Contacts of the helix formed by residues 87 - 116 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LYS* 5.0 19.1 - - + +
40H MET* 5.5 3.4 - - - -
85H GLY 3.5 3.2 + - - -
86H GLN* 1.3 75.1 - - - +
88H VAL* 1.3 66.2 + - - +
89H PRO* 3.4 11.7 - - + -
90H VAL* 3.0 16.5 + - + +
91H ILE* 2.9 20.0 + - - +
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Residues in contact with VAL 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H LEU* 4.1 13.5 - - + -
40H MET* 3.8 30.2 - - + +
42H TYR* 4.4 12.3 - - + -
45H LEU* 4.7 2.0 - - + -
87H ALA* 1.3 70.4 - - - +
89H PRO* 1.3 70.3 - - + +
91H ILE* 3.1 18.0 + - - +
92H TYR* 3.1 23.2 - - + -
146H ILE* 3.3 31.0 - - + -
154H LEU* 4.4 18.2 - - + -
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Residues in contact with PRO 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H ALA* 3.5 12.6 - - + -
88H VAL* 1.3 96.3 - - + +
90H VAL* 1.3 62.3 + - + +
92H TYR* 3.7 3.3 + - + +
93H GLU* 3.3 23.1 + - - +
143H GLY* 5.7 2.7 - - - -
146H ILE* 4.1 28.0 - - + -
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Residues in contact with VAL 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E GLU* 5.6 5.8 - - - +
86H GLN* 4.0 24.2 - - + +
87H ALA* 3.0 24.1 + - + +
89H PRO* 1.3 79.2 - - + +
91H ILE* 1.3 64.0 + - - +
93H GLU* 4.5 10.8 - - - +
94H SER* 2.8 32.8 + - - +
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Residues in contact with ILE 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H GLN* 3.6 32.5 - - + +
36H SER* 5.0 2.0 - - - -
37H LEU* 4.0 22.2 - - + -
40H MET* 5.0 5.2 - - + -
49H MET* 3.6 30.7 - - + -
86H GLN* 3.9 26.2 - - + +
87H ALA 2.9 16.7 + - - +
88H VAL* 3.5 17.7 - - + +
90H VAL* 1.3 77.1 - - - +
92H TYR* 1.3 67.5 + - + +
94H SER* 3.2 5.4 + - - -
95H ASP* 2.9 34.2 + - - +
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Residues in contact with TYR 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H LEU* 3.3 26.3 - - + +
45H LEU* 3.3 24.0 + - + +
49H MET* 4.0 10.9 - - + +
88H VAL* 3.1 38.2 + - + +
89H PRO 3.7 2.2 + - - +
91H ILE* 1.3 87.4 - - + +
93H GLU* 1.3 66.7 + - - +
95H ASP* 4.5 1.8 - - - -
96H ALA* 3.1 26.0 + - - +
138H TYR* 4.5 4.7 + + - -
139H TYR* 3.5 34.3 - + - +
142H ILE* 3.8 33.0 - - + -
143H GLY* 3.7 25.4 - - - +
146H ILE* 3.5 12.1 - - + -
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Residues in contact with GLU 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E GLU* 5.5 2.9 - - - +
89H PRO 3.3 19.4 + - - +
90H VAL* 4.1 11.3 - - - +
91H ILE 3.3 0.2 - - - -
92H TYR* 1.3 79.5 - - - +
94H SER* 1.3 63.4 + - - +
96H ALA* 3.9 4.0 - - - +
97H ASP* 3.2 34.6 + - - +
143H GLY* 5.5 0.8 - - - -
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Residues in contact with SER 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H GLN* 3.9 0.2 + - - -
86H GLN* 3.2 23.6 + - - -
90H VAL* 2.8 26.3 + - - -
91H ILE* 3.2 5.2 + - - -
93H GLU* 1.3 78.4 - - - +
95H ASP* 1.3 68.0 + - - +
97H ASP* 3.1 10.5 + - - +
98H GLN* 2.9 29.1 + - - +
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Residues in contact with ASP 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H GLN* 4.6 2.6 - - - +
30H TYR* 3.3 18.4 - - + -
33H GLN* 2.5 40.9 + - - +
49H MET* 3.2 19.4 - - - +
91H ILE 2.9 18.3 + - - +
92H TYR 4.2 0.7 - - - +
94H SER* 1.3 77.5 + - - +
96H ALA* 1.3 56.8 + - - +
98H GLN* 3.2 7.7 + - - +
99H GLU* 3.0 34.8 + - - +
139H TYR* 3.5 29.5 - - + -
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Residues in contact with ALA 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H TYR 3.1 19.1 + - - +
93H GLU* 3.9 5.2 - - - +
95H ASP* 1.3 78.7 - - - +
97H ASP* 1.3 64.7 + - - +
99H GLU 3.4 0.5 + - - -
100H ASP* 3.1 21.1 + - - +
136H LEU* 3.3 28.7 - - + +
139H TYR* 4.0 15.8 - - + +
140H GLU* 4.2 14.4 - - + +
----------------------------------------------------------
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Residues in contact with ASP 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H GLU* 3.2 25.4 + - - +
94H SER* 3.1 12.1 + - - +
96H ALA* 1.3 78.5 - - - +
98H GLN* 1.3 57.3 + - - +
100H ASP* 3.5 5.6 + - - +
101H ALA* 2.8 31.6 + - - +
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Residues in contact with GLN 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H MET 4.4 4.0 + - - -
25H HIS* 3.4 35.6 + - - -
26H ALA* 3.5 28.9 - - - +
29H GLN* 4.1 12.0 - - - +
30H TYR* 3.7 16.3 + - - +
94H SER 2.9 15.6 + - - +
95H ASP* 3.5 7.8 - - - +
96H ALA 3.2 0.2 - - - -
97H ASP* 1.3 76.2 - - - +
99H GLU* 1.3 57.0 + - - +
101H ALA* 3.7 5.7 - - + +
102H THR* 2.3 45.7 + - - +
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Residues in contact with GLU 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA* 5.1 1.0 - - - +
30H TYR* 2.4 25.1 + - - +
56H GLU* 3.3 6.3 - - - +
95H ASP 3.0 16.7 + - - +
96H ALA 4.0 1.6 - - - +
98H GLN* 1.3 76.3 + - - +
100H ASP* 1.3 56.8 + - - +
102H THR* 3.5 4.4 + - - -
103H ILE* 2.7 41.4 + - - +
132H GLU* 3.1 18.2 - - - +
135H HIS* 3.1 15.7 - - + +
136H LEU* 3.9 21.1 - - + +
139H TYR* 3.8 16.8 - - + -
200H FE 2.2 31.3 - - - -
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Residues in contact with ASP 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H ALA 3.1 18.0 + - - +
97H ASP* 3.7 5.6 - - - +
99H GLU* 1.3 75.5 - - - +
101H ALA* 1.3 67.1 + - - +
103H ILE* 3.2 7.9 + - - +
104H GLU* 2.8 35.6 + - - +
136H LEU* 4.0 23.0 - - + +
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Residues in contact with ALA 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H MET* 4.6 3.3 - - + +
97H ASP 2.8 22.3 + - - +
98H GLN* 3.7 7.9 - - + +
100H ASP* 1.3 74.4 + - - +
102H THR* 1.3 57.3 + - - +
104H GLU* 3.3 8.6 + - - +
105H ALA* 3.0 28.3 + - - +
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Residues in contact with THR 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H MET* 3.9 21.7 - - + +
23H GLU* 5.5 0.7 - - - -
98H GLN* 2.3 36.7 + - - +
99H GLU* 3.5 6.3 + - - -
101H ALA* 1.3 76.2 - - - +
103H ILE* 1.3 61.0 + - - +
105H ALA 3.3 0.7 + - - -
106H TYR* 2.8 67.2 + - + +
132H GLU* 3.2 24.5 + - - +
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Residues in contact with ILE 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H GLU 2.7 24.1 + - - +
100H ASP* 3.7 8.3 - - - +
102H THR* 1.3 72.9 - - - +
104H GLU* 1.3 65.9 + - - +
106H TYR* 4.1 5.0 - - - +
107H SER* 2.7 40.2 + - - +
129H ILE* 4.2 19.9 - - + +
132H GLU* 3.6 21.5 - - + +
133H GLN* 3.9 33.2 - - + +
136H LEU* 3.8 26.9 - - + -
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Residues in contact with GLU 104 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H ASP* 2.8 26.7 + - - +
101H ALA* 3.4 13.0 - - - +
102H THR 3.2 0.2 - - - -
103H ILE* 1.3 84.7 - - + +
105H ALA* 1.3 60.7 + - - +
107H SER* 3.4 16.4 + - - -
108H GLN* 3.5 8.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA 105 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H MET* 3.9 26.7 - - + -
101H ALA 3.0 16.6 + - - +
102H THR 3.3 3.3 + - - +
104H GLU* 1.3 72.5 - - - +
106H TYR* 1.3 62.4 + - + +
107H SER 3.0 1.8 - - - -
108H GLN* 2.8 24.7 + - - +
109H PHE* 3.0 26.0 + - + -
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Residues in contact with TYR 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ALA* 3.4 35.2 + - + -
22H MET* 4.0 12.2 - - - +
23H GLU* 2.4 37.9 + - - +
63H PHE* 4.1 3.1 - + - -
102H THR* 2.8 47.1 + - + +
105H ALA* 1.3 74.3 - - + +
107H SER* 1.3 56.6 + - - +
109H PHE* 3.2 19.4 + + - +
110H LEU* 2.8 31.0 + - - +
125H PHE* 3.8 16.2 - + + -
128H ILE* 3.8 24.0 - - + -
129H ILE* 3.5 26.7 - - + +
132H GLU* 4.3 7.6 - - + -
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Residues in contact with SER 107 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H ILE* 2.7 28.4 + - - +
104H GLU* 3.4 12.1 + - - -
105H ALA 3.0 0.2 - - - -
106H TYR* 1.3 79.0 - - - +
108H GLN* 1.3 60.2 + - - +
110H LEU* 3.6 7.4 - - - +
111H LYS* 3.3 18.4 + - - +
129H ILE* 3.9 16.2 - - - +
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Residues in contact with GLN 108 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H GLU 3.5 7.4 + - - +
105H ALA* 2.8 12.1 + - - +
107H SER* 1.3 77.2 - - - +
109H PHE* 1.3 71.1 + - + +
111H LYS* 3.1 21.8 + - - +
112H VAL* 3.1 15.3 + - - +
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Residues in contact with PHE 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H VAL* 3.8 27.2 - - + +
18H LYS* 3.8 35.7 - - + -
19H ALA* 3.8 20.4 - - + -
22H MET* 4.2 10.1 - - - -
105H ALA* 3.0 22.9 + - + -
106H TYR* 3.5 25.1 - + - +
108H GLN* 1.3 81.3 - - + +
110H LEU* 1.3 55.5 + - - +
112H VAL* 2.8 26.9 + - + +
113H CYS* 3.1 17.9 + - - -
125H PHE* 3.6 32.5 - + + -
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H TYR 2.8 14.9 + - - +
107H SER* 3.6 8.7 - - - +
108H GLN 3.2 0.2 - - - -
109H PHE* 1.3 76.4 - - - +
111H LYS* 1.3 62.9 + - - +
113H CYS* 3.4 9.7 + - - +
114H LYS* 3.1 62.6 + - + +
122H ALA* 4.0 13.6 - - + +
125H PHE* 4.1 7.8 - - + -
126H GLU* 3.3 37.5 - - + +
129H ILE* 3.7 23.1 - - + -
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Residues in contact with LYS 111 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H SER 3.3 9.6 + - - +
108H GLN* 3.1 16.5 + - - +
110H LEU* 1.3 77.2 - - - +
112H VAL* 1.3 61.6 + - + +
114H LYS* 3.9 9.4 - - + +
115H GLU* 2.9 59.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL 112 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H LYS* 3.9 26.0 - - + +
12H VAL* 5.0 0.7 - - - +
15H VAL* 4.1 22.4 - - + -
108H GLN 3.1 13.6 + - - +
109H PHE* 2.8 12.1 + - + +
111H LYS* 1.3 79.5 - - + +
113H CYS* 1.3 57.0 + - - +
115H GLU* 3.0 15.9 + - - +
116H GLN* 2.7 44.0 + - + +
----------------------------------------------------------
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Residues in contact with CYS 113 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 4.1 11.9 - - + -
15H VAL* 4.3 4.7 - - - -
109H PHE 3.1 20.4 + - - -
110H LEU* 4.0 3.8 - - - +
112H VAL* 1.3 75.0 - - - +
114H LYS* 1.3 55.5 + - - +
116H GLN* 3.1 4.8 + - - +
117H GLY 2.9 8.5 + - - -
118H ASP* 2.5 56.0 + - + +
121H THR* 3.5 28.7 - - - -
122H ALA* 3.8 8.5 - - + +
125H PHE* 3.9 17.0 - - - -
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Residues in contact with LYS 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H LEU* 3.1 46.1 + - + +
111H LYS* 3.9 8.5 - - + +
113H CYS* 1.3 75.6 - - - +
115H GLU* 1.3 59.5 + - + +
117H GLY* 3.0 18.3 + - - +
118H ASP 4.5 2.7 - - - +
119H ILE* 5.4 8.9 - - + +
122H ALA* 4.2 12.3 - - + +
126H GLU* 4.0 14.8 + - - -
114I LYS* 4.0 17.0 - - - +
126I GLU* 6.0 0.9 - - - -
1804I SO4 2.7 34.5 + - - +
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Residues in contact with GLU 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H LYS* 2.9 59.2 + - + +
112H VAL* 3.4 17.8 - - - +
114H LYS* 1.3 77.5 - - + +
116H GLN* 1.3 69.5 + - - +
117H GLY 3.2 2.6 + - - -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H GLY* 5.0 5.9 + - - -
7H ASP 4.6 0.3 - - - -
8H ARG* 2.9 54.6 + - + +
11H LYS* 3.1 48.6 - - + +
12H VAL* 3.9 17.3 - - + -
112H VAL* 2.7 32.1 + - + +
113H CYS 3.1 3.5 + - - +
115H GLU* 1.3 82.5 + - - +
117H GLY* 1.3 62.1 + - - +
118H ASP* 3.2 2.9 + - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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