Contacts of the helix formed by residues 104 - 118 (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 ASN 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B GLU* 3.1 15.5 + - - +
103B ARG* 1.3 77.2 - - - +
105B GLU* 1.4 52.1 - - - +
106B THR* 3.0 33.3 + - - -
107B MSE 3.1 24.2 + - + +
108B ILE* 2.8 37.6 + - - +
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Residues in contact with GLU 105 (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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103B ARG 3.4 12.2 + - - +
104B ASN* 1.4 72.0 + - - +
106B THR* 1.3 57.8 + - - +
108B ILE* 3.4 16.1 + - - +
109B GLN* 2.9 31.0 + - - +
128B GLU* 4.8 8.7 - - - +
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Residues in contact with THR 106 (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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104B ASN* 3.0 10.3 + - - -
105B GLU* 1.3 74.0 - - - +
107B MSE 1.3 63.0 + - - +
109B GLN* 3.2 11.7 + - + +
110B TYR* 3.0 53.5 + - + -
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Residues in contact with MSE 107 (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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52B VAL* 3.8 36.3 - - + -
53B PRO* 4.8 10.1 - - + -
81B ALA* 3.0 43.3 - - + +
82B ILE* 4.3 6.3 - - - -
102B GLU* 3.7 17.9 - - - +
104B ASN* 3.1 31.6 + - + +
106B THR* 1.3 78.1 - - - +
108B ILE* 1.4 56.4 + - - +
110B TYR* 3.3 7.1 + - - +
111B ALA* 2.9 26.7 + - - +
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Residues in contact with ILE 108 (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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102B GLU* 3.4 38.8 - - + +
103B ARG 3.9 7.4 - - - +
104B ASN 2.8 31.2 + - - +
105B GLU* 3.7 16.8 - - - +
107B MSE 1.4 71.7 - - - +
109B GLN* 1.4 54.1 + - - +
111B ALA* 3.7 4.9 - - - +
112B LYS* 2.8 51.7 + - + +
126B ILE* 4.5 8.2 - - + +
128B GLU* 3.7 45.8 - - + +
129B GLY 4.9 0.4 - - - +
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Residues in contact with GLN 109 (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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105B GLU 2.9 14.9 + - - +
106B THR* 3.2 14.6 + - + +
108B ILE* 1.4 77.9 - - - +
110B TYR* 1.3 57.1 + - + +
112B LYS* 3.4 6.6 + - - +
113B GLN* 2.9 51.8 + - + +
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Residues in contact with TYR 110 (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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46B PHE* 3.5 35.2 - + - -
50B ASN* 5.3 3.6 + - + -
52B VAL* 5.5 5.6 - - + -
82B ILE* 3.8 30.3 - - + -
106B THR* 3.0 42.4 + - + +
107B MSE 3.8 7.4 - - - +
109B GLN* 1.3 75.5 - - + +
111B ALA* 1.3 53.1 + - - +
113B GLN* 3.2 27.5 + - - +
114B ASN* 2.8 43.1 + - - +
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Residues in contact with ALA 111 (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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80B THR* 3.7 22.9 - - + -
81B ALA 3.6 12.6 - - - +
82B ILE 3.5 14.9 + - - +
83B GLY* 4.0 2.0 - - - +
107B MSE 2.9 18.6 + - - +
108B ILE* 3.7 5.2 - - - +
110B TYR* 1.3 72.3 - - - +
112B LYS* 1.4 59.2 + - - +
114B ASN* 3.2 3.1 + - - +
115B LEU* 2.9 33.2 + - + +
126B ILE* 3.8 11.9 - - + -
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Residues in contact with LYS 112 (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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108B ILE* 2.8 33.6 + - + +
109B GLN* 3.8 6.1 - - - +
111B ALA* 1.4 71.6 - - - +
113B GLN* 1.4 62.3 + - - +
115B LEU* 3.4 6.2 + - - +
116B ALA* 3.2 21.8 + - - +
121B GLU* 4.7 2.6 - - - +
126B ILE* 3.7 20.6 - - + +
128B GLU* 3.1 32.3 + - - -
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Residues in contact with GLN 113 (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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109B GLN* 2.9 43.6 + - + +
110B TYR* 3.3 30.1 - - - +
112B LYS* 1.4 74.8 - - + +
114B ASN* 1.3 55.0 + - - +
116B ALA* 3.2 7.2 + - - +
117B THR* 2.8 42.1 + - - +
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Residues in contact with ASN 114 (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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43B LEU* 3.7 27.5 - - - +
46B PHE* 6.2 0.4 - - - -
82B ILE* 2.8 35.5 + - - +
87B MSE 3.6 19.1 - - + -
110B TYR* 2.8 23.0 + - - +
111B ALA 3.7 4.0 - - - +
113B GLN* 1.3 73.7 - - - +
115B LEU* 1.4 56.9 + - - +
117B THR* 4.2 2.9 - - - +
118B TYR* 2.7 54.6 + - + +
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Residues in contact with LEU 115 (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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83B GLY* 5.3 2.7 - - - +
86B SER* 4.7 2.9 - - - +
87B MSE 3.7 28.7 - - + -
111B ALA* 2.9 22.5 + - + +
112B LYS* 3.8 5.8 - - + +
114B ASN* 1.4 71.8 - - - +
116B ALA* 1.3 56.4 + - - +
119B HIS* 3.0 9.0 + - - -
120B PHE* 2.8 36.0 + - + +
121B GLU* 3.7 22.3 + - + +
124B VAL* 3.7 46.9 - - + +
126B ILE* 3.5 28.0 - - + -
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Residues in contact with ALA 116 (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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112B LYS 3.2 10.9 + - - +
113B GLN* 3.2 10.7 + - - +
115B LEU* 1.3 74.2 - - - +
117B THR* 1.4 64.2 + - - +
119B HIS* 3.4 20.3 + - - +
121B GLU* 3.6 24.3 - - - +
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Residues in contact with THR 117 (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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113B GLN* 2.8 27.2 + - - +
114B ASN* 3.9 5.5 + - - +
116B ALA* 1.4 73.3 - - - +
118B TYR* 1.3 84.1 + - + +
119B HIS* 3.8 5.0 + - - -
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Residues in contact with TYR 118 (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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39B SER* 3.8 36.1 + - - +
40B ILE* 4.6 6.5 - - + -
42B VAL* 3.6 15.2 - - + +
43B LEU* 3.6 28.8 - - + +
87B MSE 3.8 17.9 - - + -
114B ASN* 2.7 49.0 + - + +
117B THR* 1.3 92.6 - - + +
119B HIS* 1.4 68.0 + - - +
120B PHE* 3.3 22.5 - - + -
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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