Contacts of the helix formed by residues 87 - 116 (chain K) in PDB entry 1NF4
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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K MET* 6.0 1.1 - - - -
85K GLY 3.4 3.4 + - - -
86K GLN* 1.3 74.7 - - - +
88K VAL* 1.3 66.8 + - - +
89K PRO* 3.3 11.9 - - + -
90K VAL* 2.9 17.8 + - + +
91K ILE* 2.8 20.5 + - - +
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Residues in contact with VAL 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K LEU* 4.5 11.0 - - + -
40K MET* 3.9 30.4 - - + +
42K TYR* 4.6 12.3 - - + -
45K LEU* 5.2 1.6 - - + -
86K GLN 3.9 0.4 + - - -
87K ALA* 1.3 70.0 - - - +
89K PRO* 1.3 72.6 - - + +
91K ILE* 3.1 18.1 + - - +
92K TYR* 3.1 28.2 - - + -
146K ILE* 3.3 30.7 - - + -
154K LEU* 4.4 21.5 - - + -
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Residues in contact with PRO 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87K ALA* 3.4 13.7 - - + -
88K VAL* 1.3 97.1 - - + +
90K VAL* 1.3 60.9 + - + +
92K TYR* 3.5 2.2 + - + +
93K GLU* 3.1 26.4 + - - +
143K GLY* 6.0 0.6 - - - -
146K ILE* 4.1 28.9 - - + -
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Residues in contact with VAL 90 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K GLN* 3.9 24.0 - - + +
87K ALA* 2.9 26.7 + - + +
89K PRO* 1.3 78.8 - - + +
91K ILE* 1.3 66.8 + - - +
93K GLU* 4.6 14.4 - - - +
94K SER* 3.0 34.4 + - - +
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Residues in contact with ILE 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K GLN* 3.8 35.4 - - + +
36K SER* 5.2 1.8 - - - -
37K LEU* 4.3 20.4 - - + -
40K MET* 5.0 7.0 - - + -
49K MET* 3.6 31.2 - - + -
86K GLN* 3.7 29.6 - - + +
87K ALA 2.8 15.3 + - - +
88K VAL* 3.3 16.6 - - - +
90K VAL* 1.3 77.1 - - - +
92K TYR* 1.3 70.4 + - + +
94K SER* 4.1 0.2 - - - -
95K ASP* 3.0 35.2 + - - +
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Residues in contact with TYR 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K LEU* 3.3 29.6 - - + +
45K LEU* 3.5 22.5 + - + +
49K MET* 3.9 16.2 - - + +
88K VAL* 3.1 31.2 + - + +
89K PRO* 4.4 2.7 - - + +
90K VAL 3.3 0.4 - - - -
91K ILE* 1.3 88.2 - - + +
93K GLU* 1.3 64.7 + - - +
95K ASP* 4.5 1.6 - - - -
96K ALA* 3.1 23.9 + - - +
138K TYR* 4.5 4.6 + + - -
139K TYR* 3.7 30.7 - + - +
142K ILE* 3.7 33.9 - - + -
143K GLY* 3.9 24.0 - - - -
146K ILE* 3.7 17.5 - - + -
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Residues in contact with GLU 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K PRO 3.1 18.2 + - - +
90K VAL* 4.1 17.1 - - - +
92K TYR* 1.3 76.9 - - - +
94K SER* 1.3 69.6 + - - +
96K ALA* 3.4 5.1 + - - +
97K ASP* 3.1 34.6 + - - +
143K GLY* 5.4 1.2 - - - -
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Residues in contact with SER 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K GLN* 3.8 20.7 + - - -
90K VAL* 3.0 26.2 + - - +
91K ILE 4.1 1.1 - - - -
93K GLU* 1.3 80.3 + - - +
95K ASP* 1.3 65.0 + - - +
97K ASP* 3.4 8.9 + - - +
98K GLN* 2.7 29.5 + - - +
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Residues in contact with ASP 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K GLN* 4.6 3.5 - - - +
30K TYR* 3.3 18.4 - - + -
33K GLN* 2.6 40.9 + - - +
49K MET* 3.3 15.8 - - - +
91K ILE* 3.0 20.5 + - - +
92K TYR 4.1 0.9 - - - +
94K SER* 1.3 74.0 - - - +
96K ALA* 1.3 60.4 + - - +
98K GLN* 3.0 7.4 + - - +
99K GLU* 2.8 34.0 + - - +
139K TYR* 3.4 30.0 - - + -
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Residues in contact with ALA 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K TYR 3.1 18.4 + - - +
93K GLU* 3.8 4.9 - - - +
95K ASP* 1.3 76.4 - - - +
97K ASP* 1.3 64.4 + - - +
99K GLU* 3.2 0.4 + - - -
100K ASP* 2.9 23.1 + - - +
136K LEU* 3.3 24.4 - - + +
139K TYR* 3.9 11.1 - - + +
140K GLU* 4.1 20.4 - - + +
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Residues in contact with ASP 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93K GLU* 3.1 28.0 + - - +
94K SER* 3.5 9.8 - - - +
96K ALA* 1.3 75.6 - - - +
98K GLN* 1.3 59.0 + - - +
100K ASP* 3.4 6.1 + - - +
101K ALA* 2.9 30.3 + - - +
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Residues in contact with GLN 98 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K MET 5.5 0.2 + - - -
25K HIS* 3.1 29.5 + - - -
26K ALA* 3.6 30.9 - - - +
29K GLN* 4.2 8.2 - - - +
30K TYR* 3.5 26.8 + - - +
94K SER 2.7 21.7 + - - +
95K ASP* 3.0 9.2 + - - +
97K ASP* 1.3 73.8 - - - +
99K GLU* 1.3 56.1 + - - +
101K ALA* 3.3 5.7 + - - +
102K THR* 2.9 36.7 + - - +
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Residues in contact with GLU 99 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K TYR* 2.6 26.4 + - - +
56K GLU* 3.2 2.6 - - - +
95K ASP 2.8 22.4 + - - +
96K ALA 3.8 2.9 - - - +
98K GLN* 1.3 69.7 - - - +
100K ASP* 1.3 66.4 + - - +
102K THR* 3.2 6.8 + - - -
103K ILE* 3.0 30.3 + - - +
132K GLU* 3.0 20.7 - - - +
135K HIS* 3.5 15.8 + - + +
136K LEU* 3.9 19.7 - - + +
139K TYR* 3.6 16.9 - - + -
201K FE2 2.2 31.5 - - - -
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Residues in contact with ASP 100 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K ALA 2.9 17.0 + - - +
97K ASP* 3.7 6.7 - - - +
99K GLU* 1.3 77.3 - - - +
101K ALA* 1.3 64.1 + - - +
103K ILE* 3.3 4.9 + - - +
104K GLU* 3.1 21.8 + - - +
136K LEU* 4.0 22.6 - - + +
5P ARG* 2.9 42.7 + - - -
9P LYS* 5.1 2.6 + - - -
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Residues in contact with ALA 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K MET* 4.5 4.5 - - + +
97K ASP 2.9 18.4 + - - +
98K GLN* 3.8 6.5 - - + +
100K ASP* 1.3 78.4 + - - +
102K THR* 1.3 62.6 + - - +
104K GLU* 3.5 8.6 + - - +
105K ALA* 3.0 24.8 + - - +
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Residues in contact with THR 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K MET* 4.0 19.4 - - + +
23K GLU* 5.1 0.7 - - - +
98K GLN* 2.9 27.5 + - - +
99K GLU* 3.5 15.4 + - - +
100K ASP 3.1 0.2 - - - -
101K ALA* 1.3 75.4 - - - +
103K ILE* 1.3 60.2 + - - +
104K GLU 3.3 0.2 + - - -
105K ALA 3.3 0.5 + - - -
106K TYR* 2.9 67.1 + - + +
132K GLU* 4.0 18.6 - - + -
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Residues in contact with ILE 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K GLU 3.0 20.9 + - - +
100K ASP* 3.3 5.6 + - - +
102K THR* 1.3 74.9 - - - +
104K GLU* 1.3 60.3 + - - +
106K TYR* 3.9 4.3 - - - +
107K SER* 2.7 43.5 + - - +
129K ILE* 4.1 22.4 - - + +
132K GLU* 3.8 20.2 - - + +
133K GLN* 3.9 35.4 - - + +
136K LEU* 3.9 21.3 - - + -
5P ARG* 6.3 0.4 - - - +
120P VAL* 5.5 4.0 - - + -
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Residues in contact with GLU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K ASP* 3.1 14.9 + - - +
101K ALA* 3.6 12.1 - - - +
102K THR 3.2 0.2 - - - -
103K ILE* 1.3 83.6 - - + +
105K ALA* 1.3 62.5 + - - +
107K SER* 3.5 6.2 + - - -
108K GLN* 3.4 20.1 + - - +
5P ARG* 3.3 43.3 + - - +
8P ARG* 2.9 40.8 + - - -
117P GLY 5.0 1.4 - - - +
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Residues in contact with ALA 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K MET* 4.1 25.4 - - + -
101K ALA 3.0 15.1 + - - +
102K THR 3.9 2.0 - - - +
104K GLU* 1.3 78.3 - - - +
106K TYR* 1.3 65.2 + - - +
108K GLN* 3.0 12.7 + - - +
109K PHE* 3.0 33.4 + - + -
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Residues in contact with TYR 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K ALA* 3.2 41.0 + - + -
22K MET* 4.1 17.2 - - - +
23K GLU* 2.7 30.5 + - - +
63K PHE* 3.7 3.8 - + - -
102K THR* 2.9 47.8 + - + +
103K ILE 3.9 0.2 - - - +
105K ALA* 1.3 74.4 - - + +
107K SER* 1.3 57.3 + - - +
109K PHE* 3.1 17.3 + + - +
110K LEU* 2.8 29.8 + - - +
125K PHE* 4.1 14.5 - + + -
128K ILE* 3.8 18.8 - - + -
129K ILE* 3.5 26.4 - - + +
132K GLU* 3.6 9.4 - - + -
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Residues in contact with SER 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K ILE* 2.7 30.0 + - - +
104K GLU* 3.7 8.9 + - - -
106K TYR* 1.3 77.5 - - - +
108K GLN* 1.3 61.3 + - - +
110K LEU* 3.5 4.7 + - - +
111K LYS* 3.3 20.4 + - - +
129K ILE* 3.6 17.5 - - - +
8P ARG* 5.9 1.6 - - - -
117P GLY* 4.3 16.2 + - - -
119P ILE* 3.6 24.6 + - - +
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Residues in contact with GLN 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K GLU 3.4 9.8 + - - +
105K ALA* 3.0 14.0 + - - +
107K SER* 1.3 76.6 - - - +
109K PHE* 1.3 67.8 + - + +
111K LYS* 3.0 57.6 + - - +
112K VAL* 3.0 16.8 + - + +
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Residues in contact with PHE 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K VAL* 3.7 37.9 - - + +
18K LYS* 3.8 35.9 - - + -
19K ALA* 3.9 16.2 - - + -
22K MET* 4.3 8.1 - - - -
105K ALA* 3.0 25.1 + - + -
106K TYR* 3.1 18.8 + + - +
108K GLN* 1.3 77.9 - - + +
110K LEU* 1.3 65.6 + - - +
112K VAL* 3.1 11.7 + - + +
113K CYS* 3.0 26.6 + - - -
125K PHE* 3.6 28.3 - + + -
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Residues in contact with LEU 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K TYR 2.8 12.6 + - - +
107K SER* 3.6 10.5 - - - +
108K GLN 3.2 0.2 - - - -
109K PHE* 1.3 75.8 - - - +
111K LYS* 1.3 58.0 + - - +
113K CYS* 3.0 9.7 + - - +
114K LYS* 2.9 73.8 + - + +
122K ALA* 3.7 29.4 - - + +
125K PHE* 4.1 10.5 - - + -
126K GLU* 3.7 28.3 - - + +
129K ILE* 4.4 2.0 - - + -
119P ILE* 3.9 27.1 - - + -
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Residues in contact with LYS 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K SER 3.3 10.1 + - - +
108K GLN* 3.0 49.2 + - - +
110K LEU* 1.3 79.8 - - - +
112K VAL* 1.3 54.2 + - + +
114K LYS* 3.3 15.8 + - + +
115K GLU* 2.9 54.5 + - + +
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Residues in contact with VAL 112 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K LYS* 4.2 17.5 - - + +
12K VAL* 5.1 0.4 - - - +
15K VAL* 4.0 31.0 - - + -
108K GLN* 3.0 22.1 + - - +
109K PHE* 3.1 9.4 + - + +
111K LYS* 1.3 76.9 - - + +
113K CYS* 1.3 58.1 + - - +
115K GLU* 3.3 15.9 + - - +
116K GLN* 3.0 47.1 + - + +
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Residues in contact with CYS 113 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K VAL* 3.9 17.9 - - - -
15K VAL* 4.4 3.6 - - - -
109K PHE 3.0 19.1 + - - -
110K LEU 3.0 8.2 + - - +
112K VAL* 1.3 75.1 - - - +
114K LYS* 1.3 64.9 + - - +
116K GLN 3.2 2.1 + - - -
117K GLY 3.1 3.6 + - - -
118K ASP* 2.9 44.0 + - + +
121K THR* 3.3 33.0 - - - -
122K ALA* 3.8 9.2 - - + +
125K PHE* 3.8 15.9 - - - -
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Residues in contact with LYS 114 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F LYS* 5.5 6.1 - - - -
114F LYS* 4.5 4.5 - - - +
110K LEU* 2.9 45.3 + - + +
111K LYS* 3.7 13.7 - - + +
113K CYS* 1.3 75.4 - - - +
115K GLU* 1.3 59.5 + - + +
117K GLY* 2.9 20.5 + - - -
118K ASP 4.9 1.8 - - - +
119K ILE* 5.7 8.5 - - + +
122K ALA* 4.3 10.8 - - + -
114P LYS* 3.9 15.0 - - - +
119P ILE* 4.8 8.9 - - - +
1504P SO4 2.5 48.8 + - - +
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Residues in contact with GLU 115 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K LYS* 2.9 46.8 + - + +
112K VAL* 3.4 19.8 - - - +
113K CYS 3.2 0.2 - - - -
114K LYS* 1.3 76.5 - - + +
116K GLN* 1.3 73.3 + - - +
117K GLY 3.2 1.4 + - - -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ARG* 2.8 61.7 + - + +
11K LYS* 3.9 40.4 + - + +
12K VAL* 4.0 19.7 - - + -
112K VAL* 3.0 24.9 + - + +
113K CYS 3.2 0.9 + - - +
114K LYS 3.2 0.4 - - - -
115K GLU* 1.3 91.7 + - - +
117K GLY* 1.3 63.3 + - - +
118K ASP* 3.3 2.2 + - - +
----------------------------------------------------------
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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