Contacts of the helix formed by residues 104 - 129 (chain A) in PDB entry 1UCU
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 SER 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 THR 3.4 3.9 + - - -
103A ASN* 1.3 76.6 - - - +
105A GLN* 1.3 63.5 + - - +
106A SER* 2.8 25.9 + - - -
107A ASP* 3.0 29.3 + - - +
108A LEU* 3.0 15.0 + - - +
313A ASP* 4.6 8.3 - - - -
315A ASN* 4.6 17.3 - - - -
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Residues in contact with GLN 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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104A SER* 1.3 73.9 - - - +
106A SER* 1.3 57.9 + - - +
108A LEU* 3.1 10.1 + - + +
109A ASP* 2.9 34.8 + - - +
176A GLN* 2.9 39.1 + - + +
177A LYS 3.3 14.6 + - - +
178A TYR* 3.3 34.1 - - + +
312A THR 4.3 0.2 - - - +
313A ASP* 3.3 25.2 + - + -
314A ASN* 2.8 45.1 + - + +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 2.8 21.8 + - - -
105A GLN* 1.3 79.5 - - - +
107A ASP* 1.3 64.4 + - - +
109A ASP* 3.5 6.9 + - - +
110A SER* 3.1 22.2 + - - -
178A TYR* 3.3 11.7 + - - -
313A ASP* 5.4 1.8 + - - -
317A LYS* 6.0 1.2 + - - -
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Residues in contact with ASP 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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102A THR 4.9 0.7 - - - +
103A ASN* 3.8 22.7 - - + +
104A SER* 3.0 35.3 + - - +
106A SER* 1.3 84.6 + - - +
108A LEU* 1.3 58.2 + - - +
110A SER* 3.2 7.8 + - - -
111A ILE* 3.0 34.3 + - + +
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Residues in contact with LEU 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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98A SER* 4.0 26.9 - - - +
100A ASN 5.2 0.2 - - - +
103A ASN* 4.0 24.7 - - + +
104A SER 3.0 16.9 + - - +
105A GLN* 3.5 11.7 - - - +
107A ASP* 1.3 76.5 - - - +
109A ASP* 1.3 60.2 + - - +
111A ILE* 3.4 7.9 + - + +
112A GLN* 2.9 29.8 + - - +
174A VAL* 3.5 31.5 - - + +
175A GLN* 4.1 6.2 - - - +
176A GLN* 3.8 39.0 - - + +
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLN* 2.9 19.6 + - - +
106A SER* 3.7 7.7 - - - +
107A ASP 3.2 0.2 - - - -
108A LEU* 1.3 75.2 - - - +
110A SER* 1.3 58.4 + - - +
112A GLN* 3.2 3.1 + - - +
113A ALA* 2.9 28.4 + - - +
175A GLN* 3.0 37.0 + - - +
176A GLN 4.9 1.2 + - - +
178A TYR* 2.7 36.6 + - - -
367A ASP* 4.4 0.9 - - - +
369A LYS* 3.4 16.4 + - - +
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Residues in contact with SER 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 SER 3.1 11.4 + - - -
107A ASP* 3.3 11.7 - - - -
109A ASP* 1.3 80.6 - - - +
111A ILE* 1.3 63.3 + - - +
113A ALA* 3.2 16.8 + - - +
114A GLU* 3.3 12.8 + - - +
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Residues in contact with ILE 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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94A LEU* 3.6 45.5 - - + +
97A GLN* 4.1 33.2 - - + +
98A SER* 4.3 6.3 - - - -
103A ASN* 4.2 15.9 - - - +
107A ASP* 3.0 27.0 + - + +
108A LEU* 3.7 9.0 - - + +
110A SER* 1.3 74.8 - - - +
112A GLN* 1.3 57.5 + - - +
114A GLU* 3.4 4.5 + - - +
115A ILE* 3.0 33.1 + - + +
174A VAL* 4.3 7.9 - - + -
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Residues in contact with GLN 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 LEU 2.9 18.3 + - - +
109A ASP 3.4 5.2 - - - +
111A ILE* 1.3 75.3 - - - +
113A ALA* 1.3 60.9 + - - +
115A ILE* 3.2 12.2 + - - +
116A THR* 2.8 47.5 + - - +
119A LEU* 5.9 0.2 - - - +
172A LEU 3.2 20.8 + - - -
173A ASN* 3.1 12.6 - - - +
174A VAL* 2.7 40.7 + - + +
175A GLN* 3.6 29.4 - - + +
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Residues in contact with ALA 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 ASP 2.9 13.1 + - - +
110A SER* 3.2 13.4 + - - +
112A GLN* 1.3 77.0 - - - +
114A GLU* 1.3 56.5 + - - +
116A THR* 3.3 8.1 + - - -
117A GLN* 3.0 33.3 + - + +
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Residues in contact with GLU 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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90A ARG* 2.7 45.6 + - - +
94A LEU* 3.1 27.7 - - + +
110A SER 3.3 9.6 + - - +
111A ILE* 4.1 3.6 - - - +
112A GLN 3.3 0.2 - - - -
113A ALA* 1.3 75.2 - - - +
115A ILE* 1.3 66.4 + - - +
117A GLN* 3.1 7.7 + - + +
118A ARG* 2.6 51.4 + - - +
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Residues in contact with ILE 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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91A VAL* 3.9 26.5 - - + +
94A LEU* 3.3 37.9 - - + -
95A ALA* 5.0 1.6 - - + +
111A ILE* 3.0 16.2 + - + +
112A GLN* 3.6 20.2 - - - +
114A GLU* 1.3 75.6 - - - +
116A THR* 1.3 58.4 + - - +
118A ARG* 3.2 6.3 + - - +
119A LEU* 2.9 38.0 + - + +
172A LEU* 3.9 18.2 - - + +
174A VAL* 3.9 34.8 - - + -
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Residues in contact with THR 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 GLN* 2.8 35.5 + - - +
113A ALA* 3.5 8.7 - - - +
114A GLU 3.2 0.2 - - - -
115A ILE* 1.3 77.9 - - - +
117A GLN* 1.3 61.3 + - - +
119A LEU* 3.5 7.5 + - - +
120A ASN* 2.9 43.6 + - - +
384A LYS* 3.8 26.7 - - - +
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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 ALA* 3.0 28.1 + - + +
114A GLU* 3.1 10.7 + - - +
116A THR* 1.3 79.2 - - - +
118A ARG* 1.3 79.6 + - - +
120A ASN* 3.3 15.0 + - - +
121A GLU* 3.0 29.3 + - - +
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Residues in contact with ARG 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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87A ASN* 3.3 36.9 + - + +
90A ARG* 4.1 10.8 - - + -
91A VAL* 3.5 30.5 - - + -
94A LEU* 5.0 0.4 - - + -
114A GLU* 2.6 49.9 + - - +
115A ILE 3.5 2.7 - - - +
117A GLN* 1.3 96.7 + - - +
119A LEU* 1.3 61.9 + - - +
121A GLU* 3.3 17.7 + - - +
122A ILE* 3.1 28.4 + - - +
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Residues in contact with LEU 119 (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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88A LEU* 4.3 18.8 - - + -
91A VAL* 4.7 7.6 - - + -
112A GLN* 5.9 0.4 - - - +
115A ILE* 2.9 35.1 + - + +
116A THR* 3.9 7.6 - - - +
118A ARG* 1.3 74.6 - - - +
120A ASN* 1.3 69.2 + - - +
122A ILE* 3.3 8.5 + - + +
123A ASP* 3.1 17.6 + - - -
164A SER* 3.1 29.5 + - - +
169A LEU* 3.1 42.8 - - + +
170A ASP* 5.0 4.0 - - - +
172A LEU* 4.3 12.6 - - + +
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Residues in contact with ASN 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 THR* 2.9 35.6 + - - +
117A GLN* 3.6 15.3 + - - +
119A LEU* 1.3 78.0 - - - +
121A GLU* 1.3 61.4 + - - +
123A ASP* 3.2 14.2 + - - +
124A ARG* 3.0 26.4 + - - +
384A LYS* 3.5 30.6 + - - +
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Residues in contact with GLU 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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83A GLU* 4.9 5.8 - - - +
87A ASN* 3.8 24.0 - - - +
117A GLN 3.0 16.3 + - - +
118A ARG* 3.3 19.5 + - - +
120A ASN* 1.3 73.8 - - - +
122A ILE* 1.3 60.0 + - - +
124A ARG* 2.8 44.9 + - - +
125A VAL* 2.9 34.9 + - + +
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Residues in contact with ILE 122 (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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84A ILE* 3.9 22.9 - - + +
87A ASN* 3.8 23.8 - - + +
88A LEU* 3.2 43.3 - - + +
118A ARG* 3.1 15.7 + - + +
119A LEU* 3.4 18.2 - - + +
120A ASN 3.2 0.2 - - - -
121A GLU* 1.3 77.8 - - - +
123A ASP* 1.3 56.7 + - - +
125A VAL* 3.4 8.2 + - - +
126A SER* 2.9 27.2 + - - -
162A ILE 4.6 0.6 - - - +
163A ASN* 4.2 8.7 - - - -
164A SER* 4.1 21.8 - - - +
167A LEU* 4.4 4.5 - - + -
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Residues in contact with ASP 123 (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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119A LEU 3.1 14.8 + - - +
120A ASN* 3.5 17.4 + - - +
121A GLU 3.2 0.2 - - - -
122A ILE* 1.3 75.7 - - - +
124A ARG* 1.3 58.6 + - - +
126A SER* 3.7 5.8 - - - -
127A GLY* 3.0 22.7 + - - -
163A ASN* 3.4 7.8 - - - +
164A SER* 2.8 43.1 + - - -
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Residues in contact with ARG 124 (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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120A ASN 3.0 13.8 + - - +
121A GLU* 2.8 44.6 + - - +
123A ASP* 1.3 73.6 - - - +
125A VAL* 1.3 71.8 + - - +
127A GLY* 3.1 1.3 + - - -
128A GLN* 2.8 84.5 + - + +
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Residues in contact with VAL 125 (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 ALA* 3.4 27.4 - - + +
83A GLU* 4.8 13.2 - - + +
84A ILE* 3.7 19.3 - - + -
87A ASN* 4.9 1.3 - - - +
121A GLU* 2.9 40.2 + - + +
122A ILE* 3.6 4.7 - - - +
124A ARG* 1.3 89.0 - - - +
126A SER* 1.3 61.9 + - - +
129A THR* 2.7 45.8 + - - +
137A LEU* 4.6 1.5 - - + +
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Residues in contact with SER 126 (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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84A ILE* 5.3 0.7 - - - -
122A ILE 2.9 16.6 + - - -
123A ASP 3.7 4.7 - - - -
124A ARG 3.2 0.2 - - - -
125A VAL* 1.3 79.3 - - - +
127A GLY* 1.3 60.1 + - - +
129A THR 4.5 3.5 + - - +
137A LEU* 2.9 28.1 + - - +
138A ALA* 3.4 24.3 + - - +
162A ILE 2.7 31.8 + - - -
163A ASN* 3.6 16.5 + - - +
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Residues in contact with GLY 127 (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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123A ASP 3.0 15.6 + - - -
124A ARG* 3.1 2.4 + - - -
126A SER* 1.3 79.4 - - - +
128A GLN* 1.3 61.6 + - - +
135A LYS* 3.7 20.9 - - - +
138A ALA* 4.6 8.4 - - - +
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Residues in contact with GLN 128 (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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124A ARG* 2.8 67.7 + - + +
127A GLY* 1.3 76.9 - - - +
129A THR* 1.3 65.9 + - - +
130A GLN* 3.1 15.8 + - - +
135A LYS* 3.9 7.1 - - - +
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Residues in contact with THR 129 (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 THR* 4.9 6.5 - - - +
80A ALA* 3.1 36.0 - - + +
125A VAL* 2.7 32.5 + - - +
126A SER 4.8 1.9 - - - +
127A GLY 3.8 0.2 - - - -
128A GLN* 1.3 76.1 - - - +
130A GLN* 1.3 63.1 + - - +
135A LYS* 3.3 22.2 - - - +
136A VAL* 3.5 25.1 + - + +
137A LEU* 4.7 4.0 + - - -
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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
------------------------------------------------------------
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