Contacts of the helix formed by residues 87 - 116 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F MET* 5.8 0.9 - - - -
85F GLY 3.5 3.8 + - - -
86F GLN* 1.3 75.5 - - - +
88F VAL* 1.3 61.2 + - - +
89F PRO* 3.4 13.5 - - + -
90F VAL* 3.1 17.5 + - + +
91F ILE* 2.8 25.9 + - - +
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Residues in contact with VAL 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 4.2 10.3 - - + -
40F MET* 3.7 35.4 - - + +
42F TYR* 4.5 11.2 - - + -
45F LEU* 4.8 0.9 - - + -
86F GLN 3.8 0.8 + - - -
87F ALA* 1.3 70.7 - - - +
89F PRO* 1.3 68.6 - - + +
91F ILE* 2.8 29.3 + - - +
92F TYR* 3.3 19.6 + - + -
146F ILE* 3.4 27.1 - - + -
154F LEU* 4.4 20.2 - - + -
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Residues in contact with PRO 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F ALA* 3.5 13.2 - - + -
88F VAL* 1.3 97.0 - - + +
90F VAL* 1.3 59.6 + - + +
92F TYR* 3.5 2.8 + - + +
93F GLU* 3.1 29.6 + - - +
143F GLY* 6.0 0.6 - - - -
146F ILE* 4.3 27.6 - - + -
154F LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F GLN* 3.9 24.5 - - + +
87F ALA* 3.1 25.7 + - + +
89F PRO* 1.3 78.8 - - + +
91F ILE* 1.3 56.1 + - - +
93F GLU* 4.0 20.4 - - - +
94F SER* 2.5 38.7 + - - +
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Residues in contact with ILE 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F GLN* 3.8 33.9 - - + +
36F SER* 4.9 2.0 - - - -
37F LEU* 4.1 21.5 - - + -
40F MET* 4.6 6.1 - - + -
49F MET* 3.5 30.3 - - + -
86F GLN* 3.8 26.0 - - + +
87F ALA 2.8 17.6 + - - +
88F VAL* 2.8 17.2 + - - +
90F VAL* 1.3 78.0 - - - +
92F TYR* 1.3 68.3 + - + +
94F SER* 3.4 1.9 + - - -
95F ASP* 3.1 30.1 + - - +
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Residues in contact with TYR 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 3.3 25.1 - - + +
45F LEU* 3.6 25.7 + - + +
49F MET* 3.9 15.3 - - + +
88F VAL* 3.3 28.8 + - + +
89F PRO* 3.5 3.1 + - + +
91F ILE* 1.3 83.6 - - + +
93F GLU* 1.3 65.5 + - - +
95F ASP* 4.5 1.6 - - - +
96F ALA* 3.3 24.1 + - - +
138F TYR* 4.4 9.0 + + - -
139F TYR* 3.6 42.9 - + - +
142F ILE* 3.9 27.8 - - + -
143F GLY* 4.0 17.7 - - - -
146F ILE* 3.9 13.7 - - + -
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Residues in contact with GLU 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F PRO 3.1 17.8 + - - +
90F VAL* 4.0 26.3 - - - +
91F ILE 3.4 0.2 - - - -
92F TYR* 1.3 79.6 - - - +
94F SER* 1.3 64.3 + - - +
96F ALA* 3.7 4.1 - - - +
97F ASP* 3.1 35.4 + - - +
143F GLY* 5.6 0.6 - - - -
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Residues in contact with SER 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F GLN* 3.1 21.9 + - - -
90F VAL* 2.5 26.5 + - - -
91F ILE* 3.4 3.8 + - - -
93F GLU* 1.3 83.3 - - - +
95F ASP* 1.3 57.5 + - - +
97F ASP* 3.0 8.6 + - - +
98F GLN* 2.6 37.7 + - - +
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Residues in contact with ASP 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLN* 4.5 3.3 - - - +
30F TYR* 3.3 21.1 + - + -
33F GLN* 2.3 40.6 + - - +
49F MET* 3.4 18.7 - - - +
91F ILE 3.1 16.3 + - - +
92F TYR 4.4 0.9 - - - +
93F GLU 3.4 0.2 - - - -
94F SER* 1.3 78.1 + - - +
96F ALA* 1.3 59.2 + - - +
98F GLN* 3.6 7.9 - - - +
99F GLU* 2.8 34.1 + - - +
139F TYR* 3.7 26.5 - - + -
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Residues in contact with ALA 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F TYR 3.3 18.0 + - - +
93F GLU* 3.7 4.9 - - - +
95F ASP* 1.3 77.5 - - - +
97F ASP* 1.3 63.1 + - - +
100F ASP* 3.1 21.0 + - - +
136F LEU* 3.1 17.3 - - + +
139F TYR* 3.9 16.4 - - + +
140F GLU* 4.2 24.2 - - + +
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Residues in contact with ASP 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F GLU* 3.1 29.3 + - - +
94F SER* 3.0 11.2 + - - +
96F ALA* 1.3 75.1 - - - +
98F GLN* 1.3 61.7 + - - +
100F ASP* 3.5 6.3 + - - +
101F ALA* 3.0 29.8 + - - +
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Residues in contact with GLN 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F MET 4.9 1.2 + - - -
25F HIS* 3.4 36.5 + - - -
26F ALA* 3.6 23.2 - - - +
29F GLN* 4.1 10.1 + - - +
30F TYR* 3.5 24.7 + - - +
94F SER* 2.6 21.0 + - - +
95F ASP* 3.6 9.2 - - - +
97F ASP* 1.3 71.3 - - - +
99F GLU* 1.3 60.3 + - - +
101F ALA* 3.4 6.0 + - - +
102F THR* 2.9 39.6 + - - +
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Residues in contact with GLU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F ALA* 5.2 1.2 - - - +
30F TYR* 2.4 26.0 + - - -
56F GLU* 3.2 6.0 - - - +
95F ASP 2.8 24.0 + - - +
98F GLN* 1.3 74.4 + - - +
100F ASP* 1.3 63.2 + - - +
102F THR* 3.2 5.4 + - - -
103F ILE* 2.9 29.2 + - - +
132F GLU* 3.2 17.8 - - - +
135F HIS* 3.1 18.0 - - + +
136F LEU* 4.0 21.1 - - + +
139F TYR* 3.6 21.1 - - + -
200F FE 2.2 31.3 - - - -
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Residues in contact with ASP 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ALA 3.1 18.8 + - - +
97F ASP* 3.7 8.2 - - - +
99F GLU* 1.3 78.0 - - - +
101F ALA* 1.3 63.2 + - - +
103F ILE* 3.2 7.5 + - - +
104F GLU* 3.0 21.7 + - - +
136F LEU* 3.9 25.2 - - + +
5K ARG* 2.9 44.1 + - - -
9K LYS* 5.1 4.2 + - - -
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Residues in contact with ALA 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F MET* 4.6 3.7 - - + +
97F ASP 3.0 18.6 + - - +
98F GLN* 3.7 6.5 - - - +
100F ASP* 1.3 78.0 + - - +
102F THR* 1.3 63.2 + - - +
104F GLU* 3.3 9.7 + - - +
105F ALA* 3.0 23.0 + - - +
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Residues in contact with THR 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F MET* 3.8 21.7 + - + +
23F GLU* 5.5 0.7 - - - -
98F GLN* 2.9 28.2 + - - +
99F GLU* 3.6 7.3 + - - -
101F ALA* 1.3 74.9 - - - +
103F ILE* 1.3 66.4 + - - +
104F GLU 3.2 0.2 + - - -
105F ALA 3.2 0.9 + - - -
106F TYR* 2.9 57.4 + - + +
132F GLU* 3.1 27.7 + - + +
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Residues in contact with ILE 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F GLU 2.9 20.0 + - - +
100F ASP* 3.6 7.2 - - - +
102F THR* 1.3 77.3 - - - +
104F GLU* 1.3 61.8 + - + +
106F TYR* 4.1 5.5 - - - +
107F SER* 2.8 37.8 + - - +
129F ILE* 3.9 23.7 - - + +
132F GLU* 3.7 22.7 - - + +
133F GLN* 3.8 31.6 - - + +
136F LEU* 3.8 27.1 - - + -
120K VAL* 5.4 4.3 - - + -
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Residues in contact with GLU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F ASP 3.0 13.3 + - - +
101F ALA* 3.4 12.6 - - - +
103F ILE* 1.3 79.2 - - + +
105F ALA* 1.3 64.7 + - - +
107F SER* 3.5 12.5 + - - -
108F GLN* 3.5 36.3 + - - +
5K ARG* 3.7 34.0 + - - +
8K ARG* 2.6 45.0 + - - -
117K GLY 4.5 3.3 - - - +
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Residues in contact with ALA 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F MET* 4.0 20.0 - - + -
101F ALA 3.0 16.7 + - - +
102F THR 3.9 2.5 - - - +
104F GLU* 1.3 73.8 - - - +
106F TYR* 1.3 65.4 + - - +
108F GLN* 2.8 26.2 + - - +
109F PHE* 2.9 31.6 + - + -
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Residues in contact with TYR 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ALA* 3.4 17.6 + - + -
22F MET* 3.9 17.1 - - - +
23F GLU* 2.3 50.4 + - - +
63F PHE* 3.7 11.4 - + - -
102F THR* 2.9 46.3 + - + +
103F ILE 4.1 0.4 - - - +
105F ALA* 1.3 71.9 - - - +
107F SER* 1.3 56.8 + - - +
109F PHE* 3.3 19.6 + + - +
110F LEU* 2.8 26.7 + - - +
125F PHE* 3.8 17.4 - + + -
128F ILE* 3.6 24.2 - - + -
129F ILE* 3.6 26.7 - - + +
132F GLU* 4.3 4.5 - - + -
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Residues in contact with SER 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ILE* 2.8 28.4 + - - +
104F GLU* 3.7 9.7 + - - -
105F ALA 3.0 1.2 + - - -
106F TYR* 1.3 76.2 - - - +
108F GLN* 1.3 58.7 + - - +
110F LEU* 3.1 24.1 + - - +
111F LYS* 3.2 6.9 + - - +
129F ILE* 4.0 10.4 - - - +
117K GLY* 4.2 16.6 + - - -
119K ILE* 3.6 26.3 + - - +
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Residues in contact with GLN 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F GLU* 3.5 34.2 + - - +
105F ALA* 2.8 14.1 + - - +
107F SER* 1.3 76.4 - - - +
109F PHE* 1.3 73.2 + - + +
111F LYS* 3.2 17.4 + - - +
112F VAL* 3.3 17.1 + - - +
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Residues in contact with PHE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F VAL* 3.5 44.3 - - + +
18F LYS* 3.7 31.6 - - + -
19F ALA* 3.7 18.4 - - + -
22F MET* 4.2 13.2 - - - -
105F ALA* 2.9 29.1 + - + -
106F TYR* 3.4 12.8 - + - +
108F GLN* 1.3 83.3 - - + +
110F LEU* 1.3 62.3 + - - +
112F VAL* 3.1 15.4 + - + +
113F CYS* 3.2 18.0 + - - -
125F PHE* 3.5 29.2 - + + -
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Residues in contact with LEU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F TYR 2.8 12.0 + - - +
107F SER 3.1 14.1 - - - +
109F PHE* 1.3 77.2 - - - +
111F LYS* 1.3 59.7 + - - +
113F CYS* 3.1 10.4 + - - +
114F LYS* 3.0 56.0 + - + +
122F ALA* 3.9 20.6 - - + +
125F PHE* 4.2 9.1 - - + -
126F GLU* 3.6 29.6 - - + +
129F ILE* 4.0 11.4 - - + -
119K ILE* 3.8 30.1 - - + -
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Residues in contact with LYS 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F SER 3.2 6.9 + - - +
108F GLN* 3.2 13.9 + - - +
110F LEU* 1.3 77.7 - - - +
112F VAL* 1.3 59.4 + - + +
114F LYS* 3.1 13.7 + - - +
115F GLU* 2.7 45.8 + - + +
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Residues in contact with VAL 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LYS* 4.2 25.4 - - + +
12F VAL* 5.0 0.7 - - + -
15F VAL* 4.0 23.1 - - + -
108F GLN 3.4 14.6 - - - +
109F PHE* 3.1 7.3 + - + +
111F LYS* 1.3 77.0 - - + +
113F CYS* 1.3 53.9 + - - +
115F GLU* 3.2 14.7 + - - +
116F GLN* 2.6 60.6 + - + +
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Residues in contact with CYS 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.0 19.3 - - - -
15F VAL* 4.5 3.1 - - - -
109F PHE 3.2 14.8 + - - -
110F LEU 3.1 10.1 + - - +
112F VAL* 1.3 79.3 - - - +
114F LYS* 1.3 54.8 + - - +
116F GLN 3.3 1.9 + - - -
117F GLY 3.0 7.1 + - - -
118F ASP* 2.6 38.3 + - + +
121F THR* 3.3 35.0 - - - -
122F ALA* 3.7 18.6 - - - -
125F PHE* 3.8 15.3 - - - -
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Residues in contact with LYS 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LEU* 3.0 40.7 + - + +
111F LYS* 3.4 12.3 - - - +
113F CYS* 1.3 74.8 - - - +
115F GLU* 1.3 58.6 + - + +
117F GLY* 3.0 18.2 + - - -
118F ASP 4.7 1.8 - - - +
119F ILE* 5.8 6.3 - - + +
122F ALA* 4.4 10.3 - - + -
126F GLU* 4.7 8.9 + - - -
114K LYS* 4.3 13.1 - - - +
119K ILE* 4.6 12.1 - - - +
1604K SO4 3.8 42.1 + - - +
111P LYS* 5.9 1.6 + - - +
114P LYS* 4.6 12.8 - - - +
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Residues in contact with GLU 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ALA* 4.1 18.0 + - - +
111F LYS* 2.7 31.7 + - + +
112F VAL* 3.5 21.6 + - - +
114F LYS* 1.3 70.1 - - + +
116F GLN* 1.3 71.5 + - - +
117F GLY 3.0 7.4 + - - -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ALA* 4.0 17.6 + - - +
3F GLY 4.5 1.6 + - - -
8F ARG* 2.9 57.2 + - + +
11F LYS* 3.3 41.1 - - + +
12F VAL* 3.7 20.4 - - + -
112F VAL* 2.6 39.2 + - + +
113F CYS 4.0 0.2 - - - +
115F GLU* 1.3 84.2 + - - +
117F GLY* 1.3 63.9 + - - +
118F ASP* 3.2 3.7 + - - +
----------------------------------------------------------
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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