Contacts of the helix formed by residues 87 - 116 (chain E) in PDB entry 1NF6
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 ALA 87 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E MET* 5.7 1.8 - - - -
85E GLY 3.5 2.7 + - - -
86E GLN* 1.3 73.8 - - - +
88E VAL* 1.3 63.1 + - - +
89E PRO* 3.5 11.7 - - + -
90E VAL* 3.3 16.9 + - + +
91E ILE* 2.8 31.4 + - - +
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Residues in contact with VAL 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 4.4 7.0 - - + -
40E MET* 3.7 35.1 - - + +
42E TYR* 4.8 9.0 - - + -
45E LEU* 4.9 0.7 - - + -
87E ALA* 1.3 71.1 - - - +
89E PRO* 1.3 72.5 - - + +
91E ILE* 3.1 25.4 + - + +
92E TYR* 3.3 19.1 - - + -
146E ILE* 3.3 31.6 - - + -
154E LEU* 4.7 17.7 - - + -
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Residues in contact with PRO 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ALA* 3.7 9.9 - - + -
88E VAL* 1.3 97.6 - - + +
90E VAL* 1.3 60.4 + - + +
92E TYR* 3.6 3.5 + - + +
93E GLU* 3.1 27.9 + - - +
143E GLY* 5.8 2.0 - - - -
146E ILE* 4.1 26.5 - - + -
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Residues in contact with VAL 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E GLN* 3.9 20.2 - - + +
87E ALA* 3.3 24.4 + - + +
88E VAL 3.2 0.8 - - - -
89E PRO* 1.3 77.8 - - + +
91E ILE* 1.3 56.3 + - - +
93E GLU* 3.8 17.0 - - - +
94E SER* 2.3 48.4 + - - +
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Residues in contact with ILE 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E GLN* 3.8 27.1 - - + +
36E SER* 5.3 1.8 - - - -
37E LEU* 3.9 26.5 - - + -
40E MET* 4.4 6.5 - - + -
49E MET* 3.8 28.9 - - + -
86E GLN* 3.9 19.5 - - + +
87E ALA 2.8 27.6 + - - +
88E VAL* 3.2 21.3 - - + +
90E VAL* 1.3 77.0 - - - +
92E TYR* 1.3 70.4 + - + +
94E SER* 4.0 0.8 + - - -
95E ASP* 3.0 35.5 + - - +
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Residues in contact with TYR 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 3.5 12.9 - - + +
45E LEU* 3.2 36.7 + - + +
49E MET* 4.0 10.4 - - + +
88E VAL* 3.3 37.0 + - + +
89E PRO 4.3 2.0 - - - +
91E ILE* 1.3 87.0 - - + +
93E GLU* 1.3 63.9 + - - +
95E ASP* 4.0 2.7 - - - -
96E ALA* 3.4 23.4 + - - +
138E TYR* 4.4 5.0 + + - -
139E TYR* 3.5 37.2 - + - +
142E ILE* 3.9 34.3 - - + -
143E GLY* 4.0 24.7 - - - +
146E ILE* 3.7 12.8 - - + -
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Residues in contact with GLU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E PRO 3.1 18.3 + - - +
90E VAL* 3.8 18.5 - - + +
91E ILE 3.3 0.2 - - - -
92E TYR* 1.3 77.6 - - - +
94E SER* 1.3 68.5 + - - +
96E ALA* 3.6 2.8 + - - +
97E ASP* 3.2 38.3 + - - +
143E GLY* 5.8 0.2 - - - -
90H VAL* 5.6 5.6 - - - +
93H GLU* 5.5 2.9 - - - +
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Residues in contact with SER 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E GLN* 6.4 0.7 - - - -
86E GLN* 3.2 24.6 + - - -
90E VAL* 2.3 34.3 + - - +
91E ILE 4.2 1.8 - - - -
93E GLU* 1.3 76.3 - - - +
95E ASP* 1.3 60.8 + - - +
97E ASP* 3.2 8.7 + - - +
98E GLN* 2.7 39.4 + - - +
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Residues in contact with ASP 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E GLN* 4.4 3.8 - - - +
30E TYR* 3.4 20.0 + - + -
33E GLN* 2.5 41.4 + - - +
49E MET* 3.6 4.7 - - - +
91E ILE 3.0 17.9 + - - +
92E TYR 4.4 0.2 - - - +
93E GLU 3.4 0.2 - - - -
94E SER* 1.3 76.7 - - - +
96E ALA* 1.3 62.0 + - - +
98E GLN* 3.3 3.9 + - - +
99E GLU* 2.7 34.8 + - - +
139E TYR* 3.5 41.8 - - + -
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Residues in contact with ALA 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E TYR 3.4 17.9 + - - +
93E GLU* 3.9 4.5 - - - +
94E SER 3.3 0.2 - - - -
95E ASP* 1.3 78.7 - - - +
97E ASP* 1.3 63.8 + - - +
99E GLU* 3.2 0.8 + - - -
100E ASP* 2.9 22.2 + - - +
136E LEU* 3.2 27.9 - - + +
139E TYR* 3.9 14.0 - - + +
140E GLU* 4.3 15.0 - - + +
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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 GLU* 3.2 27.0 + - - +
94E SER* 3.2 11.5 + - - +
96E ALA* 1.3 81.6 - - - +
98E GLN* 1.3 56.4 + - - +
100E ASP* 3.2 8.6 + - - +
101E ALA* 2.8 29.6 + - - +
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Residues in contact with GLN 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E MET* 4.7 3.6 + - + +
25E HIS* 2.8 41.7 + - - -
26E ALA* 3.8 21.0 - - + +
29E GLN* 4.0 14.4 - - - +
30E TYR* 4.1 15.8 + - - +
94E SER* 2.7 21.4 + - - +
95E ASP* 3.7 6.4 - - - +
97E ASP* 1.3 70.2 - - - +
99E GLU* 1.3 57.7 + - - +
101E ALA* 3.4 7.7 + - + +
102E THR* 2.6 43.8 + - - +
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Residues in contact with GLU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ALA* 5.0 2.1 - - - +
30E TYR* 2.4 26.4 + - - +
56E GLU* 3.1 7.4 - - - +
95E ASP 2.7 24.0 + - - +
96E ALA 3.2 3.6 + - - +
98E GLN* 1.3 75.8 - - - +
100E ASP* 1.3 59.4 + - - +
102E THR* 3.7 5.4 + - - -
103E ILE* 3.2 32.1 + - - +
132E GLU* 3.1 18.0 - - - +
135E HIS* 3.3 15.1 - - + +
136E LEU* 4.0 19.5 - - + +
139E TYR* 3.8 16.2 - - + -
200E FE 2.2 31.2 - - - -
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Residues in contact with ASP 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 2.9 43.0 + - - -
9D LYS* 5.2 2.4 + - - -
96E ALA 2.9 17.6 + - - +
97E ASP* 3.5 7.1 - - - +
99E GLU* 1.3 76.7 - - - +
101E ALA* 1.3 66.5 + - - +
102E THR 3.2 0.2 - - - -
103E ILE* 3.4 10.2 + - - +
104E GLU* 3.1 23.4 + - - +
136E LEU* 4.2 16.7 - - + +
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E MET* 4.4 5.7 - - + +
97E ASP 2.8 17.4 + - - +
98E GLN* 3.8 9.0 - - + +
100E ASP* 1.3 78.3 + - - +
102E THR* 1.3 57.8 + - - +
104E GLU* 3.5 7.6 + - - +
105E ALA* 3.0 29.1 + - - +
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Residues in contact with THR 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E MET* 3.8 20.6 - - + +
23E GLU* 5.1 1.1 - - - +
98E GLN* 2.6 30.3 + - - +
99E GLU* 3.7 6.8 + - - -
100E ASP 3.2 0.2 - - - -
101E ALA* 1.3 75.1 - - - +
103E ILE* 1.3 60.2 + - - +
105E ALA 3.3 0.7 + - - -
106E TYR* 2.8 69.7 + - + +
132E GLU* 3.0 29.2 + - - +
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Residues in contact with ILE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ILE* 6.3 0.2 - - + -
120D VAL* 5.5 3.6 - - + -
99E GLU 3.2 17.4 + - - +
100E ASP* 3.8 7.0 - - - +
101E ALA 3.4 0.2 - - - -
102E THR* 1.3 73.4 - - - +
104E GLU* 1.3 76.3 + - - +
106E TYR* 3.3 6.4 + - - +
107E SER* 2.8 37.2 + - - +
129E ILE* 4.2 19.7 - - + +
132E GLU* 3.7 20.9 - - + +
133E GLN* 4.0 28.3 - - + +
136E LEU* 4.0 24.7 - - + -
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Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 3.2 40.3 + - - +
8D ARG* 2.7 38.7 + - - -
117D GLY 4.9 1.9 - - - +
100E ASP* 3.1 21.7 + - - +
101E ALA* 3.7 8.1 - - - +
103E ILE* 1.3 85.0 - - - +
105E ALA* 1.3 62.6 + - - +
107E SER* 3.4 6.5 + - - -
108E GLN* 3.2 26.5 + - - +
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Residues in contact with ALA 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E MET* 4.0 26.5 - - + -
101E ALA 3.0 17.7 + - - +
102E THR 3.5 4.5 - - - +
104E GLU* 1.3 77.4 - - - +
106E TYR* 1.3 55.5 + - - +
108E GLN* 2.8 29.6 + - - +
109E PHE* 2.9 27.9 + - + -
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Residues in contact with TYR 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ALA* 3.2 25.4 + - + -
22E MET* 3.8 17.2 - - - +
23E GLU* 2.9 36.7 + - - +
63E PHE* 3.8 4.2 - + - -
102E THR* 2.8 46.1 + - + +
103E ILE* 3.8 1.1 - - - +
105E ALA* 1.3 74.0 - - + +
107E SER* 1.3 53.1 + - - +
109E PHE* 3.3 18.7 - + - +
110E LEU* 2.7 34.7 + - - +
125E PHE* 4.0 13.1 - + + -
128E ILE* 3.6 32.5 - - + -
129E ILE* 3.5 23.2 - - + +
132E GLU* 4.2 9.0 - - + -
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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
----------------------------------------------------------
8D ARG* 5.8 1.1 - - - -
117D GLY* 4.4 17.2 + - - -
119D ILE* 3.6 27.2 + - - +
103E ILE* 2.8 31.7 + - - +
104E GLU* 3.6 8.3 + - - -
106E TYR* 1.3 73.3 - - - +
108E GLN* 1.3 69.7 + - - +
110E LEU* 3.5 5.7 + - - +
111E LYS* 3.0 20.6 + - - +
129E ILE* 3.9 9.8 - - - +
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Residues in contact with GLN 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E GLU* 3.2 14.4 + - - +
105E ALA* 2.8 10.9 + - - +
107E SER* 1.3 80.6 - - - +
109E PHE* 1.3 65.0 - - + +
111E LYS* 2.8 45.4 + - + +
112E VAL* 3.0 11.9 + - + +
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Residues in contact with PHE 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 3.8 23.3 - - + +
18E LYS* 3.7 32.5 - - + -
19E ALA* 3.6 28.9 - - + -
22E MET* 4.2 8.7 - - - -
105E ALA* 2.9 24.3 + - + -
106E TYR* 3.3 22.9 - + - +
108E GLN* 1.3 77.5 - - + +
110E LEU* 1.3 66.0 + - - +
112E VAL* 2.9 16.7 + - + +
113E CYS* 3.0 18.1 + - - -
125E PHE* 3.6 32.5 - + + -
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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
----------------------------------------------------------
119D ILE* 3.7 33.9 - - + -
106E TYR 2.7 17.8 + - - +
107E SER 3.5 6.1 - - - +
109E PHE* 1.3 71.7 - - - +
111E LYS* 1.3 64.0 + - - +
113E CYS* 3.0 18.5 + - - +
114E LYS* 3.0 48.8 + - + +
122E ALA* 3.7 20.9 - - + +
125E PHE* 4.1 10.6 - - + -
126E GLU* 3.3 28.9 - - + +
129E ILE* 3.9 9.6 - - + -
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Residues in contact with LYS 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 13.2 + - - +
108E GLN* 2.8 38.0 + - - +
110E LEU* 1.3 77.2 - - - +
112E VAL* 1.3 62.6 + - + +
114E LYS* 3.3 9.6 + - - +
115E GLU* 3.2 47.6 + - + +
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Residues in contact with VAL 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LYS* 4.2 15.9 - - + +
12E VAL* 5.0 0.7 - - + -
15E VAL* 4.0 31.2 - - + -
108E GLN* 3.0 16.0 + - + +
109E PHE* 2.9 9.6 + - + +
111E LYS* 1.3 77.3 - - + +
113E CYS* 1.3 63.5 + - - +
115E GLU* 3.4 15.5 + - - +
116E GLN* 3.1 43.8 + - + +
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Residues in contact with CYS 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E VAL* 4.2 19.7 - - - -
15E VAL* 4.6 3.4 - - - -
109E PHE 3.0 16.4 + - - -
110E LEU 3.0 8.8 + - - +
112E VAL* 1.3 75.8 - - - +
114E LYS* 1.3 64.1 + - - +
116E GLN* 3.0 10.9 + - - +
117E GLY 3.0 9.0 + - - -
118E ASP* 3.0 26.1 + - + +
121E THR* 3.6 31.4 - - - -
122E ALA* 3.7 10.1 - - + -
125E PHE* 3.9 18.2 - - - -
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Residues in contact with LYS 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LYS* 5.5 9.1 - - - +
119D ILE* 5.4 5.7 - - - +
110E LEU* 3.0 41.5 + - + +
111E LYS* 3.3 8.7 + - - +
113E CYS* 1.3 76.4 - - - +
115E GLU* 1.3 58.7 + - + +
117E GLY* 2.7 21.7 + - - -
118E ASP 4.8 2.7 - - - +
119E ILE* 5.7 8.2 - - + +
122E ALA* 4.3 11.0 - - + -
126E GLU* 3.6 15.3 + - - -
1404E SO4 3.4 46.4 + - - +
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Residues in contact with GLU 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E LYS* 3.2 37.7 + - + +
112E VAL* 3.8 20.5 - - - +
113E CYS 3.3 0.2 - - - -
114E LYS* 1.3 78.8 - - + +
116E GLN* 1.3 72.0 + - - +
117E GLY 3.1 2.8 + - - -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E GLY 5.4 1.9 + - - -
8E ARG* 2.9 66.3 + - + +
11E LYS* 3.3 41.6 + - + +
12E VAL* 3.9 18.6 - - + -
112E VAL* 3.1 21.7 + - + +
113E CYS 3.0 5.1 + - - +
115E GLU* 1.3 90.6 + - - +
117E GLY* 1.3 64.2 + - - +
118E ASP* 3.2 3.4 + - + +
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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