Contacts of the helix formed by residues 83 - 91 (chain B) in PDB entry 3NTV
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 GLY 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B THR* 3.0 24.6 + - - -
81B ALA 3.3 2.2 + - - -
82B ILE* 1.3 78.8 - - - +
84B TYR* 1.3 64.3 + - - +
85B SER 3.5 2.2 - - - -
86B SER* 3.0 24.9 + - - -
87B MSE 3.1 24.3 + - - +
111B ALA* 4.3 5.2 - - - -
115B LEU* 5.6 2.5 - - - -
233B SO4 3.8 0.2 - - - -
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 3.9 23.9 - - + +
41B GLU* 2.5 33.6 + - - -
43B LEU* 4.4 9.0 - - + -
44B ARG* 2.9 35.5 + - + -
54B ILE* 3.7 22.7 - - + -
55B VAL* 3.9 7.6 - - + -
57B ARG* 4.2 0.7 - - - -
60B LEU* 3.5 25.6 - - + +
82B ILE* 3.3 14.9 + - + -
83B GLY* 1.3 77.2 - - - +
85B SER* 1.3 68.3 + - - +
87B MSE 3.9 9.6 - - - +
88B GLN* 3.0 41.6 + - + +
233B SO4 3.2 22.2 + - - +
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B VAL* 3.9 17.2 - - - +
60B LEU* 4.4 4.9 - - - -
77B GLU* 2.4 28.7 + - - -
84B TYR* 1.3 78.9 - - - +
86B SER* 1.3 60.0 + - - +
88B GLN* 3.2 5.7 + - - +
89B PHE* 3.0 45.2 + - - -
147B PHE* 4.1 2.4 - - - -
233B SO4 2.6 36.2 + - - -
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 3.3 20.8 + - - -
80B THR* 4.6 2.6 - - - +
83B GLY* 3.0 23.8 + - - -
85B SER* 1.3 80.3 + - - +
87B MSE 1.4 58.4 + - - +
89B PHE* 3.4 2.5 + - - -
90B ALA* 3.0 27.4 + - - +
98B VAL* 3.6 20.7 - - - +
100B THR* 3.6 14.8 + - - -
115B LEU* 4.7 1.2 - - - +
124B VAL* 3.8 19.2 - - - +
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Residues in contact with MSE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 3.5 18.4 - - + +
43B LEU* 3.6 23.8 - - + -
83B GLY* 3.1 25.7 + - - +
84B TYR 4.0 1.1 - - - +
86B SER* 1.4 71.7 - - - +
88B GLN* 1.3 60.3 + - - +
90B ALA* 3.3 7.8 + - - +
91B SER* 2.9 30.8 + - - -
114B ASN* 3.6 47.6 - - + +
115B LEU* 3.7 22.4 - - + -
118B TYR* 3.8 17.3 - - + -
120B PHE* 3.8 18.9 - - + -
124B VAL* 4.8 0.4 - - - -
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER* 2.7 30.9 + - - +
40B ILE* 4.0 9.3 - - + +
41B GLU* 3.2 29.9 + - - +
57B ARG* 5.9 0.2 - - - +
60B LEU* 3.7 33.1 - - + +
64B LYS* 3.0 33.5 + - - +
84B TYR* 3.0 37.8 + - + +
85B SER 3.2 4.9 + - - +
87B MSE 1.3 76.1 - - - +
89B PHE* 1.3 62.3 + - - +
91B SER* 2.6 21.8 + - - -
92B ILE* 3.7 1.4 - - - +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.9 20.4 - - + -
63B ILE* 3.6 31.2 - - + -
64B LYS* 4.6 5.8 - - + -
67B ILE* 3.6 14.6 - - + -
75B ILE* 3.7 37.5 - - + -
77B GLU* 3.6 24.2 - - + -
85B SER* 3.0 25.2 + - - +
86B SER* 3.7 7.6 - - - +
88B GLN* 1.3 76.2 - - - +
90B ALA* 1.3 64.1 + - - +
92B ILE* 3.2 20.0 + - - +
96B ILE* 3.4 19.3 - - - +
98B VAL* 4.1 3.4 - - + -
145B MSE 5.3 1.1 - - - -
147B PHE* 3.8 27.6 - + + -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B SER 3.0 17.5 + - - +
87B MSE 3.6 4.3 - - - +
89B PHE* 1.3 76.7 - - - +
91B SER* 1.4 57.8 + - - +
92B ILE 3.2 0.2 + - - -
93B SER 3.1 14.2 + - - +
96B ILE* 4.0 9.6 - - + +
98B VAL* 4.3 3.8 - - + +
120B PHE* 3.7 22.4 - - + -
123B GLN* 3.0 40.9 + - + +
124B VAL* 4.1 9.4 - - + -
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Residues in contact with SER 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER* 4.5 6.5 - - - -
40B ILE* 3.8 16.2 - - - -
64B LYS* 4.1 7.6 + - - -
87B MSE 2.9 14.8 + - - -
88B GLN* 2.6 28.2 + - - -
90B ALA* 1.4 73.4 - - - +
92B ILE* 1.3 64.3 + - - +
93B SER 3.4 0.6 + - - -
120B PHE* 3.8 14.1 - - - -
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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