Contacts of the helix formed by residues 229 - 241 (chain B) in PDB entry 5GPY
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 ASP 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B SER 4.0 1.6 + - - -
228B MET* 1.3 75.5 - - - +
230B GLU* 1.3 65.7 + - - +
231B GLU* 2.9 32.0 - - - +
232B LYS* 3.1 28.1 + - + +
233B ILE* 3.3 13.2 + - - +
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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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70A LYS* 3.6 29.8 - - + +
73A LYS* 3.2 37.4 + - - -
98A THR* 3.8 22.4 + - + +
101A ASN* 5.3 0.2 + - - -
228B MET 3.7 0.6 + - - -
229B ASP* 1.3 72.2 + - - +
231B GLU* 1.3 75.2 + - - +
233B ILE* 3.2 10.4 + - - +
234B GLU* 3.1 29.6 + - + +
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Residues in contact with GLU 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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229B ASP* 2.9 32.3 - - - +
230B GLU* 1.3 85.9 + - - +
232B LYS* 1.3 56.0 + - - +
234B GLU* 3.1 20.7 + - - +
235B GLU* 2.9 27.6 + - - +
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Residues in contact with LYS 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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228B MET* 3.5 29.7 - - + +
229B ASP* 3.1 23.9 + - + +
231B GLU* 1.3 80.8 - - - +
233B ILE* 1.3 61.0 + - - +
235B GLU* 3.3 16.5 + - - +
236B TYR* 3.1 21.5 + - - +
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Residues in contact with ILE 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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70A LYS* 3.7 36.8 - - + -
98A THR* 5.6 1.3 - - + -
101A ASN* 4.0 25.6 - - + +
102A VAL* 3.9 13.2 - - + -
105A TYR* 4.0 31.2 - - + -
225B VAL* 4.5 12.6 - - + -
228B MET* 4.1 20.2 - - + -
229B ASP 3.3 8.3 + - - +
230B GLU* 3.2 9.9 + - - +
232B LYS* 1.3 76.3 - - - +
234B GLU* 1.3 62.1 + - - +
236B TYR* 3.2 5.2 + - - +
237B LEU* 3.1 23.7 + - + +
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Residues in contact with GLU 234 (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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97A ARG* 5.1 12.5 + - - +
101A ASN* 3.3 26.8 + - - +
230B GLU* 3.1 15.3 + - + +
231B GLU* 3.4 24.5 - - - +
233B ILE* 1.3 73.7 - - - +
235B GLU* 1.3 66.0 + - - +
237B LEU* 3.3 10.3 + - - +
238B LYS* 3.0 41.7 + - - +
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Residues in contact with GLU 235 (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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231B GLU 2.9 13.5 + - - +
232B LYS* 3.6 18.8 - - - +
233B ILE 3.2 0.4 - - - -
234B GLU* 1.3 75.8 - - - +
236B TYR* 1.3 59.0 + - - +
238B LYS* 3.1 7.8 + - - +
239B ARG* 2.8 59.5 + - + +
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Residues in contact with TYR 236 (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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105A TYR* 3.5 30.1 - + + -
108A ASP* 2.6 37.3 + - + -
109A HIS* 3.2 39.7 + + - -
112A ARG* 3.4 11.3 - - - -
228B MET* 5.8 0.4 - - + -
232B LYS 3.1 8.3 + - - +
233B ILE 3.2 8.9 + - - +
235B GLU* 1.3 79.7 - - - +
237B LEU* 1.3 72.9 + - + +
239B ARG* 3.3 15.4 + - - +
240B GLN* 3.0 56.3 + - + +
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Residues in contact with LEU 237 (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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101A ASN* 3.6 46.4 - - + +
104A LYS* 4.0 13.5 - - + -
105A TYR* 3.9 27.8 - - - +
233B ILE* 3.1 16.7 + - + +
234B GLU* 3.7 8.1 - - - +
235B GLU 3.3 0.2 - - - -
236B TYR* 1.3 82.5 - - + +
238B LYS* 1.3 59.5 + - + +
240B GLN 3.3 0.9 + - - -
241B GLY 3.0 4.5 + - - -
242B ILE* 2.7 69.1 + - + +
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Residues in contact with LYS 238 (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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234B GLU* 3.0 30.5 + - - +
235B GLU* 3.6 9.4 - - - +
237B LEU* 1.3 75.3 - - + +
239B ARG* 1.3 65.4 + - - +
241B GLY* 2.9 14.4 + - - +
242B ILE 4.6 8.7 - - - +
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Residues in contact with ARG 239 (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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235B GLU* 2.8 48.2 + - + +
236B TYR* 3.4 19.3 - - + +
238B LYS* 1.3 71.1 - - - +
240B GLN* 1.3 70.0 + - + +
241B GLY 3.6 0.3 + - - -
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Residues in contact with GLN 240 (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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108A ASP* 3.8 7.9 - - - +
112A ARG* 3.2 44.1 + - - +
236B TYR* 3.0 55.2 + - + +
237B LEU 4.0 3.4 - - - +
238B LYS 3.1 0.2 - - - -
239B ARG* 1.3 84.3 - - - +
241B GLY* 1.3 61.0 + - - +
242B ILE* 3.5 14.0 - - + +
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Residues in contact with GLY 241 (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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238B LYS* 2.9 15.2 + - - -
239B ARG 3.3 0.6 + - - -
240B GLN* 1.3 80.2 - - - +
242B ILE* 1.3 66.1 + - - +
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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