Contacts of the helix formed by residues 228 - 232 (chain B) in PDB entry 6V3O
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 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A TRP* 4.5 12.0 + - - +
334A ARG* 5.7 2.7 + - - -
100B SER* 4.5 9.2 + - - -
104B HIS* 3.5 16.6 + - - -
224B ALA 4.1 6.7 + - - -
225B PHE* 3.3 20.4 - - - +
226B ARG 5.1 0.7 - - - -
227B THR* 1.3 81.1 - - - +
229B GLU* 1.3 66.7 + - - +
230B ILE* 3.0 9.2 - - - +
231B ARG* 3.1 41.7 + - + +
232B ARG* 3.6 7.8 + - - +
940B LYS* 3.8 10.5 + - + +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A SER* 4.7 0.7 + - - -
104B HIS* 5.8 0.8 - - - -
180B GLN* 3.5 21.6 + - - +
181B SER 5.3 1.6 - - - +
183B ARG* 2.5 59.7 + - - +
185B SER* 5.0 3.6 - - - -
186B LEU* 3.6 44.0 - - + +
224B ALA 5.3 1.6 + - - +
227B THR* 3.3 18.2 - - + +
228B ASP* 1.3 75.0 - - - +
230B ILE* 1.3 63.8 + - + +
231B ARG 3.2 0.7 + - - -
232B ARG* 3.4 31.1 + - - +
960B LYS* 4.7 0.2 + - - -
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Residues in contact with ILE 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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100B SER* 4.1 12.1 - - - +
103B LEU* 3.4 34.3 - - + -
104B HIS* 3.3 43.3 - - + +
107B ASN* 5.2 4.9 - - - +
180B GLN* 3.8 9.6 - - - +
228B ASP* 4.6 5.2 - - - +
229B GLU* 1.3 81.1 - - + +
231B ARG* 1.3 64.2 + - + +
232B ARG 3.8 0.2 + - - -
941B LEU* 3.6 4.2 - - - +
957B LEU* 3.3 26.5 - - + -
960B LYS* 3.0 36.6 + - + -
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Residues in contact with ARG 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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96B ILE* 3.7 32.7 - - - +
100B SER* 4.3 7.4 - - - +
228B ASP* 3.1 32.7 + - + +
230B ILE* 1.3 87.2 - - + +
232B ARG* 1.3 63.1 + - - +
233B ALA 3.6 2.4 + - - -
937B GLY 2.8 31.3 + - - -
938B LEU 3.4 4.9 + - - -
939B VAL 3.4 7.7 - - - +
940B LYS* 3.2 60.1 - - + +
941B LEU* 4.0 16.3 - - + +
953B ASP* 2.9 29.7 + - - +
957B LEU* 4.9 3.5 - - + +
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Residues in contact with ARG 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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368A ASN* 5.5 9.6 - - - +
369A GLU* 5.3 2.9 - - - -
180B GLN* 4.7 6.5 - - - +
181B SER* 4.3 16.4 + - - -
183B ARG* 3.9 28.2 - - - +
228B ASP 3.6 5.1 + - - +
229B GLU* 3.4 37.2 + - - +
230B ILE 4.3 2.1 - - - +
231B ARG* 1.3 78.1 - - - +
233B ALA* 1.3 78.4 + - - +
234B GLN* 3.5 2.4 + - - -
235B PRO* 4.6 12.3 - - - +
243B TYR* 3.8 35.9 + - - -
941B LEU* 3.9 8.0 - - - +
960B LYS* 4.4 6.4 + - - -
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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