Contacts of the helix formed by residues 224 - 233 (chain B) in PDB entry 5OA3
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 GLU 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B PRO* 5.2 6.1 - - - +
222B LYS* 3.3 23.5 + - + +
223B PHE* 1.3 90.9 - - - +
225B LEU* 1.3 66.7 + - - +
226B GLY 3.6 3.5 + - - +
227B LYS* 3.8 27.5 + - + +
228B LEU* 3.8 6.9 + - - +
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Residues in contact with LEU 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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90B ASP* 3.2 28.7 - - - +
223B PHE* 3.7 15.5 - - + -
224B GLU* 1.3 72.8 - - - +
226B GLY* 1.3 64.4 + - - +
228B LEU* 3.1 4.3 + - - +
229B MET* 2.9 41.0 + - + +
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Residues in contact with GLY 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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224B GLU* 3.4 2.2 - - - +
225B LEU* 1.3 78.8 - - - +
227B LYS* 1.3 63.2 + - - +
229B MET* 3.1 10.2 + - - +
230B GLU* 2.9 33.2 + - - +
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Residues in contact with LYS 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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131B ASP* 3.4 30.1 + - + +
133B TYR* 4.6 23.1 - - + +
180B ASP* 4.1 12.1 + - - +
181B LEU* 5.0 7.1 - - - +
182B LYS* 5.4 1.6 - - - +
224B GLU* 3.8 28.3 + - + +
225B LEU 3.3 0.4 - - - -
226B GLY* 1.3 74.1 - - - +
228B LEU* 1.3 60.4 + - + +
230B GLU* 3.2 17.0 + - + +
231B LEU* 2.9 41.9 + - + +
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Residues in contact with LEU 228 (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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89B GLU* 3.2 34.8 - - + +
90B ASP* 3.6 21.8 - - - +
97B LEU* 3.9 24.5 - - + +
98B THR 4.4 3.6 - - - +
99B ASN* 4.1 15.9 - - + +
223B PHE* 4.2 5.6 - - + -
224B GLU 3.8 7.3 + - - +
225B LEU 3.1 9.2 + - - +
227B LYS* 1.3 79.3 - - + +
229B MET* 1.3 61.1 + - + +
231B LEU* 3.0 16.5 + - + +
232B HIS* 2.9 49.4 + - + +
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Residues in contact with MET 229 (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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90B ASP* 3.4 26.2 - - + +
92B GLN* 5.1 10.5 - - - +
97B LEU* 3.9 25.4 - - + -
225B LEU* 2.9 42.3 + - + +
226B GLY* 3.3 10.1 - - - +
228B LEU* 1.3 77.8 - - + +
230B GLU* 1.3 58.6 + - + +
232B HIS* 3.4 4.3 + - - +
233B GLY 3.0 34.6 + - - +
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Residues in contact with GLU 230 (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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226B GLY* 2.9 22.8 + - - +
227B LYS* 3.3 15.4 + - + +
229B MET* 1.3 75.8 - - + +
231B LEU* 1.3 62.2 + - - +
232B HIS 3.4 0.5 + - - -
233B GLY* 3.5 14.2 + - - -
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Residues in contact with LEU 231 (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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36B PRO* 4.3 20.2 - - + -
37B ALA* 3.2 26.3 + - - +
38B MET* 4.2 24.6 - - + +
99B ASN* 3.3 31.9 - - + +
100B PHE* 6.1 0.4 - - + -
181B LEU* 6.0 5.2 - - + -
182B LYS* 4.7 19.9 + - + +
227B LYS* 2.9 30.1 + - + +
228B LEU* 3.0 19.9 + - + +
230B GLU* 1.3 78.4 - - - +
232B HIS* 1.3 57.0 + - - +
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Residues in contact with HIS 232 (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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34B LYS* 3.5 28.5 + - + +
35B ALA 3.0 32.5 + - - -
36B PRO* 3.7 3.7 - - + +
37B ALA* 3.4 19.4 - - - +
42B ARG* 3.6 20.8 + - - -
97B LEU* 3.3 37.0 - - + +
98B THR 3.0 27.8 + - - -
228B LEU* 2.9 32.3 + - + +
229B MET* 4.1 4.7 - - - +
231B LEU* 1.3 78.6 - - - +
233B GLY* 1.3 56.8 + - - +
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Residues in contact with GLY 233 (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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37B ALA* 5.1 2.0 - - - -
229B MET* 3.0 20.7 + - - +
230B GLU* 3.5 11.8 + - - -
232B HIS* 1.3 80.5 - - - +
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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