Contacts of the helix formed by residues 103 - 127 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 3.3 13.2 + - - -
102B ASP* 1.3 74.6 - - - +
104B ASN* 1.3 66.3 + - - +
105B GLU* 3.4 26.0 - - - +
106B GLY 3.5 14.4 + - - -
107B ILE* 3.5 11.3 + - - +
108C MLY 3.7 25.1 - - - -
225C ASP* 3.4 18.3 - - - +
229C SER* 3.9 3.9 + - - +
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Residues in contact with ASN 104 (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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101B SER 4.9 4.5 - - - +
102B ASP 3.5 8.3 + - - +
103B ASP* 1.3 70.3 + - - +
105B GLU* 1.3 65.4 + - - +
106B GLY 2.9 4.7 - - - -
107B ILE* 2.8 28.5 + - - +
108B MLY 3.1 31.0 + - - +
224B LEU* 3.4 48.4 + - + +
225B ASP* 5.3 1.4 + - - +
228B ALA* 3.6 18.8 - - - +
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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
----------------------------------------------------------
109A GLU* 6.0 2.0 - - - +
103B ASP* 3.4 16.5 + - - +
104B ASN* 1.3 77.3 - - - +
106B GLY* 1.3 59.1 + - - +
108B MLY 4.1 20.0 - - - +
109B GLU* 3.2 44.8 + - - +
105C GLU* 3.9 23.5 - - - +
108C MLY 5.4 0.2 - - - -
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASP* 3.5 8.5 + - - -
104B ASN 2.8 2.4 + - - -
105B GLU* 1.3 76.9 - - - +
107B ILE* 1.3 65.1 + - - -
109B GLU* 3.0 5.5 + - - +
110B ARG* 2.8 39.5 + - - +
108C MLY 3.9 19.1 - - - -
225C ASP* 3.6 10.5 - - - -
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 4.5 6.5 - - + +
95B LEU* 4.0 24.0 - - + +
98B SER* 3.7 31.0 - - - +
101B SER* 4.5 11.0 - - - +
103B ASP 3.5 7.3 + - - +
104B ASN* 2.8 25.3 + - - +
106B GLY* 1.3 70.2 - - - +
108B MLY 1.3 52.4 + - - +
110B ARG* 2.9 26.4 + - - +
111B THR* 2.6 47.8 + - - +
220B GLN* 4.3 1.1 - - - +
224B LEU* 3.6 23.1 - - + -
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Residues in contact with MLY 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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103A ASP* 3.6 15.0 - - - -
105A GLU* 5.3 1.8 - - - -
106A GLY* 4.0 15.7 - - - -
109A GLU* 3.3 28.9 - - - +
104B ASN* 3.1 20.4 + - - +
105B GLU* 4.1 27.8 - - - +
107B ILE* 1.3 74.6 + - - +
109B GLU* 1.3 63.7 + - + +
111B THR* 3.0 2.8 + - - -
112B SER* 2.8 29.9 + - - +
217B LEU* 5.1 0.2 - - - +
220B GLN* 4.0 11.7 - - - +
221B SER* 3.7 40.2 - - - +
224B LEU* 4.2 19.7 - - + -
225B ASP* 2.8 27.1 + - - -
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLU* 3.2 37.5 + - + +
106B GLY 3.0 6.5 + - - +
108B MLY 1.3 79.7 + - - +
110B ARG* 1.3 66.4 + - + +
112B SER* 3.0 13.9 + - - -
113B PHE* 3.0 15.5 + - - +
105C GLU* 6.0 1.7 - - - +
108C MLY 3.6 25.6 - - - +
221C SER* 5.0 0.9 + - - -
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 2.9 23.3 + - - +
98B SER* 2.7 27.7 + - - -
101B SER* 4.1 4.4 + - - -
103B ASP 4.1 0.4 + - - -
106B GLY 2.8 12.6 + - - +
107B ILE* 2.9 43.2 - - - +
109B GLU* 1.3 76.0 - - + +
111B THR* 1.3 63.0 + - - +
113B PHE* 3.8 1.3 + - - -
114B ARG* 3.0 27.9 + - - +
218C LEU* 3.6 28.1 - - + +
221C SER* 3.3 31.0 + - - +
222C ARG* 3.5 28.9 - - - +
225C ASP* 3.0 24.4 + - - +
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Residues in contact with THR 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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90B GLU 5.6 0.2 - - - -
91B ALA* 4.1 17.5 - - + -
94B GLU* 3.6 17.5 - - + +
107B ILE* 2.6 23.0 + - - +
108B MLY 3.4 4.7 - - - -
110B ARG* 1.3 73.1 - - - +
112B SER* 1.3 64.1 + - - +
114B ARG* 2.9 17.6 + - + +
115B LEU* 3.0 14.9 + - + +
217B LEU* 3.5 17.3 - - + -
220B GLN* 2.9 46.4 + - - +
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Residues in contact with SER 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 MLY 2.8 20.6 + - - +
109B GLU* 3.6 8.2 - - - -
111B THR* 1.3 72.0 - - - +
113B PHE* 1.3 64.1 + - - +
115B LEU* 3.0 12.8 + - - +
116B GLU* 3.0 28.6 + - - +
217B LEU* 3.4 34.3 - - - +
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Residues in contact with PHE 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 GLU 3.0 15.1 + - - +
110B ARG* 3.9 4.9 - - - +
112B SER* 1.3 76.6 - - - +
114B ARG* 1.3 63.4 + - - +
116B GLU* 3.7 17.3 + - - +
117B ARG* 3.3 41.9 + - - +
116C GLU* 4.2 18.4 - - - -
214C ALA* 3.5 32.3 - - + +
217C LEU* 4.1 23.3 - - + -
218C LEU* 4.2 22.0 - - + -
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Residues in contact with ARG 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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90B GLU* 3.2 60.9 + - + +
93B ASN* 3.0 28.7 + - - -
94B GLU* 3.1 36.2 + - - +
97B LEU* 4.7 1.0 - - - +
110B ARG 3.0 15.2 + - - +
111B THR* 2.9 8.9 + - + +
113B PHE* 1.3 76.0 - - - +
115B LEU* 1.3 66.5 + - + +
117B ARG* 2.9 20.2 + - - +
118B ARG* 3.3 5.2 + - - +
218C LEU* 3.6 25.0 - - + +
222C ARG* 4.4 4.1 - - - +
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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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87B LEU* 3.7 38.9 - - + +
90B GLU* 4.0 19.5 - - + +
91B ALA 4.6 1.8 - - - +
111B THR* 3.0 13.9 + - + +
112B SER 3.0 6.3 + - - +
114B ARG* 1.3 78.4 - - + +
116B GLU* 1.3 58.9 + - - +
118B ARG* 2.9 22.8 + - - +
119B VAL* 3.3 15.4 + - - +
213B ALA* 3.9 19.3 - - + +
216B VAL* 3.6 24.0 - - + -
217B LEU* 3.5 36.8 - - + -
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Residues in contact with GLU 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 SER* 3.0 32.0 + - - +
113B PHE* 3.7 21.3 + - + +
115B LEU* 1.3 75.5 - - - +
117B ARG* 1.3 65.4 + - - +
118B ARG 3.4 0.2 - - - -
119B VAL* 4.3 9.4 - - - +
120B ALA* 3.9 17.8 + - - +
217B LEU* 5.6 3.3 - - + +
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Residues in contact with ARG 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 PHE* 3.3 39.6 + - - +
114B ARG* 2.9 14.8 + - - +
115B LEU 2.9 0.2 + - - -
116B GLU* 1.3 83.7 + - - +
118B ARG* 1.3 61.4 + - - +
120B ALA* 4.2 3.7 - - - +
121B ALA* 3.5 19.1 + - - +
124B ARG* 5.3 2.3 + - - +
116C GLU* 5.3 3.6 + - - -
207C ALA* 4.4 5.5 + - - +
210C GLY* 3.1 30.3 + - - -
211C ASP* 2.9 39.6 + - - +
214C ALA* 3.9 12.9 - - + +
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Residues in contact with ARG 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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86B HIS* 3.6 39.9 + - - +
87B LEU* 4.0 22.4 - - + +
90B GLU* 3.1 46.2 + - - +
114B ARG 3.3 4.3 + - - +
115B LEU 2.9 8.5 + - - +
117B ARG* 1.3 78.3 - - - +
119B VAL* 1.3 67.4 + - - +
121B ALA* 2.9 10.4 + - + +
122B VAL* 2.8 33.1 + - + +
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Residues in contact with VAL 119 (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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87B LEU* 4.7 4.3 - - + -
115B LEU 3.3 12.7 + - - +
116B GLU* 4.5 7.4 - - - +
117B ARG 3.5 0.2 - - - -
118B ARG* 1.3 75.0 - - - +
120B ALA* 1.3 66.8 + - - +
122B VAL* 3.0 9.0 + - - +
123B GLY* 2.8 20.3 + - - -
206B LYS* 4.5 22.9 - - + +
209B LEU* 3.6 33.3 - - + +
210B GLY* 4.6 8.5 - - - +
213B ALA* 4.0 20.6 - - + -
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Residues in contact with ALA 120 (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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116B GLU 3.9 14.7 + - - +
117B ARG* 4.2 8.1 - - - +
118B ARG 3.3 0.4 - - - -
119B VAL* 1.3 80.6 - - - +
121B ALA* 1.3 52.1 + - - +
123B GLY* 2.9 5.0 + - - -
124B ARG* 2.7 48.9 + - - +
206B LYS* 5.4 1.9 - - - +
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Residues in contact with ALA 121 (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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117B ARG 3.5 12.2 + - - +
118B ARG* 2.9 15.9 + - + +
120B ALA* 1.3 77.0 - - - +
122B VAL* 1.3 65.5 + - + +
124B ARG* 3.0 30.0 + - - +
125B GLN* 2.9 22.3 + - - +
211C ASP* 5.1 5.6 - - - +
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Residues in contact with VAL 122 (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 LEU* 4.6 20.4 - - + -
118B ARG* 2.8 30.1 + - + +
119B VAL* 3.5 7.0 - - - +
121B ALA* 1.3 71.0 - - + +
123B GLY* 1.3 65.8 + - - +
125B GLN* 2.9 24.8 + - - +
126B MET* 3.0 35.0 + - + +
205B PHE* 4.4 6.5 - - + -
209B LEU* 3.7 28.0 - - + -
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Residues in contact with GLY 123 (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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119B VAL 2.8 16.7 + - - -
120B ALA* 3.3 4.7 - - - -
122B VAL* 1.3 72.4 - - - +
124B ARG* 1.3 56.7 + - - +
126B MET* 2.9 24.5 + - - +
127B GLY* 3.2 10.2 + - - -
202B ILE* 5.1 0.3 - - - +
205B PHE* 6.2 0.2 - - - -
206B LYS* 3.5 40.8 + - - -
209B LEU* 5.7 0.2 - - - +
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Residues in contact with ARG 124 (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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117B ARG* 5.3 2.0 + - - +
120B ALA* 2.7 22.8 + - + +
121B ALA* 3.0 32.6 + - - +
123B GLY* 1.3 72.5 - - - +
125B GLN* 1.3 59.6 + - - +
127B GLY* 3.7 3.9 + - - +
128B ARG* 3.7 16.3 + - - +
206B LYS* 4.7 2.4 - - - +
203C GLY 6.3 0.4 - - - -
204C GLY* 4.9 9.6 + - - -
207C ALA* 3.6 33.0 - - - +
208C MET* 4.8 9.1 - - - +
211C ASP* 4.3 20.4 + - - -
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LYS* 4.4 7.6 + - - -
121B ALA 2.9 10.7 + - - +
122B VAL* 2.9 19.0 + - - +
124B ARG* 1.3 74.5 - - - +
126B MET* 1.3 73.9 + - + +
128B ARG* 3.5 20.3 + - + +
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Residues in contact with MET 126 (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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44B LYS* 3.7 25.0 - - - +
47B GLU* 5.4 15.0 - - + +
48B PHE* 5.3 8.5 - - - -
51B GLN* 5.6 7.0 - - + +
83B LEU* 6.3 0.4 - - + -
122B VAL* 3.0 30.5 + - + +
123B GLY* 2.9 12.1 + - - +
125B GLN* 1.3 88.0 - - + +
127B GLY* 1.3 56.6 + - - +
128B ARG 3.2 4.4 + - - +
130B ASN* 4.7 2.4 - - - +
202B ILE* 3.5 30.1 - - + +
205B PHE* 3.4 42.2 - - + -
206B LYS* 5.8 0.4 - - + -
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Residues in contact with GLY 127 (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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123B GLY 3.2 11.0 + - - -
124B ARG* 3.7 7.3 + - - -
125B GLN 3.3 0.2 - - - -
126B MET* 1.3 75.0 - - - +
128B ARG* 1.3 59.1 + - - -
129B GLY 3.5 0.5 + - - -
130B ASN* 3.3 38.4 + - - +
131B GLY 4.6 1.2 + - - -
202B ILE* 3.9 4.9 - - - +
200C ARG* 5.2 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