Contacts of the helix formed by residues 83 - 91 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A THR* 2.9 18.0 + - - -
81A ALA 3.9 0.2 - - - -
82A ILE* 1.3 77.1 - - - +
84A TYR* 1.3 63.6 + - - +
85A SER 3.5 2.7 - - - -
86A SER* 3.4 12.7 + - - -
87A MSE 3.0 35.5 + - - +
111A ALA* 3.9 14.7 - - - +
115A LEU* 5.6 3.4 - - - -
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Residues in contact with TYR 84 (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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40A ILE* 4.0 20.4 - - + +
41A GLU* 2.6 27.8 + - - -
43A LEU* 4.5 9.2 - - + -
44A ARG* 2.8 34.2 + - - -
54A ILE* 3.7 21.8 - - + -
55A VAL* 4.0 7.4 - - + -
57A ARG* 4.3 0.5 - - - -
60A LEU* 3.5 24.8 - - + +
82A ILE* 3.3 15.9 - - + -
83A GLY* 1.3 77.6 - - - +
85A SER* 1.3 68.9 + - - +
87A MSE 3.4 10.0 + - + +
88A GLN* 3.0 48.8 + - + +
233A SO4 3.0 24.0 + - - +
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Residues in contact with SER 85 (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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55A VAL* 4.0 21.1 - - - +
60A LEU* 4.3 10.1 - - - -
77A GLU* 2.8 26.8 + - - -
80A THR* 4.8 0.9 + - - -
84A TYR* 1.3 78.6 - - - +
86A SER* 1.4 54.8 + - - +
88A GLN* 3.2 1.0 + - - +
89A PHE* 2.9 49.1 + - - -
147A PHE* 4.2 5.7 - - - -
233A SO4 2.6 28.7 + - - -
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Residues in contact with SER 86 (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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77A GLU* 2.4 32.6 + - - -
80A THR* 4.5 1.0 + - - -
83A GLY* 3.6 17.6 + - - -
84A TYR 3.3 0.2 - - - -
85A SER* 1.4 78.8 + - - +
87A MSE 1.3 58.8 + - - +
89A PHE* 3.4 1.0 + - - -
90A ALA* 3.0 28.2 + - - +
98A VAL* 3.7 12.5 - - - +
100A THR* 2.9 13.4 + - - +
115A LEU* 5.1 0.4 - - - -
124A VAL* 3.8 27.9 - - - +
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Residues in contact with MSE 87 (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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40A ILE* 4.0 14.4 - - + -
43A LEU* 3.5 32.3 - - + -
82A ILE 4.3 0.2 - - - +
83A GLY 3.0 28.2 + - - +
84A TYR* 4.0 4.9 - - - +
86A SER* 1.3 71.8 - - - +
88A GLN* 1.4 60.4 + - - +
90A ALA* 3.3 7.1 + - - +
91A SER* 2.8 31.9 + - - -
114A ASN* 3.6 40.6 - - + +
115A LEU* 3.6 22.4 - - + -
118A TYR* 4.0 7.2 - - - -
120A PHE* 3.7 31.6 - - + -
124A VAL* 4.9 0.2 - - - -
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Residues in contact with GLN 88 (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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38A SER* 2.9 28.8 + - - +
40A ILE* 3.6 11.2 - - + +
41A GLU* 3.1 27.5 + - - +
60A LEU* 3.7 33.0 - - + +
64A LYS* 3.1 33.6 + - + -
84A TYR* 3.0 38.8 + - + +
85A SER 3.2 4.7 + - - +
87A MSE 1.4 75.7 - - - +
89A PHE* 1.3 62.6 + - - +
91A SER* 2.7 21.4 + - - -
92A ILE* 3.7 1.6 - - - +
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Residues in contact with PHE 89 (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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60A LEU* 3.8 20.4 - - + -
63A ILE* 3.5 34.5 - - + -
64A LYS* 4.4 7.9 - - + -
67A ILE* 3.5 15.0 - - + -
75A ILE* 3.7 33.9 - - + -
77A GLU* 3.0 31.2 - - + -
85A SER* 2.9 22.8 + - - +
86A SER* 3.8 4.3 - - - +
88A GLN* 1.3 78.6 - - - +
90A ALA* 1.3 62.7 + - - +
92A ILE* 3.2 18.7 + - - +
96A ILE* 3.4 19.3 - - - +
98A VAL* 4.1 3.4 - - + -
145A MSE 5.2 1.1 - - - -
147A PHE* 3.8 25.8 - + + -
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Residues in contact with ALA 90 (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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86A SER 3.0 18.3 + - - +
87A MSE 3.3 1.8 + - - +
89A PHE* 1.3 76.3 - - - +
91A SER* 1.4 57.9 - - - +
93A SER 3.0 24.3 - - - +
94A ASP* 5.5 0.2 - - - +
96A ILE* 4.0 9.4 - - - +
98A VAL* 4.3 3.8 - - + +
120A PHE* 3.8 22.2 - - + -
123A GLN* 3.1 34.5 + - + +
124A VAL* 4.1 8.5 - - + -
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Residues in contact with SER 91 (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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38A SER* 4.8 5.9 - - - -
40A ILE* 4.0 10.9 - - - +
64A LYS* 4.0 11.3 + - - -
87A MSE 2.8 14.4 + - - -
88A GLN* 2.7 24.4 + - - -
89A PHE 3.2 0.2 - - - -
90A ALA* 1.4 76.6 - - - +
92A ILE* 1.4 61.9 + - - +
93A SER 3.4 1.0 + - - -
120A PHE* 3.9 18.8 - - - -
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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