Contacts of the helix formed by residues 228 - 232 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333E TRP* 3.7 11.9 + - + +
334E ARG* 4.8 4.0 + - - -
100F SER* 4.9 5.4 + - - -
104F HIS* 4.3 6.8 + - - -
224F ALA 4.2 4.7 + - - -
225F PHE* 3.7 18.3 + - - +
226F ARG* 5.2 1.1 - - - -
227F THR* 1.3 82.2 - - - +
229F GLU* 1.3 67.2 + - - +
230F ILE* 3.1 17.5 - - - +
231F ARG* 3.0 25.7 + - + +
232F ARG* 3.3 9.7 + - - +
940F LYS* 3.1 30.4 + - - +
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Residues in contact with GLU 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E SER* 4.8 0.2 + - - -
104F HIS* 5.9 1.2 - - - -
180F GLN* 3.9 15.7 + - - +
183F ARG* 2.4 48.4 + - - +
185F SER* 4.6 6.6 - - - -
186F LEU* 3.8 44.0 + - + +
224F ALA 5.3 2.3 + - - +
227F THR* 3.4 19.8 - - + +
228F ASP* 1.3 75.8 - - - +
230F ILE* 1.3 64.0 + - + +
232F ARG* 3.1 47.9 + - - +
960F LYS* 5.0 0.2 + - - -
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Residues in contact with ILE 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F SER* 4.2 17.0 - - - +
103F LEU* 3.6 37.0 - - + -
104F HIS* 3.3 38.8 - - + +
107F ASN* 4.8 9.6 - - - +
180F GLN* 3.7 19.3 - - - +
228F ASP* 4.3 8.3 - - - +
229F GLU* 1.3 79.6 - - + +
231F ARG* 1.3 71.1 + - + +
232F ARG 3.5 0.2 - - - -
941F LEU* 3.6 9.2 - - - +
957F LEU* 4.2 6.4 - - + +
960F LYS* 3.0 26.0 + - - +
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Residues in contact with ARG 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F ILE* 3.6 37.4 - - - +
100F SER* 4.4 8.1 - - - +
228F ASP* 3.0 21.8 + - + +
230F ILE* 1.3 90.2 - - + +
232F ARG* 1.3 63.0 + - - +
233F ALA 3.6 2.3 + - - -
937F GLY* 2.8 30.7 + - - -
938F LEU 3.6 0.6 - - - -
940F LYS* 3.4 68.0 - - - +
941F LEU* 3.2 21.1 - - + +
953F ASP* 2.7 30.7 + - - +
957F LEU* 4.7 4.6 - - + +
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Residues in contact with ARG 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368E ASN* 5.7 7.2 - - - +
369E GLU* 5.4 2.2 - - - -
180F GLN* 3.7 9.3 - - - +
181F SER* 3.7 25.3 + - - -
183F ARG* 3.9 34.2 - - - +
228F ASP 3.3 5.6 + - - +
229F GLU* 3.1 42.6 + - - +
231F ARG* 1.3 78.7 - - - +
233F ALA* 1.3 76.8 + - - +
234F GLN* 3.8 2.3 + - - +
235F PRO* 4.7 11.3 - - - +
243F TYR* 3.8 23.7 - - - -
941F LEU* 4.9 1.5 - - - +
960F LYS* 4.2 14.0 + - - -
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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