Contacts of the helix formed by residues 10 - 38 (chain I) 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 SER 10 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ARG* 4.0 3.1 + - - +
8I TYR 3.7 1.8 + - - -
9I HIS* 1.3 83.2 + - - +
11I ASP* 1.3 65.1 + - - +
13I GLU* 3.4 18.8 + - - +
14I ALA* 3.1 22.3 + - - +
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Residues in contact with ASP 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I HIS* 2.8 23.0 + - - +
10I SER* 1.3 72.8 - - - +
12I CYS* 1.3 62.3 + - - +
14I ALA* 3.4 7.1 + - - +
15I ALA* 2.9 29.3 + - - +
18I ARG* 4.6 1.9 + - - -
116I LEU* 3.6 21.1 - - + +
120I LYS* 3.1 22.1 + - + +
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Residues in contact with CYS 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I TYR* 4.1 10.3 - - + -
9I HIS* 3.1 24.8 + - + +
11I ASP* 1.3 80.3 - - - +
13I GLU* 1.3 57.1 + - - +
15I ALA* 3.1 3.3 + - - +
16I VAL* 2.9 36.0 + - - +
113I LEU* 4.3 1.3 - - - +
116I LEU* 4.0 25.6 - - - -
117I ALA* 4.3 7.9 - - - -
120I LYS* 4.1 15.3 - - - -
122I ASP* 5.0 5.4 - - - -
125I LEU* 4.0 26.5 - - + -
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Residues in contact with GLU 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ARG* 2.7 33.7 + - - -
8I TYR* 3.7 20.5 + - + -
9I HIS 3.1 8.5 + - - +
10I SER* 3.5 18.0 + - - +
12I CYS* 1.3 79.0 - - - +
14I ALA* 1.3 63.0 + - - +
16I VAL 3.3 0.7 + - - -
17I ASN* 3.1 22.6 + - - +
69I GLN* 3.2 27.4 + - - +
74I GLY* 3.8 1.8 - - - -
75I ARG* 2.9 33.7 + - - +
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Residues in contact with ALA 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I SER 3.1 17.0 + - - +
11I ASP* 3.7 7.9 - - - +
12I CYS 3.3 0.2 - - - -
13I GLU* 1.3 78.5 - - - +
15I ALA* 1.3 61.8 + - - +
17I ASN* 3.5 10.5 + - - +
18I ARG* 3.1 38.9 + - - +
79I GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ASP 2.9 17.9 + - - +
12I CYS 3.1 1.3 + - - +
14I ALA* 1.3 74.9 - - - +
16I VAL* 1.3 60.8 + - - +
18I ARG* 3.3 25.2 + - - +
19I MET* 2.9 29.3 + - - +
113I LEU* 3.5 27.9 - - + +
116I LEU* 3.7 11.0 - - + -
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Residues in contact with VAL 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I TYR* 3.6 14.4 - - - +
12I CYS 2.9 20.2 + - - +
13I GLU 3.6 4.9 - - - +
15I ALA* 1.3 75.9 - - - +
17I ASN* 1.3 57.1 + - - +
19I MET* 3.2 7.2 + - - +
20I LEU* 2.9 29.4 + - + +
65I PHE* 3.9 33.6 - - + +
68I TYR* 4.6 5.8 - - + -
69I GLN* 3.5 22.2 - - + +
113I LEU* 4.3 13.0 - - + -
125I LEU* 4.3 22.7 - - + -
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Residues in contact with ASN 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I GLU* 3.1 16.2 + - - +
14I ALA* 3.6 12.6 - - - +
15I ALA 3.3 0.2 - - - -
16I VAL* 1.3 76.0 - - - +
18I ARG* 1.3 61.3 + - - +
20I LEU* 3.5 17.1 - - - +
21I ASN* 3.4 19.9 + - - +
69I GLN* 3.4 11.9 + - - +
75I ARG 3.2 18.6 + - - -
76I VAL* 3.3 10.2 - - - -
77I VAL* 3.1 47.2 + - + +
79I GLN* 4.6 9.6 + - - +
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Residues in contact with ARG 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ASP 4.6 2.6 + - - -
14I ALA* 3.1 21.7 + - - +
15I ALA* 3.4 33.4 - - - +
16I VAL 3.1 0.4 - - - -
17I ASN* 1.3 79.1 - - - +
19I MET* 1.3 64.9 + - - +
21I ASN* 3.4 7.0 + - + +
22I LEU* 3.1 20.8 + - - +
79I GLN* 4.8 17.0 - - - +
116I LEU* 5.4 2.0 - - - +
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Residues in contact with MET 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ALA 2.9 16.4 + - - +
16I VAL* 3.2 6.0 + - - +
18I ARG* 1.3 76.4 - - - +
20I LEU* 1.3 64.6 + - - +
22I LEU* 3.2 13.1 + - - +
23I GLU* 2.9 28.0 + - + +
65I PHE* 3.4 30.1 - - + -
106I VAL* 4.6 3.4 - - - +
109I ALA* 3.1 50.7 - - + +
110I LEU* 3.5 21.3 - - + +
113I LEU* 3.7 19.7 - - + -
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Residues in contact with LEU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I VAL* 2.9 17.1 + - + +
17I ASN* 3.5 19.7 - - - +
19I MET* 1.3 77.4 - - - +
21I ASN* 1.3 62.0 + - + +
23I GLU* 3.4 9.2 + - - +
24I LEU* 3.1 41.8 + - + +
62I ALA* 3.7 18.0 - - + +
65I PHE* 4.2 13.6 - - + +
66I MET* 3.8 35.9 - - + +
69I GLN* 5.8 0.4 - - + +
76I VAL* 4.0 18.6 - - + -
77I VAL 5.6 0.4 - - - +
78I LEU* 3.7 17.5 - - + -
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Residues in contact with ASN 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR* 4.4 5.2 + - - +
17I ASN 3.4 7.4 + - - +
18I ARG 3.6 8.2 - - - +
19I MET 3.2 0.4 - - - -
20I LEU* 1.3 82.7 - - + +
22I LEU* 1.3 62.1 + - - +
24I LEU* 3.1 7.8 + - - +
25I TYR* 2.8 29.5 + - - +
79I GLN* 3.5 44.0 + - - +
80I ASP 3.2 27.5 + - - +
81I ILE* 4.3 7.6 - - - +
82I LYS 5.6 0.7 + - - -
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Residues in contact with LEU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG 3.1 14.4 + - - +
19I MET* 3.2 15.0 + - - +
21I ASN* 1.3 78.2 + - - +
23I GLU* 1.3 57.6 + - - +
25I TYR* 3.2 23.6 + - + -
26I ALA* 2.9 26.6 + - - +
102I LEU* 5.4 1.3 - - + -
105I THR* 4.4 17.5 - - + +
106I VAL* 3.9 31.4 - - + +
109I ALA* 3.7 30.3 - - + -
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Residues in contact with GLU 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I MET* 2.9 20.3 + - + +
20I LEU 3.4 9.0 - - - +
21I ASN 3.2 0.2 - - - -
22I LEU* 1.3 76.9 - - - +
24I LEU* 1.3 58.7 + - - +
26I ALA* 3.3 5.9 + - - +
27I SER* 2.9 28.1 + - - -
58I GLU* 2.7 20.7 - - - +
61I HIS* 3.4 18.2 - - + +
62I ALA* 3.8 13.9 - - + +
65I PHE* 4.1 19.5 - - + -
106I VAL* 4.0 15.3 - - + +
110I LEU* 4.9 2.3 - - - +
133I TYR* 3.7 14.9 - - - -
176I MG 2.4 30.3 - - - -
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Residues in contact with LEU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR* 3.6 39.7 - - + +
20I LEU* 3.1 31.0 + - + +
21I ASN* 3.1 9.4 + - - +
23I GLU* 1.3 76.0 - - - +
25I TYR* 1.3 57.2 + - - +
27I SER* 3.5 6.6 - - - +
28I TYR* 3.0 27.4 + - - +
59I ARG* 4.9 17.7 - - + -
62I ALA* 3.7 18.6 - - + -
63I GLU* 6.4 0.2 - - + -
66I MET* 5.1 6.3 - - + -
81I ILE* 3.7 22.7 - - + +
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Residues in contact with TYR 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASN* 2.8 17.7 + - - +
22I LEU* 3.4 28.0 - - + +
24I LEU* 1.3 72.3 - - - +
26I ALA* 1.3 63.3 + - - +
28I TYR* 3.2 3.9 + - - +
29I THR* 2.9 47.1 + - + +
81I ILE* 4.0 9.6 - - + +
82I LYS* 3.4 38.1 - - + +
83I LYS 3.8 12.5 + - - -
84I PRO* 4.1 1.8 - - + -
85I GLU* 3.8 25.6 + - - +
102I LEU* 4.1 16.8 - - + -
105I THR* 6.5 0.4 - - + -
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Residues in contact with ALA 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I LEU 2.9 13.6 + - - +
23I GLU* 3.3 10.1 + - - +
25I TYR* 1.3 77.3 - - - +
27I SER* 1.3 61.5 + - - +
29I THR* 3.3 3.1 + - - -
30I TYR* 3.1 32.1 + - + -
58I GLU* 4.2 15.0 - - + -
102I LEU* 4.0 25.6 - - + -
103I GLU* 6.2 0.4 - - - +
106I VAL* 4.2 19.7 - - + -
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Residues in contact with SER 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLU 2.9 17.0 + - - -
24I LEU* 3.5 11.3 - - - +
26I ALA* 1.3 75.9 - - - +
28I TYR* 1.3 61.9 + - - +
30I TYR 3.1 2.9 + - - -
31I SER* 3.0 19.5 + - - -
55I SER* 2.9 39.0 + - - +
58I GLU* 3.8 12.9 - - - +
59I ARG* 3.6 16.8 - - - +
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Residues in contact with TYR 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 5.1 0.2 - - - +
21E ASN* 4.4 3.3 + - - +
24E LEU* 3.5 28.8 - - + +
78E LEU* 3.4 36.3 - - + +
79E GLN 3.0 30.0 + - - -
81E ILE* 3.7 27.4 - - + +
24I LEU 3.0 18.8 + - - +
25I TYR* 3.2 5.6 + - - +
27I SER* 1.3 78.1 - - - +
29I THR* 1.3 60.8 + - - +
31I SER* 3.2 17.0 - - - -
32I SER* 3.2 18.2 + - - -
81I ILE* 4.0 8.1 - - + -
82I LYS 3.6 18.6 - - - +
83I LYS* 4.0 3.6 - - - -
84I PRO* 3.7 17.5 - - + +
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Residues in contact with THR 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I TYR* 2.9 30.3 + - + -
26I ALA* 3.6 8.7 - - - -
27I SER 3.2 0.4 - - - -
28I TYR* 1.3 75.5 - - - +
30I TYR* 1.3 61.9 + - - +
32I SER* 3.2 6.8 + - - -
33I MET* 3.2 38.8 + - + +
84I PRO* 3.4 20.5 - - - +
85I GLU* 5.0 0.6 + - - +
89I TRP* 4.0 15.5 - - + -
102I LEU* 3.7 25.1 - - + -
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Residues in contact with TYR 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ALA* 3.1 23.2 + - + -
27I SER 3.1 6.5 + - - +
29I THR* 1.3 74.1 - - - +
31I SER* 1.3 60.5 + - - +
33I MET* 3.2 12.4 + - + +
34I TYR* 2.8 29.3 + - - +
50I PHE* 5.9 0.2 - + - -
51I PHE* 3.6 48.0 - + - +
54I HIS* 3.9 28.7 - + + -
55I SER* 3.7 7.4 - - - -
58I GLU* 4.0 13.0 - - + -
99I ALA* 3.9 25.4 + - + +
102I LEU* 3.9 17.4 - - + +
103I GLU* 2.8 42.3 + - - +
144I ILE* 4.3 3.9 - - + +
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Residues in contact with SER 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E LEU* 6.0 0.5 - - - +
63E GLU* 4.8 6.4 + - - +
66E MET* 3.3 31.0 - - - +
78E LEU* 4.8 1.1 - - - -
27I SER 3.0 12.5 + - - -
28I TYR* 3.2 24.5 - - - -
30I TYR* 1.3 74.8 - - - +
32I SER* 1.3 61.8 + - - +
34I TYR* 3.4 12.3 + - - +
35I ALA* 3.1 22.5 + - - +
55I SER* 3.8 13.4 + - - -
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Residues in contact with SER 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E VAL* 6.3 0.2 - - - -
78E LEU* 3.3 17.4 - - - +
28I TYR 3.2 5.6 + - - -
29I THR 3.2 11.3 + - - -
30I TYR 3.2 0.2 - - - -
31I SER* 1.3 73.4 - - - +
33I MET* 1.3 59.6 + - - +
35I ALA* 3.2 7.2 + - - +
36I PHE* 2.9 28.4 + - - +
84I PRO* 3.2 29.1 - - - +
86I ARG 4.0 6.4 + - - -
87I ASP* 5.1 7.0 + - - +
89I TRP* 3.4 18.7 + - - -
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Residues in contact with MET 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I THR* 3.2 33.5 + - + +
30I TYR* 3.2 15.7 + - + +
32I SER* 1.3 76.0 - - - +
34I TYR* 1.3 65.9 + - - +
36I PHE* 3.3 0.9 + - - +
37I PHE* 3.0 33.6 + - + -
51I PHE* 3.8 42.6 - - + -
89I TRP* 3.7 43.7 - - + +
95I ALA* 3.8 22.7 - - + +
98I ALA* 4.0 8.1 - - + +
99I ALA* 4.2 9.2 - - - +
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Residues in contact with TYR 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E GLU* 5.1 12.9 + - + +
66E MET* 4.5 23.1 - - + -
67E LYS* 3.4 35.8 - - + +
30I TYR 2.8 13.3 + - - +
31I SER* 3.4 14.8 - - - +
33I MET* 1.3 77.7 - - - +
35I ALA* 1.3 72.2 + - - +
36I PHE 3.3 0.2 + - - -
37I PHE 3.4 0.5 + - - -
38I ASP* 3.2 30.6 + - + +
48I ALA* 3.2 37.1 - - + +
49I GLU* 3.6 20.2 + - - -
51I PHE* 4.0 2.4 - - - +
52I LYS* 3.7 41.8 + - + +
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Residues in contact with ALA 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E MET* 4.2 14.6 - - + -
70E ASN* 3.0 28.5 + - - +
76E VAL* 4.1 31.8 - - + +
31I SER 3.1 11.1 + - - +
32I SER* 3.2 8.9 + - - +
34I TYR* 1.3 84.7 - - - +
36I PHE* 1.3 62.6 + - - +
38I ASP* 4.4 0.9 - - - -
39I ARG* 3.5 9.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 36 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I SER 2.9 16.4 + - - +
33I MET 3.5 4.9 - - - +
34I TYR 3.1 0.2 - - - -
35I ALA* 1.3 78.9 - - - +
37I PHE* 1.3 85.6 + + - +
39I ARG* 3.3 52.9 - - - +
42I VAL* 3.3 35.0 - - + +
87I ASP 4.5 3.1 - - - +
88I GLU* 3.8 12.3 - - + -
89I TRP* 3.6 33.4 - - + -
90I GLY 3.5 41.5 - - - -
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Residues in contact with PHE 37 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I MET* 3.0 27.2 + - + +
34I TYR 3.4 0.2 + - - -
36I PHE* 1.3 90.1 - + - +
38I ASP* 1.3 60.6 + - - +
39I ARG 3.2 0.7 - - - -
42I VAL* 3.5 22.7 - - + -
43I ALA* 3.5 6.9 + - - -
44I LEU* 3.2 50.2 + - + +
45I HIS* 4.3 0.9 + - - -
47I VAL* 3.9 11.7 - - + -
48I ALA* 3.7 14.8 - - + -
51I PHE* 3.7 19.7 - + - -
89I TRP* 4.8 0.4 - - + -
91I ASN* 3.5 24.5 - - - -
92I THR* 3.6 27.4 - - - -
95I ALA* 3.7 22.7 - - + -
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Residues in contact with ASP 38 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 2.9 31.8 + - - -
67E LYS* 3.1 44.0 + - - +
70E ASN* 3.2 30.1 + - - +
34I TYR* 3.2 28.4 + - + +
35I ALA* 4.3 1.8 - - - -
36I PHE 3.2 0.4 - - - -
37I PHE* 1.3 75.1 - - - +
39I ARG* 1.3 61.9 + - - +
45I HIS* 3.4 23.2 + - - -
48I ALA* 4.1 2.8 - - + +
----------------------------------------------------------
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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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