Contacts of the helix formed by residues 147 - 153 (chain A) in PDB entry 6YBX
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A PRO* 4.3 1.0 - - - +
104A ASN 4.1 3.8 - - - +
105A ILE* 3.0 27.5 - - - +
106A LYS* 3.4 18.4 + - - +
107A GLY* 3.6 12.4 - - - +
138A LEU* 4.2 0.7 - - - -
146A ASN* 1.3 76.1 - - - +
148A ALA* 1.3 63.3 + - - +
149A CYS* 3.0 17.0 + - - +
150A THR* 2.6 43.6 + - - -
151A VAL* 3.3 19.9 + - - +
173A PHE* 4.3 10.8 - - + -
182A SER 6.1 0.7 - - - +
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 4.0 12.0 - - - +
147A ASP* 1.3 73.1 - - - +
149A CYS* 1.3 61.3 + - - +
151A VAL 3.8 0.4 - - - +
152A PHE* 2.9 35.2 + - + +
157A TYR* 3.6 32.1 - - + -
167A THR* 5.2 0.2 - - - +
169A TYR* 3.7 33.1 - - + +
173A PHE* 5.2 0.6 - - - -
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Residues in contact with CYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 5.4 1.6 - - + +
106A LYS* 5.5 9.0 - - - -
147A ASP* 3.0 10.8 + - - +
148A ALA* 1.3 75.2 - - - +
150A THR* 1.3 66.3 + - - +
153A GLN* 2.9 34.9 + - - +
157A TYR* 3.6 22.1 + - - +
158A CYS* 2.1 52.0 - - - -
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PRO* 3.7 24.8 - - + +
106A LYS* 4.8 5.7 + - - +
146A ASN* 4.0 22.4 - - - +
147A ASP* 2.6 39.3 + - - -
148A ALA 3.4 0.2 - - - -
149A CYS* 1.3 75.4 - - - +
151A VAL* 1.3 62.1 + - + +
153A GLN* 4.0 16.0 + - - +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LYS 3.8 17.7 - - - +
138A LEU* 4.0 10.5 - - + -
146A ASN* 3.5 30.1 - - + +
147A ASP 3.3 17.3 + - - +
148A ALA 3.4 0.2 + - - -
149A CYS 3.2 0.4 - - - -
150A THR* 1.3 80.5 - - + +
152A PHE* 1.3 94.5 + - + +
153A GLN* 4.8 1.9 - - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LYS* 4.1 21.3 - - + -
138A LEU* 4.3 7.4 - - + -
148A ALA* 2.9 18.3 + - - +
151A VAL* 1.3 100.8 - - + +
153A GLN* 1.3 73.6 + - - +
154A THR* 3.3 11.7 + - + +
157A TYR* 3.7 26.2 - + + -
169A TYR* 3.6 37.5 - + - -
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Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA 4.0 0.2 + - - -
149A CYS* 2.9 39.1 + - - +
150A THR* 4.0 16.0 + - - +
151A VAL 4.8 2.5 - - - +
152A PHE* 1.3 79.5 - - - +
154A THR* 1.3 62.3 + - - +
158A CYS* 4.1 12.7 - - - -
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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