Contacts of the helix formed by residues 204 - 210 (chain v) in PDB entry 6AH0
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 LYS 204 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201v ARG* 2.9 13.8 + - - +
203v THR* 1.3 76.2 - - - +
205v GLN* 1.3 67.0 + - - +
206v PHE 3.1 4.6 + - - +
207v PHE* 3.3 13.7 + - - +
208v LEU* 3.4 10.2 + - - -
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Residues in contact with GLN 205 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201v ARG* 5.8 0.2 - - - +
204v LYS* 1.3 71.7 - - - +
206v PHE* 1.3 56.6 + - - +
208v LEU* 5.7 0.2 - - - +
209v GLN* 2.9 30.0 + - - -
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Residues in contact with PHE 206 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204v LYS* 3.1 1.6 - - - +
205v GLN* 1.3 76.3 - - - +
207v PHE* 1.3 60.9 + - - +
209v GLN* 3.9 0.4 - - - +
210v PHE* 3.1 25.1 + - - +
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Residues in contact with PHE 207 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149v HIS 5.8 4.6 + - - +
203v THR 6.2 0.7 - - - +
204v LYS* 3.3 10.0 + - - +
206v PHE* 1.3 72.4 - - - +
208v LEU* 1.3 64.7 + - - +
210v PHE 5.3 0.4 - - - -
211v HIS* 3.3 26.2 + - - +
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Residues in contact with LEU 208 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200v ASN 5.7 4.7 - - - -
201v ARG 5.4 2.4 + - - -
203v THR 6.0 0.6 - - - +
204v LYS 3.4 11.1 + - - -
205v GLN 4.3 0.2 - - - -
207v PHE* 1.3 76.5 - - - +
209v GLN* 1.3 64.2 + - - +
210v PHE 3.4 0.5 + - - -
211v HIS 4.4 5.5 + - - +
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Residues in contact with GLN 209 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205v GLN 2.9 19.8 + - - -
206v PHE 3.9 0.2 - - - -
208v LEU* 1.3 77.6 - - - +
210v PHE* 1.3 56.5 + - - +
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Residues in contact with PHE 210 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206v PHE 3.1 14.3 + - - +
207v PHE* 3.9 2.5 - - - -
209v GLN* 1.3 79.2 - - - +
211v HIS* 1.3 56.6 + - - +
222v SER* 4.0 2.8 - - - -
223v LEU 3.4 35.8 + - - -
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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