Contacts of the helix formed by residues 140 - 150 (chain G) in PDB entry 3BZE
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 ALA 140 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123G TYR* 3.3 60.0 - - + +
124G LEU* 4.2 1.2 - - + +
135G ALA* 3.3 13.8 - - + +
137G ASP* 2.8 13.8 + - + +
139G ALA* 1.3 77.7 - - - +
141G GLN* 1.3 58.0 + - - +
142G ILE 3.4 1.6 - - - -
143G SER* 3.3 3.5 + - - -
144G GLU* 3.0 23.2 + - - +
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Residues in contact with GLN 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G ALA* 4.1 13.6 + - + +
137G ASP 3.8 6.5 + - - -
138G THR* 3.4 46.1 + - - +
139G ALA 3.3 2.6 - - - -
140G ALA* 1.3 74.7 - - - +
142G ILE* 1.3 69.5 + - + +
144G GLU* 3.0 14.3 + - - +
145G GLN* 2.9 26.2 + - - +
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Residues in contact with ILE 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G TYR* 3.5 42.8 - - + +
139G ALA 4.5 4.6 + - - +
140G ALA 3.4 0.4 - - - -
141G GLN* 1.3 80.3 - - + +
143G SER* 1.3 62.3 + - - +
145G GLN* 3.4 11.8 - - + +
146G LYS* 2.9 32.8 + - + +
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Residues in contact with SER 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G TYR* 3.6 2.2 + - - -
123G TYR* 2.8 38.9 + - - -
124G LEU* 4.5 4.9 - - - -
140G ALA* 3.3 7.0 + - - +
141G GLN 3.1 0.2 - - - -
142G ILE* 1.3 80.0 - - - +
144G GLU* 1.3 59.8 + - - +
146G LYS* 3.4 4.5 + - - +
147G SER* 2.9 31.8 + - - -
8S PHE 5.6 0.3 - - - +
9S LEU* 2.6 41.7 + - - +
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Residues in contact with GLU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G LEU* 3.8 14.1 - - + +
133G TRP* 3.1 30.4 - - - +
134G THR* 3.8 4.7 - - - +
135G ALA* 3.2 26.5 + - + +
140G ALA 3.0 13.5 + - - +
141G GLN* 3.3 18.3 + - - +
143G SER* 1.3 78.6 - - - +
145G GLN* 1.3 65.1 + - - +
147G SER* 3.3 3.1 + - - -
148G ASN* 3.1 41.8 + - - +
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Residues in contact with GLN 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G GLN 2.9 12.4 + - - +
142G ILE* 3.4 17.7 - - + +
144G GLU* 1.3 81.6 - - - +
146G LYS* 1.3 69.2 + - + +
148G ASN* 4.6 5.4 - - - +
149G ASP* 2.9 51.5 + - - +
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Residues in contact with LYS 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLN* 4.9 11.4 - - - +
75C ARG* 4.3 26.0 - - - +
79C ARG* 6.1 1.4 - - - +
80G THR* 4.9 4.2 + - - +
84G TYR* 4.0 9.0 + - - +
142G ILE* 2.9 23.1 + - + +
143G SER 3.4 4.9 - - - +
145G GLN* 1.3 85.2 - - + +
147G SER* 1.3 57.6 + - - +
149G ASP* 4.1 2.6 - - - +
150G ALA* 3.2 29.9 + - + +
8S PHE* 3.8 25.6 - - - +
9S LEU* 2.8 31.2 + - - +
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Residues in contact with SER 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G LEU* 4.1 2.8 - - - +
133G TRP* 3.4 32.6 + - - -
143G SER 2.9 17.4 + - - -
144G GLU 4.0 2.2 - - - -
146G LYS* 1.3 75.3 - - - +
148G ASN* 1.3 63.0 + - - +
150G ALA* 3.9 6.1 - - - -
151G SER* 3.5 1.2 + - - -
152G GLU* 3.4 24.3 + - - -
153G ALA* 4.3 0.5 + - - +
7S LEU* 3.5 28.3 - - - +
8S PHE 4.9 5.5 + - - -
9S LEU* 5.2 1.4 - - - +
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Residues in contact with ASN 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G SER* 3.7 13.6 - - - -
133G TRP* 3.0 45.8 + - - +
144G GLU* 3.1 30.0 + - - +
145G GLN* 4.2 5.5 - - - +
146G LYS 3.3 0.4 - - - -
147G SER* 1.3 75.5 - - - +
149G ASP* 1.3 70.5 + - - +
150G ALA 3.1 1.3 - - - -
151G SER* 3.1 14.5 + - - +
153G ALA* 5.8 0.2 - - - +
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Residues in contact with ASP 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ARG* 5.7 2.8 + - - -
145G GLN* 2.9 43.4 + - - +
146G LYS* 4.1 3.4 - - - +
148G ASN* 1.3 81.4 - - - +
150G ALA* 1.3 58.2 + - - +
151G SER* 3.1 5.2 + - - -
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Residues in contact with ALA 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ARG* 5.4 10.1 + - - +
72C GLN* 5.8 6.5 - - - +
146G LYS* 3.2 20.2 + - + +
147G SER* 4.3 2.2 - - - +
148G ASN 3.1 1.2 - - - -
149G ASP* 1.3 74.4 - - - +
151G SER* 1.3 58.2 + - - +
152G GLU* 2.7 36.8 + - + +
155G HIS* 5.3 3.1 - - - -
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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