Contacts of the helix formed by residues 103 - 127 (chain A) in PDB entry 5SV1
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A SER* 3.4 8.3 + - - +
102A ASP* 1.3 75.1 - - - +
104A ASN* 1.3 66.9 + - - +
105A GLU* 3.3 21.2 + - - +
106A GLY 3.5 14.0 + - - -
107A ILE* 3.8 9.7 + - - +
108B MLY 3.6 25.8 - - - -
225B ASP* 3.6 23.6 - - - +
229B SER* 3.7 3.7 + - - +
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Residues in contact with ASN 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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101A SER 4.7 4.0 - - - +
102A ASP 3.4 11.2 + - - +
103A ASP* 1.3 71.9 + - - +
105A GLU* 1.3 67.4 + - - +
106A GLY 3.0 2.5 + - - -
107A ILE* 3.3 16.3 + - - +
108A MLY 3.2 42.4 + - - +
224A LEU* 3.4 46.2 + - + +
225A ASP* 5.0 1.6 + - - +
228A ALA* 3.8 16.3 - - - +
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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
----------------------------------------------------------
103A ASP* 3.3 15.4 + - - +
104A ASN* 1.3 77.6 - - - +
106A GLY* 1.3 61.3 + - - +
108A MLY 3.7 32.6 - - - +
109A GLU* 3.1 50.3 + - - +
108B MLY 5.8 1.6 - - - -
105E GLU* 5.4 5.4 - - - +
109E GLU* 4.9 9.0 - - - +
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 3.5 8.3 + - - -
104A ASN 3.0 1.0 - - - -
105A GLU* 1.3 77.0 - - - +
107A ILE* 1.3 69.3 + - - +
109A GLU* 3.2 4.7 + - - +
110A ARG* 2.9 44.5 + - - +
108B MLY 4.0 16.6 - - - -
225B ASP* 3.6 7.4 - - - -
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Residues in contact with ILE 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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94A GLU* 4.3 7.7 - - + +
95A LEU* 3.8 28.0 - - + +
98A SER* 3.6 36.1 - - - +
101A SER* 5.1 7.4 - - - +
103A ASP 3.8 10.3 + - - +
104A ASN* 3.3 17.8 + - - +
106A GLY* 1.3 74.3 - - - +
108A MLY 1.3 65.2 + - - +
110A ARG* 3.0 14.4 + - - +
111A THR* 2.9 23.7 + - - +
220A GLN* 4.2 12.3 - - - +
224A LEU* 3.7 25.4 - - + -
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Residues in contact with MLY 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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104A ASN* 3.2 21.1 + - - +
105A GLU* 3.7 42.8 - - - +
107A ILE* 1.3 76.5 + - - +
109A GLU* 1.3 68.4 + - - +
111A THR* 3.0 12.8 + - - -
112A SER* 3.2 14.2 + - - -
217A LEU* 5.4 0.3 - - - +
220A GLN* 3.9 12.6 - - - +
221A SER* 3.8 34.8 - - - +
224A LEU* 4.6 13.5 - - + -
225A ASP* 2.7 34.8 + - - -
103E ASP* 3.6 14.4 - - - -
105E GLU 5.7 0.2 - - - -
106E GLY* 4.2 11.4 - - - -
109E GLU* 3.9 21.5 - - - +
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Residues in contact with GLU 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 43.0 + - - +
106A GLY 3.5 4.9 - - - +
108A MLY 1.3 79.9 + - - +
110A ARG* 1.3 65.8 + - + +
112A SER* 3.0 14.2 + - - -
113A PHE* 3.1 12.5 + - - +
105B GLU* 6.0 1.9 - - - +
108B MLY 3.3 30.0 - - - +
221B SER* 5.0 1.4 + - - -
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 3.2 26.7 + - - +
98A SER* 3.0 27.0 + - - -
101A SER* 4.5 3.0 + - - -
106A GLY* 2.9 22.3 + - - +
107A ILE* 3.2 32.4 - - - +
109A GLU* 1.3 73.2 - - + +
111A THR* 1.3 66.6 + - - +
113A PHE* 3.1 7.3 + - - +
114A ARG* 3.0 22.2 + - - +
218B LEU* 3.7 29.1 - - + +
221B SER* 3.1 30.4 + - - +
222B ARG* 3.9 15.2 - - - +
225B ASP* 2.5 44.7 + - - +
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Residues in contact with THR 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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90A GLU 5.6 0.2 - - - -
91A ALA* 4.1 19.5 - - + +
94A GLU* 3.8 17.2 - - + +
107A ILE 2.9 13.2 + - - -
108A MLY 3.0 4.0 + - - -
110A ARG* 1.3 74.1 - - - +
112A SER* 1.3 65.4 + - - +
114A ARG* 3.0 8.2 + - - +
115A LEU* 2.8 28.1 + - + +
216A VAL* 5.6 0.2 - - + -
217A LEU* 3.5 21.8 - - + -
220A GLN* 2.7 40.9 + - + +
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Residues in contact with SER 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 MLY 3.2 6.6 + - - -
109A GLU* 3.0 11.1 + - - -
111A THR* 1.3 77.1 - - - +
113A PHE* 1.3 65.1 + - - +
115A LEU* 3.0 1.7 + - - +
116A GLU* 2.8 36.2 + - - +
217A LEU* 3.2 34.8 - - - +
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Residues in contact with PHE 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 GLU 3.1 8.4 + - - +
110A ARG* 3.1 12.9 + - - +
112A SER* 1.3 78.4 - - - +
114A ARG* 1.3 65.1 + - - +
116A GLU* 4.3 3.1 - - + +
117A ARG* 3.3 38.5 + - + +
214B ALA* 3.6 37.2 - - + -
217B LEU* 4.3 22.7 - - + -
218B LEU* 4.1 20.9 - - + -
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Residues in contact with ARG 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 GLU* 2.7 62.6 + - + +
93A ASN* 2.9 34.3 + - - +
94A GLU* 3.4 23.1 + - - +
97A LEU* 4.8 4.6 - - - +
110A ARG 3.0 11.0 + - - +
111A THR* 3.0 7.9 + - - +
113A PHE* 1.3 73.1 - - - +
115A LEU* 1.3 69.8 + - + +
117A ARG* 3.0 9.5 + - - +
118A ARG* 2.8 22.9 + - - +
218B LEU* 3.6 33.3 - - + +
222B ARG* 5.0 3.2 - - - +
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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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87A LEU* 3.7 39.2 - - + +
90A GLU* 3.8 20.0 - - + -
91A ALA* 4.7 0.7 - - + +
111A THR* 2.8 29.4 + - + +
112A SER* 4.0 1.6 - - - +
114A ARG* 1.3 71.9 - - + +
116A GLU* 1.3 68.2 + - - +
118A ARG* 3.0 13.1 + - + +
119A VAL* 3.1 15.8 + - - +
213A ALA* 4.0 23.1 - - + +
216A VAL* 3.8 26.5 - - + -
217A LEU* 3.7 28.3 - - + -
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Residues in contact with GLU 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 SER* 2.8 35.9 + - - +
113A PHE* 4.3 4.7 - - + +
115A LEU* 1.3 73.2 - - - +
117A ARG* 1.3 62.9 + - - +
119A VAL* 2.9 18.1 + - - +
120A ALA* 3.2 9.4 + - - +
210A GLY* 5.7 2.1 - - - +
213A ALA* 5.2 6.9 - - - +
214A ALA 5.9 0.2 + - - -
217A LEU* 4.6 13.7 - - + +
113E PHE* 5.2 10.7 - - - -
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Residues in contact with ARG 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 PHE* 3.3 35.2 + - + +
114A ARG* 3.0 5.8 + - - +
116A GLU* 1.3 79.1 - - - +
118A ARG* 1.3 68.8 + - - +
120A ALA* 3.0 19.4 + - + +
121A ALA* 3.1 13.3 + - + +
124A ARG* 5.5 2.2 + - - +
207B ALA* 4.0 4.8 + - - +
210B GLY* 3.5 22.0 + - - -
211B ASP* 2.3 51.4 + - - +
214B ALA* 3.8 18.7 - - - +
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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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86A HIS* 5.7 7.3 - - + +
87A LEU* 4.1 21.3 - - + -
90A GLU* 3.1 39.8 + - - +
114A ARG 2.8 16.4 + - - +
115A LEU* 3.0 13.2 + - - +
117A ARG* 1.3 73.8 - - - +
119A VAL* 1.3 64.3 + - - +
121A ALA* 3.0 25.3 + - - +
122A VAL* 3.1 19.3 + - + +
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Residues in contact with VAL 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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87A LEU* 5.1 2.0 - - + -
115A LEU 3.1 11.5 + - - +
116A GLU* 2.9 12.6 + - - +
118A ARG* 1.3 75.6 - - - +
120A ALA* 1.3 65.5 + - - +
122A VAL* 2.9 21.6 + - - +
123A GLY 3.1 9.4 + - - -
206A LYS* 4.3 33.2 - - + +
209A LEU* 3.6 34.1 - - + +
210A GLY* 4.4 5.2 - - - +
213A ALA* 4.2 16.8 - - + -
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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 GLU 3.2 4.2 + - - +
117A ARG* 3.0 16.4 + - + +
119A VAL* 1.3 79.3 - - - +
121A ALA* 1.3 63.3 + - - +
123A GLY* 2.9 13.6 + - - +
124A ARG* 3.0 20.5 + - - +
206A LYS* 5.0 6.4 - - - +
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Residues in contact with ALA 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 ARG* 3.1 12.1 + - + +
118A ARG* 3.0 22.4 + - - +
120A ALA* 1.3 74.9 - - - +
122A VAL* 1.3 64.8 + - + +
124A ARG* 3.0 35.2 + - - +
125A GLN* 3.0 32.7 + - - +
211B ASP* 5.8 1.6 - - - +
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Residues in contact with VAL 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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83A LEU* 4.5 19.1 - - + -
118A ARG* 3.1 18.2 + - + +
119A VAL* 2.9 10.8 + - + +
121A ALA* 1.3 75.2 - - + +
123A GLY* 1.3 62.8 + - - +
125A GLN* 3.0 14.9 + - - +
126A MET* 2.9 29.7 + - + +
205A PHE* 4.0 21.8 - - + -
206A LYS* 6.0 2.9 - - + -
209A LEU* 3.6 33.0 - - + -
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Residues in contact with GLY 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 VAL 3.1 6.5 + - - -
120A ALA 2.9 8.6 + - - -
122A VAL* 1.3 77.2 - - - +
124A ARG* 1.3 60.9 + - - +
126A MET* 2.9 10.9 + - - +
127A GLY* 2.9 21.7 + - - -
202A ILE* 5.0 2.8 - - - +
206A LYS* 3.4 34.4 - - - +
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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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117A ARG* 5.5 1.6 - - - +
120A ALA* 3.0 16.7 + - - +
121A ALA* 3.0 35.2 + - - +
123A GLY* 1.3 76.4 - - - +
125A GLN* 1.3 66.1 + - - +
127A GLY* 3.8 2.2 + - - +
128A ARG* 3.6 19.6 + - - +
203B GLY 5.3 2.9 - - - -
204B GLY* 5.1 9.8 + - - -
207B ALA* 3.6 34.8 - - - +
208B MET* 5.5 3.6 - - - +
211B ASP* 4.1 20.4 + - - -
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Residues in contact with GLN 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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44A LYS* 6.1 0.5 - - - -
121A ALA* 3.0 21.3 + - - +
122A VAL* 3.5 12.9 - - - +
124A ARG* 1.3 82.9 - - + +
126A MET* 1.3 72.4 + - + +
128A ARG* 3.7 17.1 + - - +
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Residues in contact with MET 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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44A LYS* 5.3 7.3 - - - +
47A GLU* 4.6 12.6 - - + +
48A PHE* 4.6 16.6 - - - -
51A GLN* 4.2 24.7 - - - +
122A VAL* 2.9 26.5 + - + +
123A GLY* 2.9 8.5 + - - +
125A GLN* 1.3 85.6 - - + +
127A GLY* 1.3 59.7 + - - +
128A ARG 3.2 6.2 + - - +
130A ASN* 4.7 6.4 + - - -
202A ILE* 3.6 28.2 - - + +
205A PHE* 3.3 39.9 - - + -
206A LYS* 6.4 0.2 - - + -
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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 GLY 2.9 13.4 + - - -
124A ARG* 3.8 5.1 + - - -
125A GLN 3.4 0.2 - - - -
126A MET* 1.3 75.5 - - - +
128A ARG* 1.3 61.2 + - - +
129A GLY 3.3 4.0 + - - -
130A ASN* 3.3 22.7 + - - +
131A GLY 4.3 2.9 + - - -
202A ILE* 3.9 10.9 - - - +
200B ARG* 5.0 5.9 - - - +
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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