Contacts of the helix formed by residues 87 - 116 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I MET* 6.1 0.2 - - - -
85I GLY 3.5 3.8 + - - -
86I GLN* 1.3 74.9 - - - +
88I VAL* 1.3 67.1 + - - +
89I PRO* 3.8 13.5 - - + -
90I VAL* 3.0 19.4 + - + +
91I ILE* 2.9 21.2 + - - +
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Residues in contact with VAL 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LEU* 4.4 4.7 - - + -
40I MET* 3.3 38.4 - - + +
42I TYR* 4.3 12.1 - - + -
45I LEU* 5.0 3.1 - - + -
86I GLN 3.9 0.4 + - - -
87I ALA* 1.3 69.4 - - - +
89I PRO* 1.3 75.3 - - + +
91I ILE* 3.1 18.8 + - - +
92I TYR* 3.2 27.7 - - + -
146I ILE* 3.5 27.4 - - + -
154I LEU* 4.3 20.4 - - + -
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Residues in contact with PRO 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I ALA* 3.5 13.7 - - + -
88I VAL* 1.3 98.7 - - + +
90I VAL* 1.3 59.1 + - + +
92I TYR* 3.6 2.8 + - - +
93I GLU* 3.1 29.6 + - - +
143I GLY* 5.9 0.7 - - - -
146I ILE* 4.4 25.8 - - + -
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Residues in contact with VAL 90 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I GLN* 4.0 24.5 - - + +
87I ALA* 3.0 28.6 + - + +
89I PRO* 1.3 78.3 - - + +
91I ILE* 1.3 63.9 + - - +
93I GLU* 4.4 12.3 - - - +
94I SER* 2.8 34.2 + - - +
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Residues in contact with ILE 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I GLN* 3.5 48.5 - - + +
36I SER* 5.0 2.0 - - - -
37I LEU* 4.1 22.2 - - + -
40I MET* 4.5 5.8 - - + -
49I MET* 3.6 19.5 - - + -
86I GLN* 3.7 24.7 - - + +
87I ALA 2.9 19.7 + - - +
88I VAL* 3.1 17.0 + - - +
90I VAL* 1.3 76.8 - - - +
92I TYR* 1.3 73.4 + - + +
94I SER* 4.2 0.2 - - - -
95I ASP* 3.0 31.0 + - - +
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Residues in contact with TYR 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LEU* 3.4 15.9 - - + +
45I LEU* 3.2 36.3 + - + +
49I MET* 4.3 6.7 - - + +
88I VAL* 3.2 29.2 + - + -
89I PRO 4.2 3.8 - - - +
90I VAL 3.3 0.2 - - - -
91I ILE* 1.3 92.1 - - + +
93I GLU* 1.3 61.6 + - - +
95I ASP* 4.6 2.2 - - - -
96I ALA* 3.2 23.2 + - - +
138I TYR* 4.3 7.2 + + - -
139I TYR* 3.9 33.6 - + - +
142I ILE* 3.4 38.6 - - + -
143I GLY* 3.9 24.6 - - - +
146I ILE* 3.7 11.2 - - + -
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Residues in contact with GLU 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I PRO 3.1 19.6 + - - +
90I VAL* 4.1 11.5 - - - +
91I ILE 3.3 0.2 - - - -
92I TYR* 1.3 79.0 - - - +
94I SER* 1.3 63.0 + - - +
96I ALA* 3.5 5.1 + - - +
97I ASP* 3.1 39.2 + - - +
143I GLY* 5.6 0.8 - - - -
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Residues in contact with SER 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I GLN* 6.0 0.2 - - - -
86I GLN* 3.0 23.6 + - - -
90I VAL* 2.8 25.2 + - - -
91I ILE 3.6 2.6 + - - -
93I GLU* 1.3 77.5 - - - +
95I ASP* 1.3 67.9 + - - +
97I ASP* 3.3 10.7 + - - +
98I GLN* 2.8 28.4 + - - +
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Residues in contact with ASP 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I GLN* 4.5 2.6 - - - +
30I TYR* 3.4 19.6 - - + -
33I GLN* 2.5 41.4 + - - +
49I MET* 3.6 13.9 - - - +
91I ILE 3.0 19.6 + - - +
92I TYR 4.3 0.4 - - - +
94I SER* 1.3 81.1 + - - +
96I ALA* 1.3 66.2 + - - +
98I GLN* 3.1 7.8 + - - +
99I GLU* 2.9 28.8 + - - +
139I TYR* 3.7 27.1 - - + -
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Residues in contact with ALA 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I TYR 3.2 18.7 + - - +
93I GLU* 3.7 6.1 - - - +
95I ASP* 1.3 77.8 - - - +
97I ASP* 1.3 67.1 + - - +
100I ASP* 3.2 21.8 + - - +
136I LEU* 3.4 27.3 - - + +
139I TYR* 3.9 13.1 - - + +
140I GLU* 4.3 15.0 - - + +
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Residues in contact with ASP 97 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I GLU* 3.1 30.4 + - - +
94I SER* 3.5 12.6 - - - +
95I ASP 3.1 0.6 - - - -
96I ALA* 1.3 80.3 - - - +
98I GLN* 1.3 57.9 + - - +
100I ASP* 3.8 6.4 - - - +
101I ALA* 3.0 28.6 + - - +
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Residues in contact with GLN 98 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I MET 4.5 2.8 + - - -
25I HIS* 3.7 26.4 + - - -
26I ALA* 3.1 39.4 - - - +
29I GLN* 4.0 7.3 - - - +
30I TYR* 3.3 23.5 + - - +
94I SER 2.8 16.5 + - - +
95I ASP* 3.1 6.1 + - - +
97I ASP* 1.3 75.4 - - - +
99I GLU* 1.3 57.2 + - - +
101I ALA* 3.2 6.7 + - + +
102I THR* 2.6 45.4 + - - +
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Residues in contact with GLU 99 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ALA* 4.9 0.5 - - - +
30I TYR* 2.3 34.0 + - - +
56I GLU* 3.3 2.6 - - - +
95I ASP 2.9 19.8 + - - +
96I ALA 4.2 1.1 - - - +
98I GLN* 1.3 79.4 + - - +
100I ASP* 1.3 53.5 + - - +
102I THR* 3.2 6.0 + - - -
103I ILE* 2.8 39.8 + - - +
132I GLU* 3.1 17.8 - - - +
135I HIS* 3.2 14.9 - - + +
136I LEU* 4.0 20.9 - - + -
139I TYR* 3.8 17.5 - - + -
200I FE 2.2 30.9 - - - -
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Residues in contact with ASP 100 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ARG* 2.9 41.4 + - - -
9H LYS* 5.0 1.7 + - - -
96I ALA 3.2 17.5 + - - +
97I ASP* 3.8 6.0 - - - +
99I GLU* 1.3 74.0 - - - +
101I ALA* 1.3 63.9 + - - +
103I ILE* 3.5 6.6 + - - +
104I GLU* 3.2 25.1 + - - +
136I LEU* 4.3 23.1 - - + +
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Residues in contact with ALA 101 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I MET* 4.4 3.9 - - + +
97I ASP 3.0 18.8 + - - +
98I GLN* 3.6 7.6 - - + +
100I ASP* 1.3 75.8 + - - +
102I THR* 1.3 64.1 + - - +
104I GLU* 3.6 6.7 + - - +
105I ALA* 3.1 24.6 + - - +
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Residues in contact with THR 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I MET* 3.7 19.4 - - + +
23I GLU* 5.5 0.4 - - - -
98I GLN* 2.6 35.7 + - - +
99I GLU* 3.3 8.3 + - - -
101I ALA* 1.3 75.5 - - - +
103I ILE* 1.3 61.2 + - - +
105I ALA* 3.1 1.4 + - - -
106I TYR* 2.8 64.6 + - + +
132I GLU* 2.9 28.2 + - - +
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Residues in contact with ILE 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H VAL* 5.5 3.8 - - + -
99I GLU 2.8 23.0 + - - +
100I ASP* 3.9 7.9 - - - +
101I ALA 3.4 0.2 - - - -
102I THR* 1.3 73.2 - - - +
104I GLU* 1.3 64.1 + - - +
106I TYR* 3.9 4.9 - - - +
107I SER* 2.8 39.4 + - - +
129I ILE* 4.2 22.2 - - + +
132I GLU* 3.5 22.2 - - + +
133I GLN* 3.6 38.6 - - + +
136I LEU* 4.1 19.3 - - + -
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Residues in contact with GLU 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ARG* 3.5 35.8 + - - +
8H ARG* 2.7 45.9 + - - -
117H GLY 4.9 1.2 - - - +
100I ASP 3.2 21.5 + - - +
101I ALA* 3.7 7.6 - - - +
103I ILE* 1.3 80.2 - - + +
105I ALA* 1.3 61.9 + - - +
107I SER* 3.6 6.6 + - - -
108I GLN* 3.3 21.3 + - - +
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Residues in contact with ALA 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I MET* 3.9 24.5 - - + -
101I ALA 3.1 19.4 + - - +
102I THR 3.8 2.2 - - - +
104I GLU* 1.3 74.6 - - - +
106I TYR* 1.3 59.9 + - - +
107I SER 3.1 2.0 - - - -
108I GLN* 3.2 6.0 + - - +
109I PHE* 2.9 45.0 + - + -
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Residues in contact with TYR 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ALA* 3.3 28.4 + - + -
22I MET* 4.2 9.5 - - + +
23I GLU* 2.6 38.5 + - - +
63I PHE* 3.6 8.5 - + - -
102I THR* 2.8 47.6 + - + +
103I ILE 4.0 0.7 - - - +
105I ALA* 1.3 73.9 - - - +
107I SER* 1.3 58.8 + - - +
109I PHE* 3.3 18.8 + + - +
110I LEU* 2.7 29.5 + - - +
125I PHE* 3.8 14.4 - + + -
128I ILE* 3.5 32.1 - - + -
129I ILE* 3.7 22.5 - - + +
132I GLU* 4.0 8.5 - - + -
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Residues in contact with SER 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ARG* 5.9 1.3 - - - -
117H GLY* 4.3 16.3 + - - -
119H ILE* 3.4 28.7 + - - +
103I ILE* 2.8 26.9 + - - +
104I GLU* 3.7 9.3 + - - -
105I ALA 3.1 0.2 - - - -
106I TYR* 1.3 79.9 - - - +
108I GLN* 1.3 60.8 + - - +
110I LEU* 3.3 6.6 - - - +
111I LYS* 3.3 19.1 + - - +
129I ILE* 3.7 9.7 - - - +
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Residues in contact with GLN 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I GLU 3.3 11.5 + - - +
105I ALA* 3.2 9.6 + - - +
107I SER* 1.3 76.1 - - - +
109I PHE* 1.3 70.9 + - + +
111I LYS* 3.2 13.4 + - - +
112I VAL* 3.1 26.1 + - - +
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Residues in contact with PHE 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I VAL* 3.5 33.1 - - + +
18I LYS* 3.6 35.9 - - + -
19I ALA* 3.5 35.7 - - + -
22I MET* 4.2 8.3 - - - -
105I ALA* 2.9 31.0 + - + -
106I TYR* 3.5 18.8 - + - +
108I GLN* 1.3 80.6 - - + +
110I LEU* 1.3 62.6 + - - +
112I VAL* 3.0 18.0 + - + +
113I CYS* 3.1 16.7 + - - -
125I PHE* 3.7 15.5 - + + -
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Residues in contact with LEU 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H ILE* 3.7 43.3 - - + -
106I TYR 2.7 17.5 + - - +
107I SER 3.3 8.1 - - - +
109I PHE* 1.3 73.9 - - - +
111I LYS* 1.3 62.0 + - - +
113I CYS* 3.0 11.5 + - - +
114I LYS* 3.0 52.1 + - + +
122I ALA* 3.9 20.0 - - + +
125I PHE* 4.0 8.7 - - + -
126I GLU* 3.8 21.5 - - + +
129I ILE* 3.7 12.3 - - + -
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Residues in contact with LYS 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I SER 3.3 9.0 + - - +
108I GLN* 3.2 21.8 + - - +
110I LEU* 1.3 76.8 - - - +
112I VAL* 1.3 66.0 + - - +
114I LYS* 3.2 12.4 + - - +
115I GLU* 3.0 38.6 + - - +
----------------------------------------------------------
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Residues in contact with VAL 112 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I LYS* 4.1 22.7 - - + +
12I VAL* 4.8 1.6 - - + -
15I VAL* 4.0 23.3 - - + -
108I GLN* 3.1 19.5 + - - +
109I PHE* 3.0 11.2 + - + +
111I LYS* 1.3 77.9 - - + +
113I CYS* 1.3 58.1 + - - +
115I GLU* 3.1 14.7 + - - +
116I GLN* 2.8 50.8 + - + +
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Residues in contact with CYS 113 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 4.1 18.8 - - - -
15I VAL* 4.6 3.1 - - - -
109I PHE 3.1 13.7 + - - -
110I LEU 3.0 9.7 + - - +
112I VAL* 1.3 79.1 - - - +
114I LYS* 1.3 61.5 + - - +
116I GLN 3.3 2.3 + - - -
117I GLY 3.1 3.8 + - - -
118I ASP* 2.7 42.2 + - + +
121I THR* 3.3 34.5 - - - -
122I ALA* 3.8 9.2 - - + +
125I PHE* 3.8 17.0 - - - -
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Residues in contact with LYS 114 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H LYS* 4.0 17.6 - - - +
119H ILE* 5.2 5.9 - - - +
110I LEU* 3.0 39.9 + - + +
111I LYS* 3.2 12.3 + - - +
113I CYS* 1.3 77.6 - - - +
115I GLU* 1.3 58.8 + - + +
117I GLY* 2.9 20.1 + - - -
118I ASP 4.8 2.0 - - - +
119I ILE* 5.6 9.1 - - + +
122I ALA* 4.5 11.2 - - + -
126I GLU* 5.1 8.4 + - - -
1804I SO4 2.1 47.1 + - - +
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Residues in contact with GLU 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I LYS* 3.0 29.5 + - - +
112I VAL* 3.5 14.4 + - - +
114I LYS* 1.3 76.8 - - + +
116I GLN* 1.3 69.7 + - - +
117I GLY 3.1 2.6 + - - -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I GLY 4.8 4.0 + - - +
7I ASP* 3.8 2.8 - - - +
8I ARG* 2.8 62.6 + - - +
11I LYS* 3.7 39.1 + - + +
12I VAL* 3.8 23.3 - - + -
112I VAL* 2.8 35.6 + - + +
113I CYS 3.3 1.1 + - - +
114I LYS 3.2 0.2 - - - -
115I GLU* 1.3 85.2 + - - +
117I GLY* 1.3 62.2 + - - +
118I ASP* 3.3 2.3 + - - +
----------------------------------------------------------
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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