Contacts of the helix formed by residues 42 - 70 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F HIS* 4.3 8.4 - + - -
148F ASN* 5.0 9.0 + - - +
149F LEU* 4.2 13.2 - - + +
37L LEU* 2.9 13.6 + - + +
40L MET* 3.9 30.5 - - + -
41L ASP* 1.3 76.2 - - - +
43L GLY* 1.3 53.5 + - - +
44L GLU 3.4 2.5 - - - -
45L LEU* 3.1 20.0 + - + -
46L ALA* 2.9 33.1 + - - +
88L VAL* 4.2 25.1 - - + -
154L LEU* 3.7 43.9 - - + +
157L ILE* 3.7 19.1 - - + -
158L ALA* 3.7 27.4 - - + -
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Residues in contact with GLY 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ASP* 5.2 0.9 - - - -
41L ASP* 3.5 6.5 + - - -
42L TYR* 1.3 70.9 - - - +
44L GLU* 1.3 52.8 + - - +
46L ALA* 3.1 3.0 + - - -
47L ALA* 2.7 32.1 + - - +
160L THR* 3.3 29.9 + - - -
161L PRO 3.2 9.4 - - - +
162L SER* 3.4 19.7 - - - -
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Residues in contact with GLU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L TYR 3.4 0.6 - - - -
43L GLY* 1.3 72.2 - - - +
45L LEU* 1.3 65.6 + - + +
47L ALA* 4.1 3.7 - - - +
48L ASN* 3.2 38.9 + - - +
156L LYS* 6.1 0.3 - - - -
157L ILE* 3.1 32.3 - - + +
160L THR* 2.9 32.7 + - - +
161L PRO* 3.5 6.5 + - + +
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Residues in contact with LEU 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L LEU* 3.4 20.5 - - + +
42L TYR* 3.1 22.4 + - + +
44L GLU* 1.3 81.3 - - + +
46L ALA* 1.3 62.2 + - - +
48L ASN* 4.1 1.2 - - - +
49L MET* 3.1 26.0 + - - +
88L VAL* 4.7 4.3 - - + -
92L TYR* 3.2 32.4 + - + +
138L TYR* 4.0 15.2 + - - +
142L ILE* 4.0 25.4 - - + -
153L TYR* 4.7 5.6 - - + +
154L LEU* 4.2 23.1 - - + -
157L ILE* 3.9 18.2 - - + -
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Residues in contact with ALA 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L HIS* 2.7 31.4 + - + +
37L LEU* 3.7 10.3 - - + +
38L ASP* 3.6 44.9 - - + +
42L TYR 2.9 13.0 + - - +
43L GLY 3.6 7.4 - - - +
45L LEU* 1.3 76.0 - - - +
47L ALA* 1.3 64.2 + - - +
49L MET* 3.5 1.0 + - - +
50L LYS 3.3 8.0 + - - -
162L SER* 4.4 1.8 - - - -
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Residues in contact with ALA 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L HIS* 5.0 0.2 - - - -
43L GLY 2.7 19.3 + - - +
44L GLU* 4.1 4.7 - - - +
46L ALA* 1.3 72.6 - - - +
48L ASN* 1.3 59.7 + - - +
50L LYS* 3.4 5.4 + - - +
51L LEU* 3.1 34.2 + - + +
161L PRO 4.5 2.7 - - - +
162L SER* 3.3 26.9 + - - +
163L SER 3.7 14.6 - - - +
164L THR* 3.6 8.0 - - + +
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Residues in contact with ASN 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K PHE* 3.9 21.1 - - + -
44L GLU* 3.2 22.7 + - - +
45L LEU 4.2 0.2 - - - +
47L ALA* 1.3 78.5 - - - +
49L MET* 1.3 59.3 + - - +
51L LEU* 3.7 16.1 - - - +
52L ILE* 2.9 36.6 + - - +
138L TYR* 3.2 40.3 + - + +
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Residues in contact with MET 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 3.2 31.3 - - - +
33L GLN* 3.4 18.8 - - + +
34L HIS* 3.7 13.5 - - + +
37L LEU* 4.0 8.1 - - + -
45L LEU 3.1 19.8 + - - +
46L ALA 3.8 4.7 - - - +
47L ALA 3.3 0.2 - - - -
48L ASN* 1.3 78.0 - - - +
50L LYS* 1.3 56.4 + - - +
52L ILE* 3.6 5.7 + - - +
53L ALA* 3.1 24.9 + - - +
91L ILE* 3.6 17.7 - - + -
92L TYR* 3.9 14.1 - - + +
95L ASP* 3.2 18.8 - - - +
138L TYR* 4.9 1.0 + - - -
139L TYR* 3.5 31.4 - - + -
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Residues in contact with LYS 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K GLU* 2.7 28.4 + - - +
2104K FEC 2.8 47.1 + - + -
31L MET* 4.0 20.9 - - + -
34L HIS* 3.6 28.2 + - + +
46L ALA 3.3 3.2 + - - -
47L ALA 3.6 8.7 - - - +
49L MET* 1.3 77.4 - - - +
51L LEU* 1.3 59.0 + - - +
53L ALA* 3.2 3.5 + - - +
54L ILE* 2.8 36.4 + - + +
164L THR* 3.9 8.3 - - + -
2201L SO4 2.8 34.2 + - - +
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Residues in contact with LEU 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K LYS* 3.2 31.4 - - + +
170K GLY* 3.5 10.4 - - - +
171K PHE* 3.1 31.4 + - + +
47L ALA* 3.1 22.3 + - + +
48L ASN* 3.2 24.2 + - - +
50L LYS* 1.3 72.9 - - - +
52L ILE* 1.3 65.0 + - - +
54L ILE* 3.3 6.1 + - + +
55L ASP* 3.1 15.2 + - - +
163L SER 5.8 0.2 - - - +
164L THR* 3.9 33.2 - - + +
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Residues in contact with ILE 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K PHE* 3.5 25.1 - - + -
30L TYR* 4.1 11.4 - - + -
48L ASN 2.9 20.9 + - - +
49L MET* 3.9 2.5 - - - +
51L LEU* 1.3 74.0 - - - +
53L ALA* 1.3 66.8 + - - +
55L ASP* 3.0 12.5 + - - +
56L GLU* 3.1 18.7 + - - +
135L HIS* 3.7 33.2 - - + +
138L TYR* 3.5 37.2 - - + -
139L TYR* 3.3 35.2 - - + +
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Residues in contact with ALA 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L ILE* 4.3 5.8 - - - +
30L TYR* 4.2 13.0 - - + -
31L MET* 3.7 31.2 - - + -
49L MET 3.1 15.8 + - - +
50L LYS 3.2 9.4 + - - +
52L ILE* 1.3 78.0 - - - +
54L ILE* 1.3 62.3 + - - +
56L GLU* 3.0 13.4 + - - +
57L MET* 3.0 29.2 + - + +
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Residues in contact with ILE 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168K SER* 3.5 32.3 - - - +
169K LYS 3.8 22.4 - - - +
170K GLY* 4.2 4.5 - - - -
2104K FEC 4.3 27.8 - - + +
50L LYS* 2.8 44.6 + - + +
51L LEU* 3.7 11.0 - - + +
52L ILE 3.2 0.4 - - - -
53L ALA* 1.3 75.8 - - - +
55L ASP* 1.3 63.2 + - - +
57L MET* 3.2 25.4 + - + +
58L ARG* 3.1 21.0 + - - +
164L THR* 5.3 2.9 - - - +
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Residues in contact with ASP 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170K GLY* 3.1 1.4 - - - -
171K PHE* 2.9 23.4 + - - +
172K VAL* 3.0 28.2 + - - +
51L LEU 3.1 3.7 + - - -
52L ILE 3.0 8.6 + - - +
54L ILE* 1.3 76.8 - - - +
56L GLU* 1.3 57.3 - - - +
58L ARG* 2.7 39.2 + - - +
59L HIS* 2.9 36.9 + - - +
131L GLU* 4.8 0.2 - - - +
135L HIS* 2.7 34.8 + - + -
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Residues in contact with GLU 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L GLU* 3.2 23.0 - - - +
26L ALA* 4.1 8.0 - - + +
27L ILE* 3.9 15.7 - - + +
30L TYR* 3.6 18.3 - - + -
52L ILE* 3.1 18.2 - - - +
53L ALA* 3.0 12.1 + - - +
55L ASP* 1.3 72.3 - - - +
57L MET* 1.3 60.2 + - - +
59L HIS* 3.2 18.6 + - - +
60L ALA* 2.9 30.3 + - - +
99L GLU* 3.3 11.8 - - - +
132L GLU* 3.4 2.5 - - - +
135L HIS* 3.3 7.2 + - - -
200L FE 2.1 33.0 - - - -
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Residues in contact with MET 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2104K FEC 2.4 115.4 - - + +
27L ILE* 3.7 27.3 - - + +
31L MET* 4.5 6.3 - - + -
50L LYS* 6.1 0.2 - - + -
53L ALA* 3.0 32.1 + - + +
54L ILE* 3.3 18.2 - - + +
56L GLU* 1.3 77.2 - - - +
58L ARG* 1.3 57.4 + - - +
60L ALA* 3.4 2.4 + - - +
61L GLU 3.0 21.1 + - - -
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Residues in contact with ARG 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ALA* 5.3 9.2 - - - +
168K SER* 2.7 40.8 + - - +
170K GLY* 3.8 5.9 - - - -
172K VAL* 4.2 9.3 + - - +
2104K FEC 5.1 2.9 - - + +
54L ILE* 3.1 8.9 + - - +
55L ASP* 2.7 44.7 + - - +
57L MET* 1.3 73.6 - - - +
59L HIS* 1.3 62.5 + - + +
61L GLU* 3.2 20.2 + - - +
62L ASN* 2.9 48.8 + - - +
131L GLU* 3.7 27.3 + - - -
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Residues in contact with HIS 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L GLU* 3.2 24.7 + - + +
55L ASP* 2.9 20.7 + - - +
56L GLU* 3.2 30.9 + - - +
58L ARG* 1.3 80.6 - - + +
60L ALA* 1.3 56.5 + - - +
62L ASN* 3.2 5.1 + - - +
63L PHE* 2.8 36.9 + - + -
128L ILE* 3.4 41.4 - - + +
131L GLU* 2.5 41.8 + - + +
132L GLU* 3.4 14.3 + - - -
135L HIS* 4.2 3.6 - + - -
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Residues in contact with ALA 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2104K FEC 4.6 3.6 - - + -
20L ARG* 2.8 39.4 + - + +
23L GLU* 3.7 19.4 - - + +
24L LEU* 4.3 7.4 - - + -
27L ILE* 4.2 12.8 - - + -
56L GLU 2.9 17.9 + - - +
57L MET 3.5 6.1 - - - +
59L HIS* 1.3 77.0 - - - +
61L GLU* 1.3 57.4 + - - +
63L PHE* 3.5 2.6 + - - +
64L ALA 3.0 17.3 + - - -
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Residues in contact with GLU 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K MET* 4.3 1.6 - - - +
34K HIS* 4.3 7.3 + - - +
35K TYR* 3.5 19.3 + - + +
50K LYS* 2.5 39.6 + - - +
2101K SO4 4.2 6.6 + - - -
2104K FEC 3.5 21.4 - - + +
57L MET 3.0 15.8 + - - +
58L ARG* 3.5 23.3 - - - +
59L HIS 3.2 0.2 - - - -
60L ALA* 1.3 75.8 - - - +
62L ASN* 1.3 62.6 - - - +
64L ALA* 3.2 2.8 + - - +
65L GLU* 2.8 53.0 + - - +
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Residues in contact with ASN 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L ARG* 2.9 40.0 + - - +
59L HIS* 3.9 9.6 - - - +
61L GLU* 1.3 76.1 - - - +
63L PHE* 1.3 68.3 + - - +
65L GLU* 3.2 19.7 - - - +
66L ARG* 3.1 24.1 + - - +
124L LEU* 4.0 25.2 - - + +
128L ILE* 4.5 9.2 - - + +
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Residues in contact with PHE 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L LEU* 3.5 26.5 - - + +
19L ALA* 3.7 15.3 - - + -
20L ARG* 4.0 24.5 - - + -
23L GLU* 3.8 14.4 - - + -
59L HIS 2.8 25.2 + - - +
60L ALA* 3.7 4.9 - - - +
62L ASN* 1.3 78.2 - - - +
64L ALA* 1.3 61.8 + - - +
66L ARG* 3.2 3.1 + - - +
67L ILE* 3.0 27.4 + - - +
106L TYR* 3.6 30.7 - + - -
124L LEU* 3.8 13.5 - - + -
125L PHE* 3.7 29.4 - + - -
128L ILE* 3.7 25.8 - - + -
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Residues in contact with ALA 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K TYR* 3.5 32.1 - - + -
20L ARG* 3.6 14.5 - - - +
60L ALA 3.0 18.0 + - - +
61L GLU 3.2 5.1 + - - +
63L PHE* 1.3 73.8 - - - +
65L GLU* 1.3 65.3 + - - +
67L ILE* 3.3 4.9 + - - +
68L LYS* 2.9 27.4 + - - +
74L PRO* 3.9 15.7 - - + +
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Residues in contact with GLU 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K HIS* 5.2 4.1 + - - +
35K TYR* 4.6 11.4 - - + -
38K ASP* 4.4 15.5 - - - +
2101K SO4 5.3 5.9 + - - -
61L GLU* 2.8 40.6 + - + +
62L ASN* 3.2 34.1 + - - +
63L PHE 3.3 0.2 - - - -
64L ALA* 1.3 76.5 - - - +
66L ARG* 1.3 57.5 + - - +
68L LYS* 3.2 10.2 + - - +
69L GLU* 2.9 37.8 + - + +
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Residues in contact with ARG 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L LEU* 3.8 12.8 - - + -
62L ASN 3.1 16.6 + - - +
63L PHE 3.7 3.8 - - - +
65L GLU* 1.3 75.3 - - - +
67L ILE* 1.3 59.6 + - - +
69L GLU* 3.1 37.6 + - - +
70L LEU* 2.9 56.2 + - - +
118L ASP* 3.0 25.1 + - - -
120L VAL* 3.6 32.3 - - - +
121L THR* 2.8 26.0 + - + +
124L LEU* 4.1 14.4 - - + -
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Residues in contact with ILE 67 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L ILE* 4.3 12.1 - - + +
16L LEU* 3.5 35.2 - - + +
17L ASN* 3.2 31.2 - - - +
20L ARG* 4.1 10.1 - - - -
63L PHE 3.0 19.9 + - - +
64L ALA* 3.5 5.6 - - - +
66L ARG* 1.3 74.7 - - - +
68L LYS* 1.3 62.6 + - - +
70L LEU* 3.1 6.5 + - - +
71L GLY 3.0 4.3 + - - -
72L GLY* 2.8 53.2 + - - +
73L GLU 3.6 2.7 - - - +
74L PRO* 3.6 22.0 - - + -
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Residues in contact with LYS 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K ASN 5.1 0.4 - - - -
35K TYR* 3.7 45.1 - - + +
36K SER* 3.5 20.2 + - - +
39K ASP* 4.0 33.5 + - + +
64L ALA 2.9 16.5 + - - +
65L GLU* 3.3 11.9 - - - +
67L ILE* 1.3 77.0 - - - +
69L GLU* 1.3 63.0 + - + +
71L GLY* 2.9 14.7 + - - -
72L GLY 3.6 15.1 + - - +
73L GLU* 3.4 22.8 + - - -
74L PRO* 4.2 12.1 - - + -
----------------------------------------------------------
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Residues in contact with GLU 69 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K ASP* 4.9 3.1 + - - +
9L LYS* 5.2 4.2 - - - -
65L GLU* 2.9 26.0 + - + +
66L ARG* 3.1 43.1 + - - +
68L LYS* 1.3 75.9 - - + +
70L LEU* 1.3 61.3 + - - +
71L GLY 3.3 0.8 + - - -
120L VAL* 5.1 2.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L LYS* 3.8 49.4 - - + +
12L VAL* 3.5 37.2 - - + -
13L ILE* 3.5 19.9 - - + +
16L LEU* 3.7 17.0 - - + -
66L ARG* 2.9 44.3 + - - +
67L ILE 3.6 4.9 - - - +
68L LYS 3.0 0.4 - - - -
69L GLU* 1.3 78.0 - - - +
71L GLY* 1.3 60.1 + - - +
72L GLY 3.4 0.2 - - - -
118L ASP* 3.8 7.9 - - - +
121L THR* 4.1 2.9 - - - +
----------------------------------------------------------
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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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