Contacts of the helix formed by residues 87 - 116 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D MET* 6.0 0.9 - - - -
85D GLY 3.4 3.7 + - - -
86D GLN* 1.3 75.6 - - - +
88D VAL* 1.3 61.2 + - - +
89D PRO* 3.4 13.0 - - + -
90D VAL* 3.1 16.5 + - + +
91D ILE* 3.0 26.8 + - - +
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 4.1 11.0 - - + -
40D MET* 3.5 39.4 - - + +
42D TYR* 4.7 8.5 - - + -
45D LEU* 5.3 0.7 - - + -
87D ALA* 1.3 67.8 - - - +
89D PRO* 1.3 74.1 - - + +
90D VAL 3.2 0.3 + - - -
91D ILE* 3.5 9.8 + - - -
92D TYR* 3.3 27.7 - - + -
146D ILE* 3.6 30.9 - - + +
154D LEU* 4.7 16.8 - - + -
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Residues in contact with PRO 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ALA* 3.5 13.5 - - + -
88D VAL* 1.3 96.1 - - + +
90D VAL* 1.3 63.9 + - + +
92D TYR* 3.9 2.1 + - - +
93D GLU* 3.4 21.1 + - - +
143D GLY* 6.0 0.5 - - - -
146D ILE* 4.2 21.5 - - + -
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Residues in contact with VAL 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLN* 4.1 20.6 - - + +
87D ALA* 3.1 24.6 + - + +
89D PRO* 1.3 83.8 - - + +
91D ILE* 1.3 60.1 + - - +
93D GLU* 3.1 8.6 + - + +
94D SER* 2.4 44.6 + - - +
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Residues in contact with ILE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLN* 3.6 31.0 - - + +
36D SER* 5.0 1.3 - - - -
37D LEU* 4.0 27.4 - - + -
40D MET* 4.4 5.4 - - + -
49D MET* 3.7 15.0 - - + -
86D GLN* 3.8 20.8 - - + +
87D ALA 3.0 16.5 + - - +
88D VAL* 3.6 24.0 - - + +
90D VAL* 1.3 76.8 - - - +
92D TYR* 1.3 67.7 + - + +
94D SER* 3.4 3.4 + - - -
95D ASP* 3.0 48.6 + - - +
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Residues in contact with TYR 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 3.3 17.6 - - + +
45D LEU* 3.3 34.2 + - + +
49D MET* 4.0 14.4 - - + +
88D VAL* 3.3 28.3 + - + +
89D PRO 4.6 2.2 - - - +
90D VAL 3.3 0.4 - - - -
91D ILE* 1.3 87.1 - - + +
93D GLU* 1.3 65.8 + - - +
95D ASP* 4.1 3.4 - - - +
96D ALA* 3.6 20.1 + - - +
138D TYR* 4.5 4.8 + + - -
139D TYR* 3.7 28.1 - + - +
142D ILE* 3.5 39.3 - - + -
143D GLY* 3.8 24.3 - - - +
146D ILE* 3.6 15.0 - - + -
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Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D PRO 3.4 18.0 + - - +
90D VAL* 3.1 11.3 + - + +
92D TYR* 1.3 80.5 - - - +
94D SER* 1.3 61.9 + - - +
96D ALA* 3.6 2.6 + - - +
97D ASP* 3.2 35.6 + - - +
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Residues in contact with SER 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLN* 6.2 0.9 - - - -
86D GLN* 3.4 22.3 + - - -
90D VAL* 2.4 34.3 + - - +
91D ILE* 3.4 5.4 + - - -
93D GLU* 1.3 78.1 - - - +
95D ASP* 1.3 60.7 + - - +
97D ASP* 3.4 9.7 + - - +
98D GLN* 2.9 32.5 + - - +
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Residues in contact with ASP 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLN* 4.5 0.9 - - - +
30D TYR* 3.0 23.6 + - + -
33D GLN* 2.3 44.9 + - - +
49D MET* 3.3 17.2 - - - +
91D ILE* 3.0 22.7 + - - +
92D TYR* 4.6 0.4 - - - -
93D GLU 3.4 0.2 - - - -
94D SER* 1.3 77.7 + - - +
96D ALA* 1.3 58.6 + - - +
98D GLN* 3.5 4.3 + - - +
99D GLU* 2.9 32.9 + - - +
139D TYR* 3.6 27.9 - - + -
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D TYR 3.6 18.2 + - - +
93D GLU 3.9 3.4 - - - +
94D SER 3.2 0.4 - - - -
95D ASP* 1.3 77.1 - - - +
97D ASP* 1.3 69.4 + - - +
99D GLU 3.1 1.0 + - - -
100D ASP* 2.9 24.9 + - - +
136D LEU* 3.6 19.1 - - + +
139D TYR* 3.8 19.0 - - + +
140D GLU* 4.4 14.4 - - + +
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Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D GLU* 3.2 28.5 + - - +
94D SER* 3.4 10.8 + - - +
96D ALA* 1.3 78.6 - - - +
98D GLN* 1.3 57.7 + - - +
100D ASP* 3.5 8.3 + - - +
101D ALA* 3.1 26.9 + - - +
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Residues in contact with GLN 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D MET 4.9 1.4 + - - -
25D HIS* 3.3 32.2 + - - -
26D ALA* 3.7 25.5 - - - +
29D GLN* 3.9 18.6 + - - +
30D TYR* 3.8 16.4 + - - +
94D SER* 2.9 18.4 + - - +
95D ASP* 3.6 6.6 - - - +
97D ASP* 1.3 75.5 - - - +
99D GLU* 1.3 61.3 + - - +
101D ALA* 3.1 6.0 + - - +
102D THR* 2.9 39.1 + - - +
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ALA* 5.3 0.7 - - - +
30D TYR* 2.5 31.9 + - - -
56D GLU* 3.3 1.8 - - - +
95D ASP 2.9 21.2 + - - +
96D ALA 3.1 3.3 + - - +
98D GLN* 1.3 75.7 - - - +
100D ASP* 1.3 58.1 + - - +
102D THR* 3.4 6.1 + - - +
103D ILE* 3.0 35.2 + - - +
132D GLU* 3.1 16.1 - - - +
135D HIS* 3.2 17.9 - - + +
136D LEU* 4.0 19.7 - - + +
139D TYR* 3.7 17.5 - - + -
200D FE 2.2 30.7 - - - -
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Residues in contact with ASP 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ALA 2.9 16.5 + - - +
97D ASP* 3.6 8.8 - - - +
99D GLU* 1.3 79.7 - - - +
101D ALA* 1.3 57.9 + - - +
103D ILE* 3.7 5.9 + - - +
104D GLU* 3.2 34.5 + - - +
136D LEU* 4.3 23.7 - - + +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D MET* 4.3 4.2 - - + +
97D ASP 3.1 16.4 + - - +
98D GLN* 3.1 6.5 + - - +
100D ASP* 1.3 76.5 + - - +
102D THR* 1.3 62.2 + - - +
104D GLU* 3.3 7.7 + - - +
105D ALA* 2.8 30.3 + - - +
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Residues in contact with THR 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D MET* 3.4 22.4 - - - +
23D GLU* 5.6 0.2 - - - -
98D GLN* 2.9 25.6 + - - +
99D GLU* 3.6 4.8 + - - -
101D ALA* 1.3 77.4 - - - +
103D ILE* 1.3 52.9 + - - +
105D ALA 3.2 0.2 + - - -
106D TYR* 2.7 75.0 + - + +
132D GLU* 2.8 31.2 + - + +
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Residues in contact with ILE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D GLU 3.0 21.6 + - - +
100D ASP* 3.9 7.4 - - - +
102D THR* 1.3 76.3 - - - +
104D GLU* 1.3 61.1 + - - +
106D TYR* 4.0 5.0 - - - +
107D SER* 2.5 46.6 + - - +
129D ILE* 4.2 18.1 - - + +
132D GLU* 3.6 20.2 - - + +
133D GLN* 3.7 44.9 - - + +
136D LEU* 3.9 15.9 - - + -
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ASP* 3.2 25.3 + - - +
101D ALA* 3.5 11.2 - - - +
102D THR 3.3 0.2 - - - -
103D ILE* 1.3 86.5 - - - +
105D ALA* 1.3 60.1 + - - +
107D SER* 3.5 8.9 + - - -
108D GLN* 3.2 32.9 + - - +
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Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D MET* 3.7 24.2 - - + -
101D ALA 2.8 19.9 + - - +
104D GLU* 1.3 72.7 - - - +
106D TYR* 1.3 59.9 + - - +
108D GLN* 3.1 7.1 + - - +
109D PHE* 2.9 50.9 + - + -
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Residues in contact with TYR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ALA* 3.4 31.0 + - + -
22D MET* 4.1 14.9 - - - +
23D GLU* 2.8 35.5 + - - +
63D PHE* 3.7 4.4 - + - -
102D THR* 2.7 47.2 + - + +
103D ILE* 4.0 1.3 - - - +
105D ALA* 1.3 73.0 - - + +
107D SER* 1.3 57.9 + - - +
109D PHE* 3.4 17.2 - + - +
110D LEU* 2.8 29.5 + - - +
125D PHE* 4.0 12.5 - + + -
128D ILE* 3.6 33.0 - - + -
129D ILE* 3.5 25.6 - - + +
132D GLU* 4.2 7.0 - - + -
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ILE* 2.5 32.0 + - - +
104D GLU* 3.7 12.0 + - - -
106D TYR* 1.3 78.5 - - - +
108D GLN* 1.3 63.0 + - - +
110D LEU* 3.8 6.2 - - - +
111D LYS* 3.6 21.1 + - - +
114D LYS* 5.7 0.9 + - - -
129D ILE* 4.1 14.6 - - - +
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Residues in contact with GLN 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLU* 3.2 21.5 + - - +
105D ALA* 3.1 11.0 + - - +
107D SER* 1.3 79.2 - - - +
109D PHE* 1.3 70.0 + - + +
111D LYS* 3.0 52.1 + - - +
112D VAL* 3.4 11.8 + - - +
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Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D VAL* 4.0 21.1 - - + +
18D LYS* 3.6 39.5 - - + -
19D ALA* 3.9 17.9 - - + -
22D MET* 4.2 7.4 - - - -
105D ALA* 2.9 36.3 + - + +
106D TYR* 3.4 29.8 - + - +
108D GLN* 1.3 79.8 - - + +
110D LEU* 1.3 65.9 + - - +
112D VAL* 3.2 17.8 + - + +
113D CYS* 3.3 15.9 + - - -
125D PHE* 3.5 27.3 - + + -
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D TYR 2.8 13.7 + - - +
107D SER* 3.8 9.4 - - - +
109D PHE* 1.3 76.5 - - - +
111D LYS* 1.3 62.1 + - - +
113D CYS* 3.1 7.5 + - - +
114D LYS* 3.1 62.1 + - + +
122D ALA* 4.0 14.6 - - + +
125D PHE* 3.8 11.6 - - + -
126D GLU* 3.5 44.2 - - + +
129D ILE* 3.4 28.7 - - + -
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Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D SER 3.6 9.4 + - - +
108D GLN* 3.0 52.8 + - - +
109D PHE 3.1 0.2 - - - -
110D LEU* 1.3 79.5 - - - +
112D VAL* 1.3 59.0 + - + +
114D LYS* 3.1 22.9 + - + +
115D GLU* 2.8 47.8 + - + +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 3.7 25.4 - - + +
12D VAL* 5.1 0.9 - - + +
15D VAL* 4.0 22.0 - - + -
108D GLN 3.5 15.3 - - - +
109D PHE* 3.2 9.2 + - + +
111D LYS* 1.3 77.6 - - + +
113D CYS* 1.3 53.0 + - - +
115D GLU* 3.0 17.6 + - - +
116D GLN* 2.7 56.8 + - + +
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Residues in contact with CYS 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL* 4.3 18.4 - - - -
15D VAL* 4.6 3.8 - - - -
109D PHE 3.6 12.8 - - - -
110D LEU 3.1 8.0 + - - +
112D VAL* 1.3 77.8 - - - +
114D LYS* 1.3 62.2 + - - +
116D GLN 3.1 1.9 + - - -
117D GLY 3.0 4.2 + - - -
118D ASP* 2.8 42.7 + - + +
121D THR* 3.5 32.8 - - - -
122D ALA* 3.9 9.9 - - - +
125D PHE* 3.8 17.9 - - - -
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D SER 5.7 0.6 + - - -
110D LEU* 3.1 45.0 + - + +
111D LYS* 3.1 22.5 + - + +
113D CYS* 1.3 76.3 - - - +
115D GLU* 1.3 57.0 + - + +
117D GLY* 2.6 28.2 + - - -
118D ASP 4.8 1.1 - - - +
119D ILE* 5.6 7.2 - - + -
122D ALA* 4.8 8.2 - - + +
126D GLU* 5.0 3.1 - - - -
114E LYS* 5.5 7.6 - - - +
1404E SO4 4.1 30.7 + - - +
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D LYS* 2.8 36.5 + - + +
112D VAL* 3.0 23.6 + - - +
114D LYS* 1.3 77.4 - - + +
116D GLN* 1.3 71.4 + - - +
117D GLY 3.4 0.9 + - - -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D GLY* 4.8 5.9 + - - -
8D ARG* 2.8 58.6 + - + +
11D LYS* 3.5 48.1 + - + +
12D VAL* 3.9 17.9 - - + -
112D VAL* 2.7 34.6 + - + +
113D CYS 3.9 3.4 - - - +
114D LYS 3.0 0.2 - - - -
115D GLU* 1.3 84.0 + - - +
117D GLY* 1.3 63.1 + - - +
118D ASP* 3.3 3.2 + - + +
----------------------------------------------------------
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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