Contacts of the helix formed by residues 133 - 139 (chain O) in PDB entry 6CNB
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 SER 133 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56O HIS* 5.6 0.2 - - - -
129O ILE 2.8 15.1 + - - -
130O LEU 2.3 28.5 + - - -
132O TYR* 1.3 73.0 - - - +
134O GLY* 1.3 56.7 + - - -
135O LEU 2.7 1.9 + - - -
136O ILE* 2.4 36.8 + - - +
137O ILE* 2.8 12.4 + - - +
164O ILE* 4.9 8.0 - - - +
58Q TYR* 3.5 12.1 - - - -
61Q PHE* 3.2 37.6 - - - -
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Residues in contact with GLY 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O TYR 2.9 3.4 + - - -
133O SER* 1.3 78.1 - - - +
135O LEU* 1.3 56.5 + - - +
137O ILE* 3.1 27.2 - - - +
138O ASP* 2.8 19.4 + - - +
54Q LEU* 3.1 20.6 - - - +
58Q TYR* 3.0 23.8 + - - +
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Residues in contact with LEU 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O TYR* 3.3 29.0 + - + +
133O SER 2.7 4.6 + - - -
134O GLY* 1.3 69.4 - - - +
136O ILE* 1.3 58.1 + - - +
137O ILE 3.0 1.1 - - - -
138O ASP* 2.6 45.2 + - + +
139O GLU 3.0 8.1 + - - -
287O PHE* 3.5 26.9 - - + -
291O ARG* 5.0 4.3 - - + -
294O LYS* 6.0 7.0 - - + -
642O SER* 6.0 0.9 - - - +
645O LEU* 3.8 17.5 - - + -
649O GLU* 3.9 9.6 - - - +
54Q LEU* 3.7 15.9 - - + +
58Q TYR* 4.5 0.8 - - - -
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Residues in contact with ILE 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128O HIS* 6.3 0.9 - - + -
129O ILE* 3.6 44.9 - - + +
132O TYR* 3.6 12.8 - - + -
133O SER* 2.4 20.0 + - - +
135O LEU* 1.3 70.9 - - - +
137O ILE* 1.3 55.2 + - - +
139O GLU* 3.0 26.3 - - + +
140O ILE* 5.8 0.2 - - - +
160O VAL* 4.4 10.9 - - + +
164O ILE* 3.7 20.2 - - + -
282O ILE* 4.3 21.1 - - + -
284O LEU* 6.4 1.8 - - + -
287O PHE* 3.5 41.7 - - + -
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Residues in contact with ILE 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133O SER 2.8 9.5 + - - +
134O GLY* 3.1 26.9 - - - +
136O ILE* 1.3 73.1 - - - +
138O ASP* 1.3 56.7 + - - +
139O GLU 2.9 10.7 + - - -
140O ILE* 2.9 37.6 + - + +
157O ALA* 5.1 9.6 - - + -
160O VAL* 5.2 6.7 - - + -
161O GLN* 4.3 31.6 - - + +
164O ILE* 5.5 3.8 - - + -
57Q LYS* 3.5 54.3 - - + +
61Q PHE* 4.6 11.9 - - + -
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Residues in contact with ASP 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O GLY 2.8 12.3 + - - +
135O LEU* 2.6 36.6 + - + +
137O ILE* 1.3 70.9 - - - +
139O GLU* 1.3 59.4 + - - -
140O ILE* 2.9 3.8 + - - +
141O ILE* 3.0 39.4 + - - +
142O THR 4.7 0.2 + - - -
294O LYS* 5.4 9.4 + - - +
50Q LYS* 5.0 10.1 - - - -
54Q LEU* 4.6 9.0 - - + -
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Residues in contact with GLU 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135O LEU 3.0 5.5 + - - -
136O ILE* 3.0 25.1 - - + +
137O ILE 2.9 0.2 + - - -
138O ASP* 1.3 77.7 - - - +
140O ILE* 1.3 68.1 + - - +
141O ILE 3.1 1.1 + - - -
142O THR* 3.3 12.4 + - - +
143O GLN* 2.7 59.1 + - - +
160O VAL* 4.8 6.8 - - - +
198O GLY* 5.0 4.7 - - - -
199O TYR* 3.7 28.7 + - - +
287O PHE* 4.7 17.5 - - + -
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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