Contacts of the helix formed by residues 96 - 121 (chain A) in PDB entry 1L6N
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 ASP 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.7 8.7 - - - +
20A ARG* 3.3 32.0 - - + +
21A LEU 4.4 3.1 - - - +
94A VAL* 4.5 0.9 - - - +
95A LYS* 1.3 81.7 + - - +
97A THR* 1.3 66.9 + - - +
98A LYS* 3.4 14.4 - - + +
99A GLU* 2.9 59.2 + - - +
100A ALA* 3.2 6.8 + - - +
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Residues in contact with THR 97 (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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19A ILE* 3.9 0.2 - - - +
20A ARG 3.2 14.7 + - - -
21A LEU* 3.6 14.9 + - - -
22A ARG* 5.1 1.6 - - - -
29A TYR* 3.3 24.2 + - - +
80A ASN* 2.8 68.4 - - + +
84A VAL* 3.4 8.3 - - + -
96A ASP* 1.3 74.2 - - - +
98A LYS* 1.3 59.4 + - - +
100A ALA* 2.9 24.6 + - - +
101A LEU 3.2 4.3 + - - -
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 5.8 12.3 - - + -
80A ASN* 4.8 5.5 - - - +
96A ASP* 3.2 11.3 + - + +
97A THR* 1.3 80.0 - - - +
99A GLU* 1.3 62.2 + - - +
101A LEU* 3.1 28.6 + - + +
102A ASP* 3.2 12.6 + - - +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP 4.5 1.1 - - - +
94A VAL* 4.0 4.9 - - - -
95A LYS* 3.7 30.6 - - - +
96A ASP* 2.9 45.8 + - - +
98A LYS* 1.3 79.4 - - - +
100A ALA* 1.3 50.3 + - - +
102A ASP* 3.4 4.8 + - - +
103A LYS* 2.7 62.6 + - + +
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Residues in contact with ALA 100 (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 ALA* 4.8 0.4 - - + -
84A VAL* 3.1 52.7 - - + +
87A CYS* 4.2 4.7 - - + -
94A VAL* 3.8 13.4 - - + +
96A ASP 3.2 5.3 + - - +
97A THR 2.9 2.8 + - - +
99A GLU* 1.3 76.0 - - - +
101A LEU* 1.3 57.4 + - - +
104A ILE* 2.4 46.7 + - + +
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Residues in contact with LEU 101 (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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76A ARG* 5.5 9.6 - - - +
79A TYR* 3.8 20.2 - - + +
80A ASN* 2.8 34.5 - - - +
83A ALA* 3.6 23.1 - - + -
97A THR 3.2 2.2 + - - -
98A LYS* 3.1 23.9 + - + +
100A ALA* 1.3 79.9 - - - +
102A ASP* 1.3 50.1 + - - +
104A ILE* 3.5 6.5 - - + +
105A GLU* 2.5 54.7 + - - +
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Residues in contact with ASP 102 (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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98A LYS 3.2 9.1 + - - +
99A GLU* 3.7 9.2 - - - +
100A ALA 3.2 0.2 - - - -
101A LEU* 1.3 75.6 - - - +
103A LYS* 1.3 94.0 + - - +
105A GLU* 3.1 26.9 + - - +
106A GLU* 3.1 25.7 + - - +
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Residues in contact with LYS 103 (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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92A ILE* 3.0 35.8 - - + +
93A ASP* 3.1 23.1 - - - +
94A VAL* 3.3 14.6 - - + -
99A GLU* 2.7 47.2 + - + +
100A ALA* 3.7 1.1 - - - +
102A ASP* 1.3 98.4 + - - +
104A ILE* 1.3 67.7 + - + +
105A GLU 2.9 1.1 - - - -
106A GLU* 3.0 25.6 + - - +
107A GLU* 3.2 11.0 + - - +
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Residues in contact with ILE 104 (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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61A LEU* 3.8 14.6 - - + -
79A TYR* 5.0 3.6 - - - +
83A ALA* 2.9 57.0 - - + +
86A TYR* 4.0 13.8 - - + -
87A CYS* 3.6 23.1 - - + +
92A ILE* 5.0 2.0 - - - +
100A ALA 2.4 46.5 + - - +
101A LEU* 3.5 15.7 - - + +
103A LYS* 1.3 67.5 - - - +
105A GLU* 1.3 59.0 + - + +
107A GLU* 3.5 9.3 - - - +
108A GLN* 2.8 35.7 + - - +
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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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101A LEU* 2.5 47.2 + - + +
102A ASP* 3.1 18.4 + - - +
103A LYS 2.9 0.4 - - - -
104A ILE* 1.3 80.5 - - + +
106A GLU* 1.3 64.1 + - - +
108A GLN* 3.2 5.7 + - - +
109A ASN* 2.9 24.2 + - - +
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Residues in contact with GLU 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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102A ASP* 3.1 29.6 + - - +
103A LYS* 3.0 17.1 + - - +
105A GLU* 1.3 78.3 - - - +
107A GLU* 1.3 64.7 + - - +
109A ASN* 3.1 9.6 + - + +
110A LYS* 2.8 24.2 + - - +
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Residues in contact with GLU 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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86A TYR* 4.6 11.4 - - + +
90A GLN* 2.4 55.2 + - + +
92A ILE* 3.5 18.3 - - + +
103A LYS 3.2 8.8 + - - +
104A ILE* 3.5 12.3 - - - +
106A GLU* 1.3 78.0 - - - +
108A GLN* 1.3 52.3 + - - +
110A LYS* 2.8 24.6 + - - +
111A SER* 2.8 34.1 + - - -
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Residues in contact with GLN 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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58A ARG* 4.4 18.4 + - - +
61A LEU* 4.3 18.8 - - - +
62A GLY* 6.1 1.6 - - - +
86A TYR* 3.1 39.6 + - - -
104A ILE* 2.8 21.1 + - + +
105A GLU* 3.5 7.4 - - - +
107A GLU* 1.3 73.5 - - - +
109A ASN* 1.3 57.1 + - - +
110A LYS 2.9 0.5 + - - -
111A SER* 2.9 11.5 + - - +
112A LYS* 2.7 39.8 + - + +
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Residues in contact with ASN 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 2.9 13.2 + - - +
106A GLU* 3.4 12.8 - - + +
108A GLN* 1.3 75.5 - - - +
110A LYS* 1.3 61.2 + - - +
112A LYS* 3.2 42.4 + - - +
113A LYS* 3.2 14.7 - - - +
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Residues in contact with LYS 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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106A GLU 2.8 11.3 + - - +
107A GLU* 2.8 30.9 + - - +
109A ASN* 1.3 77.4 - - - +
111A SER* 1.3 63.5 - - - +
113A LYS* 2.9 21.7 - - + +
114A LYS* 3.2 32.3 + - - +
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Residues in contact with SER 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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58A ARG* 4.6 14.4 + - - -
86A TYR* 5.2 4.4 + - - -
107A GLU* 2.8 15.9 + - - -
108A GLN* 2.9 18.1 + - - -
110A LYS* 1.3 69.6 - - - +
112A LYS* 1.3 68.0 - - - -
114A LYS* 2.7 23.1 + - - +
115A ALA* 3.1 9.4 + - - +
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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 GLN* 2.7 21.6 + - + +
109A ASN* 3.2 46.2 + - - +
111A SER* 1.3 73.5 - - - +
113A LYS* 1.3 74.9 + - - +
115A ALA* 3.1 11.5 + - - +
116A GLN* 2.8 62.2 + - - +
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Residues in contact with LYS 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 ASN* 3.2 13.5 - - - +
110A LYS* 2.9 19.1 - - + +
111A SER 2.8 0.8 + - - -
112A LYS* 1.3 95.2 - - - +
114A LYS* 1.3 71.5 + - - +
116A GLN* 2.9 25.1 + - - +
117A GLN* 2.8 33.2 + - + +
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Residues in contact with LYS 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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110A LYS* 3.2 32.0 + - - +
111A SER* 2.7 18.0 + - - +
113A LYS* 1.3 82.4 - - - +
115A ALA* 1.3 62.9 + - - +
117A GLN* 3.1 26.3 + - - +
118A ALA* 2.9 22.8 + - - +
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Residues in contact with ALA 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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111A SER 3.1 6.6 + - - +
112A LYS* 3.1 15.9 + - - +
114A LYS* 1.3 76.4 - - - +
116A GLN* 1.3 64.7 + - - +
118A ALA* 3.0 8.9 + - - +
119A ALA* 2.8 25.5 + - - +
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Residues in contact with GLN 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* 2.8 52.9 + - - +
113A LYS* 3.3 21.1 - - - +
115A ALA* 1.3 72.8 - - - +
117A GLN* 1.3 64.5 + - - +
119A ALA* 3.2 9.9 + - + +
120A ALA* 2.9 22.0 + - - +
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Residues in contact with GLN 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 LYS* 2.8 25.4 + - + +
114A LYS* 3.3 32.6 - - - +
116A GLN* 1.3 72.7 - - - +
118A ALA* 1.3 65.9 + - - +
120A ALA* 2.8 28.4 - - + +
121A ASP* 3.2 14.0 + - - +
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Residues in contact with ALA 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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114A LYS 2.9 11.9 + - - +
115A ALA* 3.3 10.5 - - - +
117A GLN* 1.3 80.2 - - - +
119A ALA* 1.3 55.0 + - - +
120A ALA 2.6 5.4 + - - -
121A ASP* 2.6 7.7 + - - +
122A THR* 2.6 36.1 + - - -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA 2.8 16.6 + - - +
116A GLN* 3.4 14.4 - - + +
118A ALA* 1.3 73.2 - - - +
120A ALA* 1.3 62.6 + - - +
122A THR* 2.7 25.7 + - - +
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Residues in contact with ALA 120 (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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116A GLN 2.9 11.3 + - - +
117A GLN* 2.8 19.1 - - + +
118A ALA 2.6 4.0 + - - -
119A ALA* 1.3 78.2 - - - +
121A ASP* 1.3 56.2 + - + +
122A THR* 3.2 3.1 + - - -
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Residues in contact with ASP 121 (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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117A GLN* 3.2 15.2 + - - +
118A ALA* 2.6 12.0 + - - +
120A ALA* 1.3 75.1 - - + +
122A THR* 1.3 71.8 + - - +
123A GLY* 3.5 1.2 + - - -
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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
------------------------------------------------------------
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