Contacts of the helix formed by residues 87 - 116 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N MET* 5.8 1.6 - - - -
85N GLY 3.5 3.2 + - - -
86N GLN* 1.3 75.4 - - - +
88N VAL* 1.3 68.3 + - - +
89N PRO* 3.3 11.2 - - + -
90N VAL* 2.9 18.3 + - + +
91N ILE* 2.7 19.6 + - - +
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Residues in contact with VAL 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N LEU* 4.1 13.7 - - + -
40N MET* 3.6 32.2 - - + +
42N TYR* 4.7 10.5 - - + -
45N LEU* 5.1 0.7 - - + -
86N GLN 3.9 0.6 + - - -
87N ALA* 1.3 69.8 - - - +
89N PRO* 1.3 72.4 - - + +
91N ILE* 3.0 19.3 + - - +
92N TYR* 3.2 24.3 + - + -
146N ILE* 3.3 30.1 - - + -
154N LEU* 4.7 18.4 - - + -
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Residues in contact with PRO 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87N ALA* 3.5 11.2 - - + -
88N VAL* 1.3 98.4 - - + +
90N VAL* 1.3 64.0 + - + +
92N TYR* 3.5 1.9 + - + +
93N GLU* 3.1 25.7 + - - +
143N GLY* 6.1 0.4 - - - -
146N ILE* 4.2 25.4 - - + -
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Residues in contact with VAL 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86N GLN* 3.9 27.4 - - + +
87N ALA* 2.9 25.9 + - + +
89N PRO* 1.3 78.3 - - + +
91N ILE* 1.3 55.1 + - - +
93N GLU* 4.4 11.2 - - - +
94N SER* 2.5 43.1 + - - +
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Residues in contact with ILE 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N GLN* 3.8 32.3 - - + +
36N SER* 5.0 1.6 - - - -
37N LEU* 4.2 20.9 - - + -
40N MET* 4.8 5.6 - - + -
49N MET* 3.7 30.1 - - + -
86N GLN* 3.7 29.4 - - + +
87N ALA 2.7 14.3 + - - +
88N VAL* 3.0 17.7 + - + +
90N VAL* 1.3 78.7 - - - +
92N TYR* 1.3 73.3 + - + +
94N SER* 3.3 4.6 + - - -
95N ASP* 3.1 31.2 + - - -
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Residues in contact with TYR 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N LEU* 3.3 17.9 - - + +
45N LEU* 3.2 39.5 + - + +
49N MET* 3.9 12.7 - - + +
88N VAL* 3.2 30.6 + - + +
89N PRO 4.4 1.8 - - - +
91N ILE* 1.3 85.5 - - + +
93N GLU* 1.3 64.5 + - - +
95N ASP* 4.0 2.5 - - - -
96N ALA* 3.4 23.0 + - - +
138N TYR* 4.2 4.5 + + - -
139N TYR* 3.6 38.4 - + - +
142N ILE* 3.7 30.5 - - + -
143N GLY* 4.0 24.8 - - - +
146N ILE* 3.8 11.9 - - + -
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Residues in contact with GLU 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89N PRO 3.1 18.7 + - - +
90N VAL* 3.9 11.5 - - - +
92N TYR* 1.3 77.7 - - - +
94N SER* 1.3 64.5 + - - +
96N ALA* 3.7 2.8 + - - +
97N ASP* 3.1 36.0 + - - +
143N GLY* 5.6 1.1 - - - -
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Residues in contact with SER 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86N GLN* 2.9 27.5 + - - -
90N VAL* 2.5 27.2 + - - +
91N ILE* 3.3 7.3 + - - -
93N GLU* 1.3 79.4 + - - +
95N ASP* 1.3 62.3 + - - +
97N ASP* 3.4 10.4 + - - +
98N GLN* 3.0 29.0 + - - +
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Residues in contact with ASP 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N GLN* 4.7 1.0 - - - +
30N TYR* 3.3 18.2 + - + -
33N GLN* 2.5 40.7 + - - +
49N MET* 3.3 19.2 - - - +
91N ILE* 3.1 17.3 + - - +
92N TYR 4.3 1.1 - - - +
93N GLU 3.3 0.4 - - - -
94N SER* 1.3 80.3 + - - +
96N ALA* 1.3 56.7 + - - +
98N GLN* 3.2 9.9 + - - +
99N GLU* 3.0 32.9 + - - +
139N TYR* 3.6 29.0 - - + -
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Residues in contact with ALA 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N TYR 3.4 16.8 + - - +
93N GLU* 4.2 3.6 - - - +
94N SER 3.4 0.6 - - - -
95N ASP* 1.3 74.8 - - - +
97N ASP* 1.3 60.7 + - - +
100N ASP* 3.1 15.8 + - - +
136N LEU* 2.9 37.8 - - + +
139N TYR* 4.0 16.5 - - + +
140N GLU* 4.1 16.6 - - + +
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Residues in contact with ASP 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N GLU* 3.1 27.1 + - - +
94N SER* 3.4 11.8 + - - +
95N ASP 3.3 0.2 - - - -
96N ALA* 1.3 76.8 - - - +
98N GLN* 1.3 59.7 + - - +
100N ASP* 3.8 6.1 - - - +
101N ALA* 3.1 27.9 + - - +
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Residues in contact with GLN 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N MET 4.5 2.8 + - - -
25N HIS* 3.3 35.9 + - - -
26N ALA* 3.5 27.5 - - - +
29N GLN* 4.1 6.6 + - - +
30N TYR* 3.4 24.8 + - - +
94N SER 3.0 15.8 + - - +
95N ASP* 3.2 8.2 + - - +
97N ASP* 1.3 76.1 - - - +
99N GLU* 1.3 59.1 + - - +
101N ALA* 3.3 5.7 + - - +
102N THR* 2.8 42.1 + - - +
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Residues in contact with GLU 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N ALA* 5.1 1.2 - - - +
30N TYR* 2.5 30.7 + - - +
56N GLU* 3.3 2.1 - - - +
95N ASP 3.0 18.8 + - - +
96N ALA 4.1 1.3 - - - +
98N GLN* 1.3 73.6 + - - +
100N ASP* 1.3 62.4 + - - +
102N THR* 3.4 6.1 + - - -
103N ILE* 2.9 36.5 + - - +
132N GLU* 3.2 17.2 - - - +
135N HIS* 3.1 16.3 - - + +
136N LEU* 3.9 20.6 - - + +
139N TYR* 3.9 17.5 - - + -
200N FE 2.2 31.0 - - - -
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Residues in contact with ASP 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 2.9 44.6 + - - -
9B LYS* 4.9 0.3 + - - -
96N ALA 3.1 19.4 + - - +
97N ASP* 3.8 7.1 - - - +
99N GLU* 1.3 74.2 - - - +
101N ALA* 1.3 67.5 + - - +
103N ILE* 3.1 8.3 + - - +
104N GLU* 2.9 23.4 + - - +
136N LEU* 4.0 21.0 - - + +
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Residues in contact with ALA 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N MET* 4.7 3.8 - - + -
97N ASP 3.1 17.1 + - - +
98N GLN* 3.6 6.7 - - - +
100N ASP* 1.3 82.1 + - - +
102N THR* 1.3 57.8 + - - +
104N GLU* 3.2 10.4 + - - +
105N ALA* 2.9 28.6 + - - +
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Residues in contact with THR 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N MET* 3.4 24.6 - - + +
23N GLU* 5.5 0.4 - - - -
98N GLN* 2.8 32.3 + - - +
99N GLU* 3.6 7.9 + - - -
101N ALA* 1.3 74.6 - - - +
103N ILE* 1.3 59.7 + - - +
105N ALA 3.2 0.3 + - - -
106N TYR* 2.8 62.5 + - + +
132N GLU* 3.2 26.9 + - - +
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Residues in contact with ILE 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B VAL* 5.7 3.1 - - + -
99N GLU 2.9 23.3 + - - +
100N ASP* 3.1 9.2 + - - +
102N THR* 1.3 76.5 - - - +
104N GLU* 1.3 68.8 + - - +
106N TYR* 4.0 5.1 - - - +
107N SER* 2.8 39.0 + - - +
129N ILE* 4.4 18.7 - - + +
132N GLU* 3.7 20.2 - - + +
133N GLN* 3.8 44.0 - - + +
136N LEU* 4.1 15.3 - - + -
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Residues in contact with GLU 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ARG* 3.8 36.9 + - - +
8B ARG* 3.1 36.8 + - - -
117B GLY 4.9 2.4 - - - +
100N ASP* 2.9 18.4 + - - +
101N ALA* 3.3 12.6 - - - +
103N ILE* 1.3 86.1 - - - +
105N ALA* 1.3 60.9 - - - +
107N SER* 3.5 7.6 + - - -
108N GLN* 3.1 35.6 + - - +
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Residues in contact with ALA 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N MET* 4.1 18.8 - - + -
101N ALA 2.9 15.5 + - - +
102N THR 3.8 2.9 - - - +
104N GLU* 1.3 75.6 - - - +
106N TYR* 1.3 60.9 + - - +
108N GLN* 3.0 16.8 + - - +
109N PHE* 2.9 49.7 + - + -
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Residues in contact with TYR 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N ALA* 3.4 27.3 + - + -
22N MET* 4.1 10.1 - - - +
23N GLU* 2.8 39.1 + - - +
63N PHE* 3.8 8.1 - + - -
102N THR* 2.8 46.5 + - + +
103N ILE 4.1 0.2 - - - +
105N ALA* 1.3 73.6 - - - +
107N SER* 1.3 58.6 + - - +
109N PHE* 3.1 19.7 + + - +
110N LEU* 2.8 29.3 + - - +
125N PHE* 4.0 14.5 - + + -
128N ILE* 3.6 31.2 - - + -
129N ILE* 3.7 23.6 - - + +
132N GLU* 4.0 9.0 - - + -
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Residues in contact with SER 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 6.1 0.7 - - - -
117B GLY* 4.4 15.8 + - - -
119B ILE* 3.5 27.9 + - - +
103N ILE* 2.8 29.7 + - - +
104N GLU* 3.6 9.5 + - - -
105N ALA 3.1 0.2 - - - -
106N TYR* 1.3 77.9 - - - +
108N GLN* 1.3 61.6 + - - +
110N LEU* 3.2 18.0 - - - +
111N LYS* 3.3 8.3 + - - +
129N ILE* 3.8 10.7 - - - +
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Residues in contact with GLN 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104N GLU* 3.1 25.3 + - - +
105N ALA* 3.0 12.8 + - - +
107N SER* 1.3 73.7 - - - +
109N PHE* 1.3 73.1 + - + +
110N LEU 3.2 0.2 - - - -
111N LYS* 3.4 10.5 + - - +
112N VAL* 3.2 24.5 + - - +
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Residues in contact with PHE 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N VAL* 3.6 36.8 - - + +
18N LYS* 3.8 27.8 - - + -
19N ALA* 3.9 19.3 - - + -
22N MET* 4.3 6.7 - - - -
105N ALA* 2.9 34.1 + - + -
106N TYR* 3.4 30.3 - + - +
108N GLN* 1.3 82.1 - - + +
110N LEU* 1.3 66.0 + - - +
112N VAL* 3.2 9.9 + - + +
113N CYS* 3.0 27.0 + - - -
125N PHE* 3.6 20.9 - + + -
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Residues in contact with LEU 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 5.1 0.2 - - - +
119B ILE* 4.1 16.8 - - + -
106N TYR 2.8 10.1 + - - +
107N SER 3.2 12.8 - - - +
109N PHE* 1.3 77.4 - - - +
111N LYS* 1.3 58.7 + - - +
113N CYS* 3.0 10.2 + - - +
114N LYS* 2.8 63.3 + - + +
122N ALA* 4.0 12.1 - - + +
125N PHE* 3.9 8.6 - - + -
126N GLU* 3.3 48.5 - - + +
129N ILE* 3.8 17.5 - - + -
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Residues in contact with LYS 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107N SER 3.3 8.7 + - - +
108N GLN* 3.5 12.8 - - - +
109N PHE 3.3 0.2 - - - -
110N LEU* 1.3 79.8 - - - +
112N VAL* 1.3 52.7 + - + +
114N LYS* 3.2 10.2 + - - +
115N GLU* 2.7 49.0 + - + +
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Residues in contact with VAL 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N LYS* 4.0 25.6 - - + +
12N VAL* 4.9 0.9 - - - -
15N VAL* 4.1 22.7 - - + -
108N GLN 3.2 13.6 + - - +
109N PHE* 3.4 8.5 - - + +
110N LEU 3.2 0.2 - - - -
111N LYS* 1.3 78.3 - - + +
113N CYS* 1.3 57.6 + - - +
115N GLU* 2.9 17.6 + - - +
116N GLN* 2.8 43.4 + - + +
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Residues in contact with CYS 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N VAL* 4.1 19.1 - - - -
15N VAL* 4.5 4.5 - - - -
109N PHE 3.0 17.2 + - - -
110N LEU 3.0 9.3 + - - +
112N VAL* 1.3 75.9 - - - +
114N LYS* 1.3 58.1 + - - +
116N GLN 3.3 1.7 + - - -
117N GLY 3.2 4.0 + - - -
118N ASP* 2.7 45.7 + - + +
121N THR* 3.3 33.7 - - - -
122N ALA* 3.7 9.6 - - + +
125N PHE* 3.7 16.4 - - - -
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Residues in contact with LYS 114 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS* 3.3 25.3 - - - +
119B ILE* 5.5 1.2 - - - +
111G LYS* 6.1 1.4 - - - -
114G LYS* 3.3 17.3 - - - +
110N LEU* 2.8 43.0 + - + +
111N LYS* 3.6 10.6 - - - +
113N CYS* 1.3 73.6 - - - +
115N GLU* 1.3 62.4 + - + +
117N GLY* 3.2 12.9 + - - +
118N ASP 4.8 1.6 - - - +
119N ILE* 5.1 9.7 - - + +
122N ALA* 4.2 11.2 - - + -
126N GLU* 4.4 6.3 - - - -
1204N SO4 2.4 56.7 + - - +
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Residues in contact with GLU 115 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111N LYS* 2.7 30.7 + - - +
112N VAL* 2.9 19.2 + - - +
114N LYS* 1.3 75.1 - - + +
116N GLN* 1.3 68.8 + - - +
117N GLY 3.2 2.8 + - - -
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Residues in contact with GLN 116 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3N GLY 4.7 5.3 + - - +
7N ASP 4.4 0.5 - - - -
8N ARG* 3.0 69.0 + - + +
11N LYS* 3.7 37.8 - - + +
12N VAL* 3.6 24.5 - - + -
112N VAL* 2.8 26.3 + - + +
113N CYS 3.3 0.9 + - - +
115N GLU* 1.3 83.8 + - - +
117N GLY* 1.3 63.6 + - - +
118N ASP* 3.3 2.1 + - - +
----------------------------------------------------------
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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