Contacts of the helix formed by residues 45 - 71 (chain K) in PDB entry 1MFR
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 HIS 45 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LYS* 4.0 2.5 - - - -
146D ASP* 3.0 33.9 + - + -
150D ASN* 5.9 0.4 - - - -
37K PHE 4.6 1.3 - - - -
38K ASP* 3.4 44.7 + - - -
43K ALA* 3.3 15.0 + - - -
44K LEU* 1.3 69.0 - - - +
46K ASN* 1.3 65.0 + - - +
48K ALA* 3.5 6.7 - - - +
49K GLU* 3.1 30.0 + - + +
167K ASP* 3.6 3.4 + - - +
67W LYS* 5.0 5.1 + - - -
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Residues in contact with ASN 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K HIS* 1.3 77.3 - - - +
47K VAL* 1.3 65.8 + - - +
49K GLU* 3.3 9.5 + - - +
50K PHE 3.0 17.3 + - - -
167K ASP* 3.0 46.4 + - - +
168K LYS* 4.4 10.7 - - - +
171K VAL* 3.2 28.0 - - + +
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Residues in contact with VAL 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K PHE* 3.9 20.2 - - + -
44K LEU* 3.5 18.6 - - + +
46K ASN* 1.3 76.9 - - - +
48K ALA* 1.3 61.2 + - - +
50K PHE* 3.2 9.6 + - - +
51K PHE* 3.2 45.5 + - + -
92K THR* 4.1 25.4 - - + +
96K MET* 4.6 4.9 - - + -
163K GLU 5.8 0.4 - - - +
166K PHE* 4.3 14.1 - - + -
167K ASP* 3.1 22.3 + - + +
171K VAL* 4.4 4.9 - - + +
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Residues in contact with ALA 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K TYR* 3.2 40.9 - - + +
37K PHE* 3.7 23.5 - - + +
38K ASP* 4.1 4.5 - - + +
44K LEU 3.0 15.3 + - - +
45K HIS* 3.5 15.0 - - - +
46K ASN 3.2 0.2 - - - -
47K VAL* 1.3 77.2 - - - +
49K GLU* 1.3 57.4 + - - +
51K PHE* 3.4 2.3 + - - -
52K LYS 3.0 20.6 + - - -
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Residues in contact with GLU 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K TYR* 3.6 23.2 + - - -
45K HIS* 3.1 18.2 + - + +
46K ASN* 3.3 11.2 + - - +
48K ALA* 1.3 74.4 - - - +
50K PHE* 1.3 62.4 + - - +
52K LYS* 3.6 23.9 + - - +
53K GLU* 2.9 39.7 + - - +
67W LYS* 5.8 1.2 - - - -
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Residues in contact with PHE 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K TYR* 5.9 0.4 - + - -
46K ASN 3.0 14.2 + - - +
47K VAL* 3.2 10.5 + - - +
49K GLU* 1.3 76.7 - - - +
51K PHE* 1.3 93.4 + + - +
53K GLU* 3.5 7.9 + - - +
54K HIS* 3.2 54.6 + + - -
96K MET* 4.0 20.6 - - + -
143K ARG* 3.9 17.7 - - - -
144K ILE* 4.5 12.6 - - + -
147K PHE* 3.7 29.2 - + - -
171K VAL* 3.7 19.5 - - + +
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Residues in contact with PHE 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K TYR* 3.6 49.9 - + + +
33K MET* 3.8 30.1 - - + -
34K TYR 4.0 4.9 - - - +
37K PHE* 3.7 22.7 - + - -
47K VAL* 3.2 35.7 + - + -
48K ALA* 3.9 5.2 - - - +
49K GLU 3.2 0.2 - - - -
50K PHE* 1.3 98.7 - + - +
52K LYS* 1.3 59.6 + - - +
54K HIS* 3.2 5.8 + - + +
55K SER* 2.9 24.1 + - - -
92K THR 5.7 0.2 - - - -
95K ALA* 4.1 11.7 - - + -
96K MET* 3.7 23.1 - - + -
99K ALA* 4.2 8.1 - - + -
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Residues in contact with LYS 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K TYR* 3.7 37.2 + - + +
48K ALA 3.0 17.6 + - - +
49K GLU* 3.6 32.0 + - - +
50K PHE 3.3 0.2 - - - -
51K PHE* 1.3 76.2 - - - +
53K GLU* 1.3 63.1 + - + +
55K SER* 3.2 22.0 + - - +
56K HIS* 3.3 30.2 + - + +
63W GLU* 3.6 25.3 + - - +
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Residues in contact with GLU 53 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K GLU* 2.9 26.6 + - + +
50K PHE* 3.6 9.0 - - + +
51K PHE 3.2 0.2 - - - -
52K LYS* 1.3 78.6 - - + +
54K HIS* 1.3 61.7 + - + +
56K HIS* 3.3 10.9 + - - +
57K GLU* 3.1 34.9 + - - +
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Residues in contact with HIS 54 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K TYR* 3.9 23.2 - + + -
50K PHE* 3.2 40.3 + + - +
51K PHE* 3.2 11.4 + - - +
53K GLU* 1.3 80.7 - - + +
55K SER* 1.3 63.0 + - - +
57K GLU* 3.4 16.9 + - - +
58K GLU* 3.2 32.1 + - - +
103K GLU* 3.6 17.9 + - - -
140K ASP* 3.7 26.2 - - + -
143K ARG* 3.1 27.3 + - - -
144K ILE* 4.9 5.4 - - + -
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Residues in contact with SER 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K SER* 2.9 47.2 + - - +
30K TYR* 3.7 14.6 - - - +
31K SER* 3.8 14.2 - - - -
51K PHE 2.9 10.0 + - - -
52K LYS* 3.2 16.6 + - - +
53K GLU 3.3 0.2 - - - -
54K HIS* 1.3 74.6 - - - +
56K HIS* 1.3 75.8 + - - +
58K GLU 3.4 1.0 + - - -
59K ARG* 3.1 12.4 + - - +
63W GLU* 4.4 5.5 + - - -
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Residues in contact with HIS 56 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K LYS* 3.3 35.2 + - + +
53K GLU* 3.3 12.5 + - - +
54K HIS 3.2 0.4 - - - -
55K SER* 1.3 90.6 + - - +
57K GLU* 1.3 55.4 + - + +
59K ARG* 3.5 7.4 + - + +
60K GLU* 3.1 26.3 + - - +
59W ARG* 6.0 3.3 - - + +
63W GLU* 3.1 27.4 + - - -
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Residues in contact with GLU 57 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K GLU* 3.1 21.0 + - - +
54K HIS* 3.6 25.3 + - - +
55K SER 3.2 0.4 - - - -
56K HIS* 1.3 76.3 - - - +
58K GLU* 1.3 63.9 + - + +
60K GLU* 3.2 6.5 + - - +
61K HIS* 2.9 45.2 + - + +
140K ASP* 4.1 17.3 - - - +
143K ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLU* 2.7 31.4 - - - +
26K ALA* 4.2 9.8 - - + +
27K SER* 3.8 12.3 - - - +
30K TYR* 4.0 16.2 - - + -
54K HIS* 3.2 21.8 + - - +
55K SER 3.4 0.2 + - - -
57K GLU* 1.3 80.2 - - - +
59K ARG* 1.3 58.4 + - - +
61K HIS* 3.1 11.5 + - - +
62K ALA* 3.0 26.3 + - - +
103K GLU* 3.4 14.7 - - - +
106K VAL* 4.9 1.2 - - - +
176K MG 2.0 31.6 - - - -
177K MG 2.6 24.2 - - - -
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Residues in contact with ARG 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K LEU* 4.9 11.7 - - + -
27K SER* 3.6 13.2 + - - +
55K SER 3.1 18.0 + - - +
56K HIS* 3.6 9.6 - - + +
58K GLU* 1.3 74.2 - - - +
60K GLU* 1.3 63.8 + - - +
62K ALA* 3.2 8.7 + - - +
63K GLU* 3.1 36.1 + - + +
56W HIS* 6.0 2.7 - - + +
59W ARG* 5.8 9.0 - - + -
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Residues in contact with GLU 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K HIS 3.1 15.1 + - - +
57K GLU* 3.2 10.7 + - + +
59K ARG* 1.3 76.1 - - - +
61K HIS* 1.3 61.8 + - + +
63K GLU* 3.5 12.0 + - - +
64K LYS* 3.1 32.2 + - - +
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Residues in contact with HIS 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLU* 3.4 15.7 + - - +
57K GLU* 2.9 30.6 + - + +
58K GLU* 3.1 17.9 + - - +
59K ARG 3.2 0.2 - - - -
60K GLU* 1.3 77.3 - - + +
62K ALA* 1.3 65.5 - - - +
64K LYS* 4.4 18.7 + - - -
65K PHE* 3.3 12.2 + - - -
132K GLU 4.6 6.9 + - - -
133K TYR* 3.0 39.2 + + + -
136K GLU* 5.1 13.9 - - + +
137K GLN* 5.1 1.3 - - - -
140K ASP* 5.6 0.4 - - - -
176K MG 2.7 23.6 - - - -
177K MG 4.3 10.3 - - - -
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Residues in contact with ALA 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 3.7 16.7 - - + +
23K GLU* 3.8 10.7 - - + +
24K LEU* 3.7 35.4 - - + -
58K GLU 3.0 12.5 + - - +
59K ARG 3.2 8.9 + - - +
61K HIS* 1.3 75.2 - - - +
63K GLU* 1.3 64.0 + - + +
65K PHE* 3.3 8.0 + - - +
66K MET* 3.1 27.1 + - + +
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Residues in contact with GLU 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K LEU* 6.4 0.4 - - + -
59K ARG* 3.1 25.9 + - + +
60K GLU* 3.8 11.8 - - - +
61K HIS 3.3 0.2 - - - -
62K ALA* 1.3 74.9 - - + +
64K LYS* 1.3 62.9 + - - +
66K MET* 3.2 24.6 + - + +
67K LYS* 3.1 24.8 + - - +
31W SER* 4.8 5.1 + - - +
34W TYR* 5.1 11.3 - - + -
52W LYS* 3.6 21.3 - - - +
55W SER* 4.4 5.9 + - - -
56W HIS* 3.1 34.4 + - - -
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Residues in contact with LYS 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K GLU* 3.1 20.7 + - - +
61K HIS* 3.6 17.8 + - - +
62K ALA 3.3 0.4 - - - -
63K GLU* 1.3 75.9 - - - +
65K PHE* 1.3 57.8 + - - +
67K LYS* 3.5 7.4 + - - +
68K TYR* 2.9 27.2 + - - +
128K PHE* 3.7 9.7 - - + -
132K GLU* 2.9 53.8 + - + +
133K TYR* 3.2 21.8 - - + +
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Residues in contact with PHE 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K VAL* 3.9 29.0 - - + +
19K MET* 3.4 33.7 - - + -
20K LEU* 4.2 19.5 - - + +
23K GLU* 4.1 15.0 - - + -
61K HIS 3.3 17.1 + - - -
62K ALA 3.3 8.2 + - - +
63K GLU 3.2 0.4 - - - -
64K LYS* 1.3 78.4 - - - +
66K MET* 1.3 64.4 + - - +
68K TYR* 3.5 3.5 - + + +
69K GLN* 3.0 24.6 + - - +
110K LEU* 4.0 10.8 - - + -
113K LEU* 4.5 8.3 - - + -
125K LEU* 5.3 0.4 - - + -
128K PHE* 3.5 24.5 - + - -
129K LEU* 4.0 12.1 - - + -
133K TYR* 3.4 31.0 - + - -
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Residues in contact with MET 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 3.8 29.8 - - + -
24K LEU* 5.1 8.1 - - + -
62K ALA* 3.1 20.7 + - + +
63K GLU* 3.2 23.3 + - + +
65K PHE* 1.3 75.9 - - - +
67K LYS* 1.3 61.6 + - - +
69K GLN* 3.4 4.2 - - - +
70K ASN* 3.3 28.3 + - - -
76K VAL* 3.9 20.7 - - + +
78K LEU* 4.7 8.3 - - + -
28W TYR* 5.6 0.2 - - + -
31W SER* 3.3 39.9 - - - +
34W TYR* 4.5 15.0 - - + -
35W ALA* 4.2 13.5 - - + -
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Residues in contact with LYS 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K GLU 3.1 10.3 + - - +
64K LYS* 3.6 11.0 - - - +
66K MET* 1.3 78.6 - - - +
68K TYR* 1.3 57.6 + - - +
70K ASN* 3.5 3.1 + - - +
71K LYS* 3.0 45.2 + - + +
142P LYS* 6.0 1.0 - - - +
34W TYR* 3.4 28.7 + - - +
38W ASP* 3.1 33.7 + - - +
45W HIS* 5.0 5.9 + - - -
49W GLU* 5.8 1.6 - - - -
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Residues in contact with TYR 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K TYR* 3.9 18.4 - + - -
16K VAL* 4.6 7.6 - - + -
64K LYS 2.9 18.6 + - - +
65K PHE* 3.5 6.1 - - - +
66K MET 3.2 0.2 - - - -
67K LYS* 1.3 74.5 - - - +
69K GLN* 1.3 66.9 + - - +
71K LYS* 3.1 17.9 + - + +
72K ARG* 2.8 52.2 + - + +
124K HIS* 2.8 42.0 + + - -
125K LEU* 3.2 36.6 - - + +
128K PHE* 3.6 43.3 - + + -
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Residues in contact with GLN 69 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K TYR* 3.0 36.5 + - - -
13K GLU* 3.2 28.7 + - - +
16K VAL* 3.5 14.5 - - + +
17K ASN* 3.4 18.4 + - - -
20K LEU* 5.8 0.6 - - + +
65K PHE 3.0 14.6 + - - +
66K MET 3.4 7.0 - - - +
68K TYR* 1.3 83.1 - - - +
70K ASN* 1.3 59.7 - - - +
72K ARG* 3.2 4.9 + - - +
73K GLY 3.1 3.6 + - - -
74K GLY* 2.9 43.6 + - - -
75K ARG 4.0 6.3 - - - -
76K VAL* 3.7 24.7 - - + +
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Residues in contact with ASN 70 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K VAL* 4.5 0.5 - - - +
66K MET 3.3 12.5 + - - -
67K LYS 3.9 3.4 - - - +
68K TYR 3.3 0.2 - - - -
69K GLN* 1.3 76.1 - - - +
71K LYS* 1.3 65.1 + - - +
73K GLY* 3.2 10.9 + - - -
74K GLY 3.9 12.2 - - - +
75K ARG* 4.0 1.6 + - - +
76K VAL* 4.6 8.8 + - - +
142P LYS* 3.3 17.8 - - - +
35W ALA* 3.0 30.5 + - - +
38W ASP* 3.2 39.6 + - - +
39W ARG* 3.2 28.2 - - - +
40W ASP* 4.8 3.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K VAL* 3.4 17.7 - - - +
67K LYS* 3.0 29.4 + - + +
68K TYR* 3.1 21.9 + - + +
70K ASN* 1.3 76.5 - - - +
72K ARG* 1.3 63.6 + - + +
128K PHE* 6.2 2.4 - - - -
135P GLU* 2.8 35.6 + - - +
138P VAL* 4.3 23.7 - - + +
139P LYS* 4.6 11.8 - - - +
142P LYS* 4.1 28.4 - - + +
----------------------------------------------------------
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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