Contacts of the helix formed by residues 90 - 115 (chain E) in PDB entry 4GTU
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 GLU 90 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E THR* 1.3 73.4 + - - +
91E GLU* 1.3 64.8 + - - +
93E LYS* 2.7 24.5 + - - +
94E ILE* 2.9 30.9 + - + +
67F HIS* 5.2 7.6 - - + +
78F TYR* 4.0 21.3 - - + -
81F ARG* 3.1 38.9 + - - +
82F LYS* 4.3 14.2 - - - +
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Residues in contact with GLU 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E THR* 3.1 15.8 + - + +
90E GLU* 1.3 79.7 - - - +
92E GLU* 1.3 69.3 + - + +
94E ILE* 3.4 14.0 + - - +
95E ARG* 3.5 23.3 + - - +
148E VAL 5.7 1.1 - - - +
67F HIS* 6.4 0.9 - - - -
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Residues in contact with GLU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E GLY* 3.9 7.2 - - - -
88E GLU* 3.4 16.1 + - - +
89E THR* 2.9 25.0 + - + +
91E GLU* 1.3 84.9 - - + +
93E LYS* 1.3 62.3 + - - +
94E ILE 3.3 0.2 + - - -
95E ARG* 3.5 5.3 + - - +
96E VAL* 2.9 32.5 + - - +
148E VAL* 3.6 32.8 - - + +
149E GLY* 5.0 0.5 - - - -
150E ASP* 4.8 8.5 + - - +
151E LYS* 3.3 38.7 + - - +
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Residues in contact with LYS 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E GLY* 3.5 23.9 + - - +
88E GLU* 3.3 8.5 + - - +
89E THR* 2.8 42.0 + - - +
90E GLU* 2.7 22.2 + - - +
92E GLU* 1.3 79.0 - - - +
94E ILE* 1.3 56.8 + - - +
96E VAL* 3.7 4.6 + - - +
97E ASP* 2.7 30.8 + - - +
81F ARG* 3.3 39.3 - - - +
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Residues in contact with ILE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E GLU* 2.9 32.2 + - + +
91E GLU* 3.9 7.6 - - - +
92E GLU 3.3 0.2 - - - -
93E LYS* 1.3 77.2 - - - +
95E ARG* 1.3 59.7 + - - +
97E ASP* 3.2 9.4 + - - +
98E ILE* 3.0 30.4 + - + +
67F HIS* 3.8 25.1 - - + -
68F LYS 5.9 0.2 - - - -
69F ILE* 3.2 36.8 - - + -
74F ALA* 5.0 2.1 - - - +
78F TYR* 3.6 33.9 - - + -
81F ARG* 5.1 3.6 - - - +
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Residues in contact with ARG 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E GLU* 3.5 22.8 - - - +
92E GLU* 3.9 8.3 - - - +
94E ILE* 1.3 73.8 - - - +
96E VAL* 1.3 64.4 + - - +
98E ILE* 3.4 10.1 - - + +
99E LEU* 3.1 29.0 + - - +
139E GLN 5.5 0.2 + - - -
140E PHE* 3.0 67.6 + - + +
144E ARG* 3.4 23.7 - - - +
147E PHE 2.7 31.1 + - - +
148E VAL* 3.6 22.4 - - - +
55F ASP* 4.0 10.3 + - - -
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Residues in contact with VAL 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E CYS* 5.2 1.3 - - + -
87E GLY 4.0 20.9 - - - +
92E GLU 2.9 27.8 + - - +
93E LYS* 3.8 6.3 - - - +
95E ARG* 1.3 76.6 - - - +
97E ASP* 1.3 70.7 + - - +
99E LEU 3.7 0.2 + - - -
100E GLU* 3.1 9.3 + - - +
148E VAL* 3.5 29.6 - - + -
153E THR* 4.5 3.6 - - + +
154E PHE* 3.8 20.9 - - + -
155E VAL* 3.0 43.0 - - + +
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Residues in contact with ASP 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LYS* 2.7 21.5 - - - +
94E ILE* 3.2 8.3 + - - +
96E VAL* 1.3 82.8 - - - +
98E ILE* 1.3 69.8 + - - +
100E GLU* 3.0 13.5 + - - +
101E ASN* 2.8 29.1 + - - +
74F ALA* 4.0 19.1 - - + +
77F CYS* 3.4 18.8 - - - +
81F ARG* 2.9 34.2 + - - -
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Residues in contact with ILE 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ILE* 3.0 21.3 + - + +
95E ARG* 3.4 15.5 - - - +
97E ASP* 1.3 80.3 - - - +
99E LEU* 1.3 54.2 + - - +
101E ASN* 3.0 3.3 + - - +
102E GLN* 2.7 37.2 + - + +
140E PHE* 3.6 26.9 - - + -
55F ASP* 5.7 2.7 - - - +
56F PHE* 3.8 19.7 - - + -
68F LYS 4.9 3.1 - - - +
69F ILE* 3.6 18.8 - - + -
70F THR* 3.5 42.0 - - - +
71F GLN* 4.6 2.8 - - + +
74F ALA* 4.1 5.6 - - - +
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ARG 3.1 13.6 + - - +
96E VAL 4.0 2.9 - - - +
98E ILE* 1.3 78.8 - - - +
100E GLU* 1.3 59.5 - - - +
102E GLN* 4.3 3.1 - - + -
103E ALA* 2.6 39.4 + - + +
137E PHE* 4.6 12.1 - - + -
140E PHE* 3.7 21.5 - - + -
147E PHE* 3.2 54.7 - - + -
148E VAL* 5.2 0.2 - - + -
155E VAL* 4.1 29.4 - - + +
158E LEU* 5.4 0.2 - - - -
159E ALA* 5.2 4.9 - - + -
56F PHE* 4.4 16.4 - - + -
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Residues in contact with GLU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASN* 3.0 42.9 + - - +
77E CYS* 3.8 18.7 - - - -
96E VAL* 3.1 10.5 + - - +
97E ASP* 3.0 20.9 + - - +
99E LEU* 1.3 78.3 - - - +
101E ASN* 1.3 64.0 + - - +
104E MET* 3.3 22.5 + - - +
154E PHE* 3.6 24.7 - - + -
155E VAL* 4.1 6.2 - - + +
158E LEU* 4.0 15.1 - - + +
100F GLU* 4.0 14.5 - - - +
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Residues in contact with ASN 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASN* 5.1 3.9 + - - +
97E ASP* 2.8 33.3 + - - +
98E ILE 3.7 3.1 - - - +
100E GLU* 1.3 92.5 + - - +
102E GLN* 1.3 59.8 + - - +
104E MET* 3.6 3.4 + - - +
105E ASP 2.8 22.9 + - - -
71F GLN* 3.0 38.2 + - + +
72F SER* 5.5 0.2 + - - -
73F ASN* 2.8 45.9 + - - +
74F ALA 4.2 7.0 - - - +
100F GLU* 4.5 2.1 + - - +
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Residues in contact with GLN 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ILE* 2.7 28.3 + - + +
99E LEU* 3.9 4.0 - - - +
101E ASN* 1.3 71.6 - - - +
103E ALA* 1.3 66.3 - - - +
105E ASP* 3.0 29.6 + - - +
106E VAL* 2.9 37.3 + - + +
137E PHE* 4.8 5.6 - - + -
56F PHE* 3.6 52.7 - - + +
58F ASN* 5.0 9.6 - - - +
70F THR* 4.3 4.5 + - - -
71F GLN* 3.9 17.4 - - + +
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Residues in contact with ALA 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E LEU* 2.6 28.1 + - + +
100E GLU 4.8 1.1 - - - +
102E GLN* 1.3 73.1 - - - +
104E MET* 1.3 59.1 + - - +
106E VAL* 3.1 22.9 - - - +
107E SER* 3.1 7.3 + - - -
137E PHE* 4.7 10.9 - - + -
158E LEU* 4.5 19.3 - - + -
159E ALA* 4.6 8.1 - - - +
162E VAL* 3.3 26.6 - - + +
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Residues in contact with MET 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 4.8 19.5 - - + -
72E SER* 4.5 20.2 - - - +
73E ASN* 4.1 23.8 - - - +
100E GLU 3.3 20.2 + - - +
101E ASN* 3.6 4.5 + - - +
102E GLN 3.2 0.4 - - - -
103E ALA* 1.3 74.9 - - - +
105E ASP* 1.3 68.0 + - - +
107E SER* 2.7 25.6 + - - +
108E ASN* 2.8 46.9 + - - +
158E LEU* 5.6 10.0 - - + +
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Residues in contact with ASP 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ASN 2.8 17.6 + - - +
102E GLN* 3.0 29.0 + - - +
104E MET* 1.3 75.4 - - - +
106E VAL* 1.3 58.2 + - - +
108E ASN* 3.2 9.4 + - - +
109E GLN* 2.9 42.9 + - - +
112E ARG* 4.8 4.8 + - - -
58F ASN* 6.2 1.8 - - - -
71F GLN* 3.6 16.4 + - - +
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Residues in contact with VAL 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E GLN* 2.9 32.9 + - + +
103E ALA* 3.1 20.0 - - - +
105E ASP* 1.3 74.3 - - - +
107E SER* 1.3 59.3 + - - +
108E ASN 3.3 0.2 - - - -
109E GLN* 3.2 24.5 - - - +
110E LEU* 3.0 27.0 + - - +
126E TYR* 4.3 10.2 + - - +
133E MET* 4.5 19.3 - - + -
137E PHE* 4.9 8.1 - - + -
162E VAL* 3.5 26.0 - - + -
166E HIS* 4.7 4.5 + - + -
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Residues in contact with SER 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 6.0 1.7 - - - +
103E ALA 3.1 14.3 + - - -
104E MET* 2.7 23.9 + - - +
106E VAL* 1.3 76.9 - - - +
108E ASN* 1.3 56.3 + - - +
110E LEU* 3.4 6.8 + - - +
111E ALA* 3.0 28.8 + - - +
161E ASP* 4.9 4.5 + - - -
162E VAL* 4.6 9.9 - - - +
165E LEU* 4.6 16.8 - - - +
166E HIS* 6.0 1.3 - - - -
208E TYR* 5.1 0.9 + - - -
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Residues in contact with ASN 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 6.0 1.6 - - - +
104E MET* 2.8 54.8 + - - +
105E ASP* 3.5 8.1 + - - +
107E SER* 1.3 74.5 - - - +
109E GLN* 1.3 61.2 + - - +
111E ALA* 4.0 6.7 - - - +
112E ARG* 2.8 45.7 + - - +
108F ASN* 5.9 2.0 - - - -
112F ARG* 5.3 11.2 - - - +
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Residues in contact with GLN 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ASP* 2.9 29.3 + - - +
106E VAL* 3.2 20.6 - - - +
108E ASN* 1.3 79.8 - - - +
110E LEU* 1.3 57.1 + - - +
112E ARG* 4.0 25.3 + - - +
113E VAL* 3.1 25.6 + - - +
126E TYR* 3.5 29.2 + - + -
133E MET* 3.9 13.7 - - - +
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Residues in contact with LEU 110 (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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106E VAL 3.0 15.0 + - - +
107E SER* 3.8 7.2 - - - +
109E GLN* 1.3 75.9 - - - +
111E ALA* 1.3 65.3 + - - +
113E VAL* 2.9 20.7 + - + +
114E CYS* 3.0 18.6 + - - -
126E TYR* 3.8 17.7 - - + -
165E LEU* 4.6 20.0 - - + -
166E HIS* 3.7 31.4 - - + +
169E PHE* 3.5 37.2 - - + -
208E TYR* 3.4 19.5 - - - +
214E TRP* 5.3 4.3 - - + -
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Residues in contact with ALA 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E SER 3.0 18.3 + - - +
108E ASN* 4.0 7.6 - - - +
110E LEU* 1.3 76.2 - - - +
112E ARG* 1.3 62.9 + - - +
114E CYS* 2.9 4.0 + - - +
115E TYR* 2.9 45.5 + - + +
208E TYR* 3.8 28.0 + - + -
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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
----------------------------------------------------------
105E ASP* 4.8 4.6 + - - -
108E ASN* 2.8 30.1 + - - +
109E GLN* 4.0 37.9 + - - +
111E ALA* 1.3 75.4 - - - +
113E VAL* 1.3 59.6 + - + +
115E TYR* 3.5 11.2 + - - +
116E SER* 2.9 28.4 + - - +
122E LEU* 5.6 0.2 - - - -
112F ARG* 4.5 28.6 - - - +
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Residues in contact with VAL 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E GLN* 3.1 21.1 - - + +
110E LEU* 2.9 16.0 + - + +
112E ARG* 1.3 73.2 - - + +
114E CYS* 1.3 61.8 + - - +
115E TYR 3.0 3.6 - - - -
116E SER* 2.8 34.5 + - - +
119E PHE* 4.7 12.7 - - + -
122E LEU* 3.6 44.4 - - + +
123E LYS* 4.3 5.8 - - - +
126E TYR* 4.8 17.3 - - + -
169E PHE* 5.7 2.9 - - + -
213E VAL* 4.6 0.7 - - - +
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Residues in contact with CYS 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E LEU* 3.0 21.0 + - - +
111E ALA 2.9 8.6 + - - +
113E VAL* 1.3 78.5 - - - +
115E TYR* 1.3 59.0 + - - +
116E SER 3.4 0.2 - - - -
119E PHE* 4.5 8.5 - - - -
169E PHE* 4.7 2.5 - - - -
208E TYR* 4.1 22.0 - - + -
212E ALA* 3.5 3.3 - - - +
213E VAL* 3.0 37.3 + - - +
214E TRP* 3.3 51.4 - - + +
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Residues in contact with TYR 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E ALA* 2.9 36.2 + - + +
112E ARG* 3.8 9.2 - - - +
113E VAL 3.0 0.2 - - - -
114E CYS* 1.3 78.2 - - - +
116E SER* 1.3 62.9 + - - +
117E PRO* 3.6 7.4 - - - +
208E TYR* 3.9 19.3 - + + +
209E THR* 4.9 10.7 + - - +
211E VAL* 5.3 4.5 - - + -
212E ALA* 3.5 33.7 - - + +
213E VAL* 4.9 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) + - + + + + + -
------------------------------------------------------------
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