 + - - +
232A LYS* 3.2 13.9 + - + +
234A LEU* 1.3 76.8 - - - +
236A ASP* 1.3 53.8 + - - +
238A THR* 4.3 0.4 - - - -
239A GLN* 2.7 36.9 + - - -
240A PHE 4.3 2.9 - - - +
242A ALA* 3.6 26.0 - - + -
252A ILE* 3.7 39.9 - - + -
256A HIS* 3.6 32.1 - - + +
258A ARG* 4.0 13.2 - - + -
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Residues in contact with ASP 236 (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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232A LYS* 3.1 36.8 + - - +
233A LYS* 3.6 12.9 - - - +
235A ILE* 1.3 75.7 - - - +
237A LEU* 1.3 67.9 + - + +
239A GLN* 2.8 30.3 + - - +
256A HIS* 2.6 35.7 + - - -
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Residues in contact with LEU 237 (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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233A LYS* 3.0 24.3 + - + +
234A LEU 4.3 0.7 - - - +
236A ASP* 1.3 83.7 - - + +
238A THR* 1.3 60.2 + - - +
239A GLN* 4.8 1.7 - - - +
334A LEU* 3.7 24.7 - - + +
337A ILE* 3.6 33.7 - - + -
338A ALA* 4.1 34.9 - - + +
341A ALA* 5.0 1.2 - - - +
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Residues in contact with THR 238 (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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208A VAL* 4.9 0.9 - - - +
216A ILE* 3.8 11.2 - - + -
234A LEU* 2.9 26.3 + - + +
235A ILE 3.9 0.9 - - - +
237A LEU* 1.3 80.2 - - - +
239A GLN* 1.3 71.2 + - - +
240A PHE* 2.7 72.3 + - + +
283A LEU* 5.5 0.9 - - + -
337A ILE* 4.8 12.2 - - - +
341A ALA* 3.4 17.6 - - - +
344A TYR* 3.9 6.6 - - - -
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Residues in contact with GLN 239 (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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235A ILE 2.7 20.9 + - - -
236A ASP* 2.8 34.1 + - - +
237A LEU 4.8 2.0 - - - +
238A THR* 1.3 74.6 - - - +
240A PHE* 1.3 61.1 + - - +
256A HIS* 4.6 5.9 - - - -
257A PRO* 5.9 0.3 - - - +
258A ARG* 2.7 60.0 + - - +
344A TYR* 3.5 5.2 - - + -
346A PRO* 4.7 16.3 - - + +
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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