Contacts of the helix formed by residues 108 - 129 (chain E) in PDB entry 4HHM
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 108 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ASP* 4.9 0.2 + - - -
106E ALA* 3.2 1.8 - - + +
107E ASN* 1.3 74.0 - - - +
109E ARG* 1.3 65.6 + - - +
110E ASP* 3.2 16.2 - - - +
111E VAL* 3.1 23.6 + - + +
112E ARG* 3.3 14.4 + - - +
334F ARG* 2.8 51.1 + - - +
337F GLN* 3.8 8.6 + - - +
365F ALA 5.3 0.7 - - - +
368F ARG* 3.2 24.5 + - - +
370F MET* 4.0 9.4 - - - +
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Residues in contact with ARG 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ASN 3.2 2.8 + - - -
108E ASP* 1.3 71.8 - - - +
110E ASP* 1.3 64.3 + - - +
112E ARG* 3.1 38.3 + - - +
113E ARG* 3.1 53.8 + - - +
337F GLN* 2.9 24.1 - - + +
340F GLU* 4.4 17.3 - - - -
341F PRO 3.1 24.3 + - - -
342F THR* 3.2 10.1 + - - +
343F ALA* 4.7 1.6 - - - +
344F ALA 5.1 1.8 - - - +
345F ASP* 4.2 7.7 + - - -
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Residues in contact with ASP 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E ASP* 3.2 8.8 - - - +
109E ARG* 1.3 78.0 + - - +
111E VAL* 1.3 68.2 + - - -
113E ARG* 3.6 12.6 + - - +
114E TYR* 3.3 21.3 + - - +
337F GLN* 4.5 1.6 + - - +
355F THR 5.9 0.7 - - - +
356F ALA* 5.6 1.2 - - - -
360F PHE* 3.7 25.9 - - + -
365F ALA* 4.5 0.7 - - - +
368F ARG* 2.9 43.4 + - - -
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Residues in contact with VAL 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E VAL* 3.6 41.1 - - + +
99E PHE* 3.9 13.4 - - + -
102E GLY 3.7 18.2 - - - +
103E ALA 4.4 0.9 - - - +
106E ALA* 3.8 9.0 - - + -
108E ASP* 3.1 20.1 + - + +
110E ASP* 1.3 90.4 + - - +
112E ARG* 1.3 66.9 + - - +
114E TYR* 3.3 2.6 + - + +
115E ALA* 2.9 21.8 + - - +
360F PHE* 4.3 9.6 - - + -
365F ALA* 4.6 0.9 - - + +
368F ARG* 4.0 8.3 - - - +
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Residues in contact with ARG 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E ALA 3.2 20.1 - - - +
104E PHE* 3.2 24.9 - - - +
105E THR* 4.3 0.4 - - - +
106E ALA 2.8 43.9 + - - +
107E ASN 2.9 20.8 + - - -
108E ASP 3.6 2.9 - - - +
109E ARG* 3.1 28.9 + - - +
111E VAL* 1.3 77.8 - - - +
113E ARG* 1.3 61.9 + - - +
115E ALA* 3.3 4.9 + - - +
116E LEU* 3.2 24.9 + - - +
157E ARG* 3.5 15.1 - - - +
337F GLN 2.9 14.8 + - - -
338F LEU* 3.7 5.5 - - - +
340F GLU 2.7 29.7 + - - -
342F THR* 2.7 32.6 + - + +
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Residues in contact with ARG 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E ARG* 3.1 45.2 + - - +
110E ASP* 3.9 11.4 - - - +
112E ARG* 1.3 76.4 - - - +
114E TYR* 1.3 62.5 + - - +
116E LEU* 3.2 5.8 + - - +
117E ARG* 3.1 27.7 + - - +
342F THR* 2.9 40.1 + - + +
343F ALA* 3.5 6.9 - - - +
345F ASP* 3.1 33.5 + - - -
350F LEU* 3.6 28.6 - - + +
353F ASP* 2.5 36.8 + - - +
355F THR* 5.6 0.8 + - - -
356F ALA* 4.2 10.1 - - + +
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Residues in contact with TYR 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E PHE* 3.2 33.3 - + - -
98E VAL* 4.4 4.9 - - + -
99E PHE* 3.7 33.9 - + - -
110E ASP 3.3 15.9 + - - +
111E VAL 3.3 3.8 + - - +
113E ARG* 1.3 78.4 - - - +
115E ALA* 1.3 56.7 + - - +
117E ARG* 3.1 2.8 + - - -
118E LYS* 2.8 43.4 + - + +
356F ALA 3.3 22.6 + - - +
357F TYR* 4.0 29.5 - + - -
360F PHE* 3.4 36.6 - + + -
362F VAL* 3.9 16.1 - - + +
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Residues in contact with ALA 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E LEU* 3.7 11.7 - - + +
99E PHE* 3.9 8.1 - - + -
103E ALA* 3.6 37.9 - - + -
104E PHE* 3.9 9.4 - - + -
111E VAL 2.9 13.4 + - - +
112E ARG 3.3 9.8 + - - +
114E TYR* 1.3 76.3 - - - +
116E LEU* 1.3 59.6 + - - +
118E LYS* 3.5 2.9 + - - +
119E THR* 2.9 29.5 + - - -
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Residues in contact with LEU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 3.9 14.1 - - + -
112E ARG* 3.2 8.0 + - + +
113E ARG* 3.4 7.6 - - - +
115E ALA* 1.3 76.5 - - - +
117E ARG* 1.3 60.7 + - - +
119E THR* 3.9 2.4 - - - -
120E ILE* 3.0 39.2 + - + +
161E ALA* 3.8 39.3 - - + +
164E LEU* 3.8 17.9 - - + -
165E LEU* 4.3 12.8 - - + -
342F THR* 3.6 31.2 - - + -
350F LEU* 3.8 25.4 - - + -
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Residues in contact with ARG 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ARG 3.1 14.5 + - - +
114E TYR 3.1 7.0 + - - +
116E LEU* 1.3 76.1 - - - +
118E LYS* 1.3 63.4 + - - +
120E ILE* 4.1 3.8 - - - +
121E ARG* 3.3 23.6 + - - +
350F LEU* 3.0 35.0 + - + -
351F LEU* 3.0 40.2 + - - +
353F ASP 2.9 28.5 + - - -
356F ALA* 3.7 20.2 - - + +
357F TYR* 3.8 26.1 - - + +
358F GLU* 3.9 19.8 + - - -
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Residues in contact with LYS 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E ASP* 2.6 32.4 + - - +
56E ASP* 2.8 22.2 + - - -
61E PHE* 4.1 16.4 - - - -
91E THR* 4.2 2.9 - - + -
92E ASN 3.1 19.7 + - - +
93E LEU* 4.1 5.6 - - + -
96E HIS* 6.2 0.9 - - - -
99E PHE* 4.1 23.3 - - + -
114E TYR* 2.8 40.4 + - + +
115E ALA* 3.6 6.7 - - - +
117E ARG* 1.3 79.0 - - - +
119E THR* 1.3 61.0 + - - +
121E ARG* 3.7 4.7 + - - +
122E ASN* 3.4 19.9 + - - +
357F TYR* 4.5 12.5 - - + -
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Residues in contact with THR 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E THR* 3.3 34.2 + - - +
93E LEU* 3.5 12.7 - - + +
104E PHE* 3.9 6.9 - - + -
115E ALA 2.9 15.9 + - - -
116E LEU 3.9 4.3 - - - -
118E LYS* 1.3 76.8 - - - +
120E ILE* 1.3 66.1 + - - +
121E ARG 3.2 0.2 - - - -
122E ASN* 2.9 5.0 + - - +
123E ILE* 2.8 24.5 + - + +
134E TYR* 3.7 14.6 - - + -
165E LEU* 4.1 27.1 - - + -
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Residues in contact with ILE 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU* 3.0 30.8 + - + +
117E ARG* 4.1 9.0 - - - +
119E THR* 1.3 75.4 - - - +
121E ARG* 1.3 65.9 + - - +
123E ILE* 3.0 20.5 + - - +
124E ASP* 3.2 14.5 + - - +
164E LEU* 5.7 2.0 - - + +
165E LEU* 4.0 18.4 - - + -
168E TYR* 3.6 42.2 - - + +
347F LEU* 4.0 15.9 - - + -
350F LEU* 5.2 2.9 - - + -
351F LEU* 3.6 28.7 - - + -
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Residues in contact with ARG 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E ALA 5.3 6.1 + - - -
65E ASP* 3.0 33.9 + - - -
68E ARG* 3.3 51.2 + - - +
117E ARG 3.3 16.5 + - - +
118E LYS* 3.9 5.4 - - - +
119E THR 3.2 0.4 - - - -
120E ILE* 1.3 81.6 - - - +
122E ASN* 1.3 60.8 + - - +
124E ASP* 3.4 13.9 + - + +
125E LEU* 3.3 18.2 + - - +
357F TYR* 2.6 50.0 + - + -
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Residues in contact with ASN 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E PHE* 3.6 19.2 - - - -
55E ASP* 3.2 37.7 - - + +
68E ARG* 5.3 2.8 + - - +
89E ALA* 4.4 0.6 - - - +
90E THR 2.8 30.1 + - - +
118E LYS 3.4 9.6 + - - +
119E THR* 2.9 6.2 + - - +
121E ARG* 1.3 75.5 - - - +
123E ILE* 1.3 60.1 + - - +
124E ASP 3.2 0.4 - - - -
125E LEU* 3.7 14.6 - - - +
126E ALA* 2.9 26.2 + - - +
134E TYR* 2.9 22.3 + - - +
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Residues in contact with ILE 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E THR* 2.8 20.4 + - + +
120E ILE* 3.0 12.5 + - - +
122E ASN* 1.3 77.9 - - - +
124E ASP* 1.3 64.0 + - - +
126E ALA* 3.2 2.2 + - - +
127E VAL* 3.0 23.2 + - - +
134E TYR* 3.9 24.9 - - + -
165E LEU* 4.1 19.3 - - + +
168E TYR* 4.6 7.2 - - + -
169E VAL* 4.1 11.2 - - + -
174E TYR* 4.2 12.3 - - + -
176E ILE* 3.3 28.3 - - + -
178E PHE* 3.7 29.8 - - + -
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Residues in contact with ASP 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ILE* 3.2 12.1 + - - +
121E ARG* 3.6 14.9 - - + +
122E ASN 3.2 0.2 - - - -
123E ILE* 1.3 78.3 - - - +
125E LEU* 1.3 61.5 + - - +
127E VAL* 3.5 2.8 + - - +
128E GLU* 3.0 24.3 + - - +
168E TYR* 2.6 32.6 + - - -
174E TYR* 2.9 29.8 + - - +
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Residues in contact with LEU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E PHE* 4.1 11.7 - - + -
58E LEU* 4.5 2.5 - - + -
59E ILE* 3.6 31.0 - - + -
68E ARG* 4.0 10.1 - - - +
72E VAL* 3.7 24.7 - - + -
121E ARG 3.3 11.0 + - - +
122E ASN* 3.7 24.5 - - - +
123E ILE 3.2 0.2 - - - -
124E ASP* 1.3 75.7 - - - +
126E ALA* 1.3 67.7 + - - +
128E GLU* 3.3 24.7 + - - +
129E LEU* 3.1 37.3 + - + +
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Residues in contact with ALA 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E PHE* 4.7 3.1 - - - -
89E ALA* 3.7 27.4 - - + -
122E ASN 2.9 16.3 + - - +
123E ILE* 3.2 11.2 + - + +
125E LEU* 1.3 76.1 - - - +
127E VAL* 1.3 65.9 + - + +
129E LEU* 2.9 16.8 + - - +
130E GLY 3.0 8.7 + - - -
131E ALA* 3.2 19.8 + - + +
133E VAL 5.8 0.4 - - - +
134E TYR* 4.0 11.9 - - + -
176E ILE* 5.7 2.7 - - + -
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Residues in contact with VAL 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ILE 3.0 18.8 + - - +
124E ASP 3.9 4.5 - - - +
126E ALA* 1.3 74.3 - - - +
128E GLU* 1.3 59.1 + - - +
130E GLY* 2.9 19.6 + - - -
131E ALA 4.2 7.0 - - - -
174E TYR* 3.6 56.5 - - + -
175E ASP 5.2 2.0 - - - +
176E ILE* 4.0 20.6 - - + -
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Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E GLU* 4.2 15.2 - - - +
72E VAL* 4.6 4.5 - - - +
76E ARG* 2.9 33.4 + - - +
124E ASP 3.0 15.1 + - - +
125E LEU* 3.3 29.8 - - + +
126E ALA 3.1 0.4 - - - -
127E VAL* 1.3 77.4 - - - +
129E LEU* 1.3 58.3 + - - +
130E GLY 3.7 0.2 + - - -
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Residues in contact with LEU 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E PHE* 3.5 39.3 - - + -
58E LEU* 4.5 9.6 - - + -
72E VAL* 5.4 5.6 - - + +
75E PHE* 4.8 10.8 - - + -
76E ARG* 3.7 40.8 - - + +
79E LEU* 5.0 0.4 - - + -
85E THR* 5.3 2.4 + - - -
86E VAL* 4.5 30.6 + - + +
125E LEU* 3.1 26.4 + - + +
126E ALA* 2.9 9.0 + - - +
128E GLU* 1.3 78.0 - - - +
130E GLY* 1.3 59.5 + - - +
131E ALA* 3.5 1.5 + - + +
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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
------------------------------------------------------------
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