Contacts of the helix formed by residues 104 - 118 (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 ASN 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLU* 2.9 17.8 + - - +
103A ARG* 1.3 79.2 - - + +
105A GLU* 1.3 53.5 + - - +
106A THR* 2.9 33.3 + - - -
107A MSE 3.1 29.3 + - + +
108A ILE* 2.8 35.0 + - - +
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Residues in contact with GLU 105 (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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103A ARG 3.4 7.4 + - - +
104A ASN* 1.3 70.7 + - - +
106A THR* 1.4 56.7 + - - +
108A ILE* 3.5 13.7 + - + +
109A GLN* 3.1 36.5 + - + +
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Residues in contact with THR 106 (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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104A ASN* 2.9 11.7 + - - -
105A GLU* 1.4 77.3 - - - +
107A MSE 1.3 65.3 + - + +
109A GLN* 3.3 13.7 + - + +
110A TYR* 3.1 61.3 + - + +
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Residues in contact with MSE 107 (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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51A GLU 5.6 1.8 - - - +
52A VAL* 4.2 15.5 - - + -
53A PRO* 5.0 9.0 - - + -
80A THR 3.5 18.4 - - - +
81A ALA* 3.0 40.5 - - - +
102A GLU* 3.8 10.3 - - + +
104A ASN* 3.1 33.0 + - + +
106A THR* 1.3 77.4 - - + +
108A ILE* 1.4 58.8 + - - +
110A TYR* 3.3 18.0 + - + -
111A ALA* 2.9 32.6 + - - +
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Residues in contact with ILE 108 (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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102A GLU* 3.3 37.9 - - + +
103A ARG 3.9 12.3 - - - +
104A ASN 2.8 25.7 + - - +
105A GLU* 3.7 13.5 - - + +
106A THR 3.4 0.2 - - - -
107A MSE 1.4 72.5 - - - +
109A GLN* 1.4 54.7 + - + +
111A ALA* 3.3 5.4 + - - +
112A LYS* 2.8 45.7 + - + +
126A ILE* 4.4 8.6 - - + +
128A GLU* 3.6 48.5 - - + +
129A GLY 4.7 0.7 - - - +
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Residues in contact with GLN 109 (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 GLU* 3.1 24.5 + - + +
106A THR* 3.6 11.0 + - - +
108A ILE* 1.4 77.3 - - + +
110A TYR* 1.4 58.6 + - + +
112A LYS* 3.4 6.3 + - - +
113A GLN* 3.0 31.0 + - - +
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Residues in contact with TYR 110 (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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46A PHE* 3.9 31.1 - + + -
50A ASN* 5.2 5.2 + - - +
52A VAL* 4.2 14.2 - - + +
81A ALA 4.1 6.5 - - - +
82A ILE* 3.6 31.0 - - + -
106A THR* 3.1 40.8 + - + +
107A MSE 3.6 15.3 - - + +
109A GLN* 1.4 75.7 - - + +
111A ALA* 1.4 63.5 + - - +
113A GLN* 3.4 5.3 + - - +
114A ASN* 3.0 30.8 + - - +
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Residues in contact with ALA 111 (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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80A THR* 4.2 12.6 - - + -
82A ILE 3.5 11.2 + - - -
83A GLY* 3.9 21.9 - - - +
107A MSE 2.9 18.0 + - - +
108A ILE* 3.7 5.4 - - - +
110A TYR* 1.4 76.1 - - - +
112A LYS* 1.4 56.7 + - - +
114A ASN* 3.2 3.1 + - - +
115A LEU* 2.9 33.4 + - + +
126A ILE* 3.7 19.1 - - + -
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Residues in contact with LYS 112 (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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108A ILE* 2.8 26.7 + - + +
109A GLN* 3.7 7.2 - - - +
111A ALA* 1.4 69.4 - - - +
113A GLN* 1.4 62.4 + - - +
115A LEU* 3.4 7.2 + - + +
116A ALA* 3.2 22.0 + - - +
121A GLU* 4.6 6.2 - - - +
126A ILE* 3.6 35.1 + - + +
128A GLU* 3.9 22.5 + - - +
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Residues in contact with GLN 113 (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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109A GLN 3.0 17.2 + - - +
110A TYR* 3.9 5.2 - - - +
112A LYS* 1.4 75.6 - - - +
114A ASN* 1.3 60.8 + - - +
116A ALA* 3.2 12.7 + - - +
117A THR* 2.9 49.0 + - - +
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Residues in contact with ASN 114 (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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43A LEU* 3.5 35.8 - - - +
46A PHE* 6.0 1.2 - - - -
82A ILE* 2.8 34.2 + - - +
87A MSE 3.6 20.0 - - + -
110A TYR* 3.0 19.1 + - - +
111A ALA 3.2 4.5 + - - +
113A GLN* 1.3 79.2 - - - +
115A LEU* 1.4 56.7 + - - +
117A THR* 4.4 2.6 + - - -
118A TYR* 2.9 45.2 + - + +
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Residues in contact with LEU 115 (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 GLY* 5.1 4.7 - - - +
86A SER* 5.1 0.7 - - - -
87A MSE 3.6 29.6 - - + -
111A ALA* 2.9 18.4 + - + +
112A LYS* 3.4 7.4 + - + +
114A ASN* 1.4 74.4 - - - +
116A ALA* 1.4 58.1 + - - +
119A HIS* 3.0 8.5 + - - -
120A PHE* 2.8 33.4 + - + +
121A GLU* 3.7 21.1 + - + +
124A VAL* 3.6 49.6 - - + +
126A ILE* 3.5 28.3 - - + -
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Residues in contact with ALA 116 (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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112A LYS 3.2 11.6 + - - +
113A GLN* 3.5 17.7 - - - +
115A LEU* 1.4 73.1 - - - +
117A THR* 1.4 63.9 + - - +
119A HIS* 3.3 22.2 + - - -
121A GLU* 3.6 29.6 - - - +
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Residues in contact with THR 117 (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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113A GLN* 2.9 34.7 + - - +
114A ASN* 3.8 6.4 + - - +
116A ALA* 1.4 74.3 - - - +
118A TYR* 1.3 85.7 + - + +
119A HIS* 3.4 20.5 + - - -
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Residues in contact with TYR 118 (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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39A SER* 4.2 24.0 + - - -
40A ILE* 3.6 22.0 - - + -
42A VAL* 4.9 10.2 - - - +
43A LEU* 3.9 31.8 - - + +
87A MSE 4.0 4.9 - - - -
114A ASN* 2.9 37.4 + - - +
115A LEU 3.8 0.2 - - - -
117A THR* 1.3 95.3 - - + +
119A HIS* 1.3 76.3 + - - +
120A PHE* 3.4 32.1 - - + -
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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