Contacts of the helix formed by residues 42 - 70 (chain C) 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 TYR 42 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 3.0 13.7 + - + +
40C MET* 3.7 42.8 - - + -
41C ASP* 1.3 74.3 - - - +
43C GLY* 1.3 53.2 + - - +
44C GLU 3.4 2.2 - - - -
45C LEU* 3.2 15.0 + - + -
46C ALA* 2.8 35.7 + - - +
88C VAL* 4.6 8.7 - - + -
154C LEU* 3.4 48.3 - - + +
157C ILE* 3.5 20.4 - - + -
158C ALA* 3.5 27.6 - - + -
145E HIS* 4.7 6.1 + - - -
148E ASN* 5.1 6.8 + - - +
149E LEU* 3.9 19.7 - - + +
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 5.3 0.7 - - - -
41C ASP* 3.4 7.8 + - - -
42C TYR* 1.3 69.5 - - - +
44C GLU* 1.3 59.6 - - - +
46C ALA* 3.6 2.0 - - - +
47C ALA* 2.8 27.7 + - - +
160C THR* 3.2 26.4 + - - -
161C PRO 3.1 12.0 - - - +
162C SER* 3.4 18.6 - - - -
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR 3.4 0.4 - - - -
43C GLY* 1.3 75.5 - - - +
45C LEU* 1.3 64.9 + - + +
47C ALA* 3.9 4.0 - - + +
48C ASN* 3.0 44.5 + - - +
153C TYR* 5.1 2.9 + - - -
157C ILE* 3.8 24.8 - - + +
160C THR* 2.9 22.2 + - + +
161C PRO 3.4 6.0 + - - +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.6 17.1 - - + +
42C TYR* 3.2 21.9 + - + +
44C GLU* 1.3 81.6 - - + +
46C ALA* 1.3 61.1 + - - +
48C ASN* 4.2 1.0 - - - +
49C MET* 3.2 25.6 + - - +
88C VAL* 4.9 2.9 - - + -
92C TYR* 3.4 30.6 + - + +
138C TYR* 3.9 14.8 + - - +
142C ILE* 3.8 23.3 - - + -
153C TYR* 4.1 13.9 - - + +
154C LEU* 4.0 27.4 - - + -
157C ILE* 3.9 13.6 - - + +
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Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C HIS* 2.8 30.7 + - + +
37C LEU* 3.9 11.4 - - + +
38C ASP* 3.7 39.9 - - - +
42C TYR 2.8 20.3 + - - +
43C GLY* 3.2 7.2 + - - +
45C LEU* 1.3 74.0 - - - +
47C ALA* 1.3 61.7 + - - +
49C MET* 3.4 1.7 + - - +
50C LYS 3.1 9.7 + - - -
162C SER* 4.3 2.7 - - - -
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C HIS* 5.0 0.4 - - - -
43C GLY 2.8 18.5 + - - +
44C GLU* 3.9 5.4 - - + +
46C ALA* 1.3 71.2 - - - +
48C ASN* 1.3 68.8 + - - +
49C MET 3.0 0.3 + - - -
50C LYS* 3.0 4.4 + - - +
51C LEU* 2.9 29.7 + - + +
161C PRO 4.8 1.1 - - - +
162C SER* 3.3 25.0 + - - +
163C SER 3.7 8.3 - - - +
164C THR* 3.6 18.3 - - + +
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Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 3.0 38.2 + - - +
45C LEU 4.3 0.2 - - - +
47C ALA* 1.3 80.4 - - - +
49C MET* 1.3 56.8 + - - +
51C LEU* 3.4 18.5 + - - +
52C ILE* 2.9 34.7 + - - +
138C TYR* 3.1 40.8 + - + +
171D PHE* 4.0 15.5 - - + -
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Residues in contact with MET 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 3.1 39.0 - - - +
33C GLN* 3.3 14.6 - - + +
34C HIS* 3.8 10.3 - - + +
37C LEU* 4.1 6.5 - - + -
45C LEU 3.2 18.7 + - - +
46C ALA 3.7 4.5 - - - +
47C ALA 3.0 0.2 - - - -
48C ASN* 1.3 75.8 - - - +
50C LYS* 1.3 66.7 + - - +
52C ILE* 3.3 6.7 + - - +
53C ALA* 3.0 22.6 + - - +
91C ILE* 3.7 18.6 - - + -
92C TYR* 4.1 12.1 - - + +
95C ASP* 3.3 17.5 - - - +
138C TYR* 4.9 2.4 + - + -
139C TYR* 3.2 33.2 - - + -
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C MET* 3.9 24.7 - - + -
34C HIS* 3.6 31.8 + - + +
46C ALA 3.1 5.8 + - - +
47C ALA 3.0 7.9 + - - +
49C MET* 1.3 77.5 - - - +
51C LEU* 1.3 57.3 + - - +
53C ALA* 3.3 3.3 + - - +
54C ILE* 2.9 37.2 + - + +
164C THR* 3.8 28.5 + - + +
1305C FEC 3.8 28.7 - - + +
61D GLU* 2.8 32.2 + - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA* 2.9 23.8 + - + +
48C ASN* 3.7 21.1 - - - +
50C LYS* 1.3 75.2 - - - +
52C ILE* 1.3 64.7 + - - +
54C ILE* 3.2 8.7 + - + +
55C ASP* 3.2 15.8 + - - -
163C SER 5.8 0.2 - - - +
164C THR* 3.8 35.7 - - + +
169D LYS* 3.3 28.7 - - + +
170D GLY* 3.6 22.8 - - - +
171D PHE* 3.2 19.4 + - + +
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Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 4.1 5.8 - - + -
48C ASN 2.9 20.5 + - - +
49C MET* 3.3 4.7 + - - +
51C LEU* 1.3 76.6 - - - +
53C ALA* 1.3 63.3 + - - +
55C ASP* 3.0 14.3 + - - +
56C GLU* 3.0 19.8 + - - +
135C HIS* 3.7 30.1 - - + +
138C TYR* 3.4 37.0 - - + -
139C TYR* 3.6 32.3 - - + +
171D PHE* 3.5 28.5 - - + -
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Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ILE* 4.2 7.2 - - - +
30C TYR* 4.2 15.8 - - + -
31C MET* 3.7 31.2 - - + -
49C MET 3.0 13.4 + - - +
50C LYS 3.4 9.0 - - - +
52C ILE* 1.3 77.4 - - - +
54C ILE* 1.3 57.2 + - - +
56C GLU* 3.2 12.8 + - - +
57C MET* 3.0 33.3 + - + +
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Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LYS* 2.9 34.2 + - + +
51C LEU* 3.6 17.5 - - + +
52C ILE 3.1 0.6 - - - -
53C ALA* 1.3 76.0 - - - +
55C ASP* 1.3 61.1 + - - +
57C MET* 3.2 28.5 - - + +
58C ARG* 3.1 21.5 + - - +
164C THR* 5.3 1.8 - - - +
1305C FEC 4.4 28.9 - - + -
168D SER* 3.8 30.3 - - - +
169D LYS 3.8 21.3 - - - +
170D GLY* 4.2 4.7 - - - -
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Residues in contact with ASP 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU 3.2 6.5 + - - -
52C ILE 3.0 9.3 + - - +
54C ILE* 1.3 74.9 - - - +
56C GLU* 1.3 65.5 + - - +
58C ARG* 2.6 36.8 + - - +
59C HIS* 3.1 27.9 + - - -
131C GLU* 4.6 2.5 - - - +
135C HIS* 2.7 33.3 + - + -
170D GLY* 3.5 7.1 - - - -
171D PHE* 3.1 22.5 + - - +
172D VAL* 2.9 23.2 + - - +
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLU* 3.3 25.4 - - - +
26C ALA* 4.2 6.7 - - + +
27C ILE* 4.1 15.0 - - + +
30C TYR* 3.5 18.2 - - + -
52C ILE* 3.0 17.4 + - - +
53C ALA* 3.2 13.2 + - - +
55C ASP* 1.3 76.1 - - - +
57C MET* 1.3 57.9 + - - +
59C HIS* 3.0 19.7 + - - +
60C ALA* 2.8 28.4 + - - +
99C GLU* 3.2 11.8 - - - +
132C GLU* 3.4 1.7 - - - +
135C HIS* 3.2 8.2 + - - -
200C FE 2.1 32.4 - - - -
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Residues in contact with MET 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ILE* 3.6 24.2 - - + +
31C MET* 4.5 5.2 - - + -
50C LYS* 6.0 0.2 - - + -
53C ALA* 3.0 32.7 + - + +
54C ILE* 3.2 20.2 - - + +
56C GLU* 1.3 77.3 - - - +
58C ARG* 1.3 61.6 + - - +
60C ALA* 3.4 3.6 + - - +
61C GLU* 3.0 22.5 + - - +
1305C FEC 2.4 109.2 - - + +
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Residues in contact with ARG 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ILE* 3.1 7.9 + - - +
55C ASP* 2.6 43.5 + - - +
57C MET* 1.3 79.3 - - - +
59C HIS* 1.3 59.9 + - - +
61C GLU* 3.5 11.3 + - - +
62C ASN* 2.9 46.6 + - - +
131C GLU* 3.7 17.5 + - - -
1305C FEC 3.6 20.9 - - + +
167D ALA* 5.3 5.6 - - - -
168D SER* 2.8 37.7 + - - +
170D GLY* 5.4 0.4 - - - -
172D VAL* 3.6 18.8 - - - +
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Residues in contact with HIS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLU* 3.0 30.9 + - + +
55C ASP 3.1 13.9 + - - -
56C GLU* 3.0 30.6 + - - +
58C ARG* 1.3 81.1 - - + +
60C ALA* 1.3 67.5 + - - +
61C GLU 3.0 1.1 - - - -
62C ASN* 3.1 3.8 + - - +
63C PHE* 2.9 31.5 + - - -
128C ILE* 3.7 38.7 - - + +
131C GLU* 2.7 38.5 + - + +
132C GLU* 3.6 13.2 - - - -
135C HIS* 4.2 3.8 - + - -
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ARG* 2.6 37.0 + - + +
23C GLU* 3.9 17.1 - - + +
24C LEU* 4.5 5.2 - - + -
27C ILE* 4.5 5.2 - - + -
56C GLU 2.8 15.0 + - - +
57C MET 3.6 7.4 - - - +
59C HIS* 1.3 72.8 - - - +
61C GLU* 1.3 56.0 + - - +
63C PHE* 3.7 2.4 + - - +
64C ALA 3.0 16.1 + - - -
1305C FEC 3.6 25.8 - - + +
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C MET 3.0 16.3 + - - +
58C ARG* 3.6 10.4 - - - +
59C HIS 3.0 0.4 - - - -
60C ALA* 1.3 75.8 - - - +
62C ASN* 1.3 64.4 + - - +
64C ALA* 3.2 1.9 + - - +
65C GLU* 2.9 52.9 + - - +
1305C FEC 3.5 32.3 + - + +
31D MET* 4.3 0.5 - - - +
34D HIS* 4.1 8.3 + - - -
35D TYR* 3.5 21.5 - - + +
50D LYS* 3.0 35.9 + - - +
1401D SO4 4.1 7.4 + - - -
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Residues in contact with ASN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ARG* 2.9 34.2 + - - +
59C HIS* 3.1 7.1 + - - +
61C GLU* 1.3 76.5 + - - +
63C PHE* 1.3 66.3 + - - +
65C GLU* 3.1 22.1 + - - +
66C ARG* 2.9 24.1 + - - +
124C LEU* 3.8 27.2 - - + +
127C ARG* 5.0 7.7 + - - +
128C ILE* 4.6 4.7 - - + +
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Residues in contact with PHE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.3 27.6 - - + +
19C ALA* 3.6 11.9 - - + -
20C ARG* 3.9 31.4 - - + -
23C GLU* 3.9 17.3 - - + -
59C HIS 2.9 20.8 + - - +
60C ALA 3.8 3.8 - - - +
62C ASN* 1.3 75.6 - - - +
64C ALA* 1.3 53.3 + - - +
66C ARG* 2.9 3.8 + - - +
67C ILE* 2.8 39.3 + - - +
106C TYR* 3.9 5.6 - + - -
124C LEU* 3.7 16.4 - - + -
125C PHE* 3.7 35.4 - + - -
128C ILE* 3.3 35.9 - - + -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ARG* 3.5 7.5 - - - +
60C ALA 3.0 16.2 + - - +
61C GLU 3.2 2.0 + - - +
63C PHE* 1.3 75.9 - - - +
65C GLU* 1.3 57.5 + - - +
67C ILE* 3.2 4.2 + - - +
68C LYS* 2.9 32.7 + - - +
74C PRO* 3.6 17.1 - - + +
35D TYR* 3.3 45.5 - - + -
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLU* 2.9 40.7 + - + +
62C ASN* 3.1 30.7 + - - +
64C ALA* 1.3 73.8 - - - +
66C ARG* 1.3 62.6 + - - +
68C LYS* 3.1 9.2 + - - +
69C GLU* 3.0 31.2 + - + +
34D HIS* 4.9 3.6 + - - -
35D TYR* 4.6 10.8 - - + -
38D ASP* 4.3 13.3 - - - +
1401D SO4 5.3 3.3 + - - -
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.6 15.5 - - + -
62C ASN 2.9 12.6 + - - +
63C PHE 2.9 8.4 + - - +
65C GLU* 1.3 76.3 - - - +
67C ILE* 1.3 64.5 + - - +
69C GLU* 2.8 57.6 + - - +
70C LEU* 3.1 33.9 + - + +
118C ASP* 3.1 22.8 + - - -
120C VAL* 3.4 30.4 - - - +
121C THR* 2.7 27.8 + - + +
124C LEU* 3.9 15.0 - - + -
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Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 4.3 10.7 - - + +
16C LEU* 3.5 39.3 - - + +
17C ASN* 3.0 33.4 - - - +
20C ARG* 4.2 6.3 - - - -
63C PHE 2.8 19.3 + - - +
64C ALA 3.5 6.7 - - - +
66C ARG* 1.3 72.4 - - - +
68C LYS* 1.3 59.3 + - - +
70C LEU* 3.5 5.8 + - - +
71C GLY 3.5 2.6 + - - -
72C GLY* 2.8 52.7 + - - +
73C GLU 3.5 5.8 - - - +
74C PRO* 3.5 23.1 - - + -
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Residues in contact with LYS 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA 2.9 17.5 + - - +
65C GLU* 3.5 11.7 - - - +
66C ARG 3.0 0.2 - - - -
67C ILE* 1.3 77.2 - - - +
69C GLU* 1.3 64.5 + - - +
71C GLY* 3.1 14.0 + - - -
72C GLY 3.6 16.0 + - - +
73C GLU* 3.6 21.0 + - - -
74C PRO* 3.8 11.9 - - + -
35D TYR* 3.6 43.1 - - + +
36D SER* 3.8 18.9 + - - +
39D ASP* 3.9 38.1 + - + +
85D GLY* 6.2 0.2 - - - -
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 3.0 19.3 + - - +
66C ARG* 2.8 46.3 + - - +
68C LYS* 1.3 77.1 - - + +
70C LEU* 1.3 60.5 + - - +
71C GLY 3.3 1.0 + - - -
120C VAL* 4.7 4.0 - - - +
39D ASP* 5.2 3.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LYS* 3.8 43.0 - - + +
12C VAL* 3.7 23.3 - - + -
13C ILE* 3.8 25.3 - - + +
16C LEU* 3.9 17.9 - - + -
66C ARG* 3.1 42.1 + - - +
67C ILE 3.5 0.9 + - - +
68C LYS 3.1 0.8 - - - -
69C GLU* 1.3 77.8 - - - +
71C GLY* 1.3 59.3 - - - +
72C GLY 3.4 0.8 + - - -
118C ASP* 3.7 20.0 - - - +
----------------------------------------------------------
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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).
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