Contacts of the helix formed by residues 10 - 38 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ARG* 4.0 4.4 + - - +
8G TYR 3.7 1.6 + - - -
9G HIS* 1.3 83.1 + - - +
11G ASP* 1.3 66.0 + - - +
13G GLU* 3.4 19.5 + - - +
14G ALA* 3.1 22.5 + - - +
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Residues in contact with ASP 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G HIS* 2.8 23.5 + - - +
10G SER* 1.3 73.7 - - - +
12G CYS* 1.3 62.4 + - - +
14G ALA* 3.4 6.9 + - - +
15G ALA* 2.9 29.1 + - - +
18G ARG* 4.6 2.1 + - - -
116G LEU* 3.6 21.5 - - + +
120G LYS* 3.1 22.5 + - - +
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Residues in contact with CYS 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G TYR* 4.1 9.9 - - + -
9G HIS* 3.1 24.8 + - + +
11G ASP* 1.3 80.3 - - - +
13G GLU* 1.3 56.5 + - - +
15G ALA* 3.1 3.3 + - - +
16G VAL* 2.9 36.4 + - - +
113G LEU* 4.3 1.5 - - - +
116G LEU* 4.0 24.9 - - - -
117G ALA* 4.3 8.1 - - - -
120G LYS* 4.1 15.9 - - - -
122G ASP* 5.0 4.9 - - - -
125G LEU* 4.0 26.7 - - + -
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Residues in contact with GLU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ARG* 2.7 33.8 + - - -
8G TYR* 3.7 20.7 + - + -
9G HIS 3.1 8.7 + - - +
10G SER* 3.5 17.7 + - - +
12G CYS* 1.3 78.8 - - - +
14G ALA* 1.3 62.7 + - - +
16G VAL 3.3 0.3 + - - -
17G ASN* 3.1 23.0 + - - +
69G GLN* 3.2 27.0 + - - +
74G GLY* 3.8 2.7 - - - -
75G ARG* 2.9 31.9 + - - +
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Residues in contact with ALA 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G SER 3.1 17.0 + - - +
11G ASP* 3.7 8.1 - - - +
12G CYS 3.3 0.2 - - - -
13G GLU* 1.3 78.4 - - - +
15G ALA* 1.3 60.7 - - - +
17G ASN* 3.5 10.0 + - - +
18G ARG* 3.1 39.4 + - - +
79G GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ASP 2.9 18.1 + - - +
12G CYS 3.5 1.3 - - - +
14G ALA* 1.3 74.7 - - - +
16G VAL* 1.3 60.8 + - - +
18G ARG* 3.3 25.6 + - - +
19G MET* 2.9 28.9 + - - +
113G LEU* 3.5 27.6 - - + +
116G LEU* 3.7 11.2 - - + -
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Residues in contact with VAL 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G TYR* 3.6 13.7 - - - +
12G CYS 2.9 20.4 + - - +
13G GLU 3.6 5.4 - - - +
14G ALA 3.3 0.2 - - - -
15G ALA* 1.3 77.5 - - - +
17G ASN* 1.3 56.9 + - - +
19G MET* 3.2 8.0 + - - +
20G LEU* 2.9 29.4 + - + +
65G PHE* 3.9 34.1 - - + +
68G TYR* 4.6 4.5 - - + -
69G GLN* 3.5 22.2 - - + +
113G LEU* 4.3 11.4 - - + -
125G LEU* 4.3 24.5 - - + -
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Residues in contact with ASN 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G GLU* 3.1 15.4 + - - +
14G ALA* 3.6 12.0 - - - +
15G ALA 3.3 0.2 - - - -
16G VAL* 1.3 76.7 - - - +
18G ARG* 1.3 62.6 + - - +
20G LEU* 3.5 16.0 - - - +
21G ASN* 3.4 20.1 + - - +
69G GLN* 3.4 11.9 + - - +
75G ARG 3.2 19.2 + - - -
76G VAL* 3.3 10.0 - - - -
77G VAL* 3.1 47.0 + - - +
79G GLN* 4.6 8.8 + - - +
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Residues in contact with ARG 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ASP 4.6 2.8 + - - -
14G ALA* 3.1 21.7 + - - +
15G ALA* 3.4 33.9 - - - +
17G ASN* 1.3 78.8 - - - +
19G MET* 1.3 64.1 + - - +
21G ASN* 3.4 6.8 + - - +
22G LEU* 3.1 21.0 + - - +
79G GLN* 4.8 17.0 - - - +
116G LEU* 5.4 2.6 - - - +
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Residues in contact with MET 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ALA 2.9 16.0 + - - +
16G VAL* 3.2 6.5 + - - +
18G ARG* 1.3 76.5 - - - +
20G LEU* 1.3 63.6 + - - +
22G LEU* 3.2 13.3 + - - +
23G GLU* 2.9 27.8 + - + +
65G PHE* 3.4 30.1 - - + -
106G VAL* 4.6 3.4 - - - +
109G ALA* 3.1 50.9 - - + +
110G LEU* 3.5 21.3 - - + +
113G LEU* 3.7 18.6 - - + -
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 5.2 0.2 - - - +
16G VAL* 2.9 15.5 + - + +
17G ASN* 3.5 19.7 - - - +
19G MET* 1.3 76.7 - - - +
21G ASN* 1.3 62.9 + - + +
23G GLU* 3.4 7.9 + - - +
24G LEU* 3.1 42.7 + - + +
62G ALA* 3.7 16.4 - - + +
65G PHE* 4.2 13.4 - - + +
66G MET* 3.8 35.9 - - + +
69G GLN* 5.8 0.7 - - - +
76G VAL* 4.0 18.6 - - + -
77G VAL 5.6 0.7 - - - +
78G LEU* 3.7 17.3 - - + -
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Residues in contact with ASN 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.4 4.6 + - - +
17G ASN 3.4 7.6 + - - +
18G ARG* 3.6 8.1 - - + +
19G MET 3.2 0.4 - - - -
20G LEU* 1.3 82.5 - - + +
22G LEU* 1.3 61.1 + - - +
24G LEU* 3.1 8.4 + - - +
25G TYR* 2.8 29.8 + - - +
79G GLN* 3.5 44.6 + - - +
80G ASP 3.2 27.7 + - - +
81G ILE* 4.3 7.2 - - - +
82G LYS 5.6 0.9 + - - -
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Residues in contact with LEU 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG 3.1 13.6 + - - +
19G MET* 3.2 14.1 + - - +
21G ASN* 1.3 78.7 + - - +
23G GLU* 1.3 58.2 + - - +
25G TYR* 3.2 23.7 + - + -
26G ALA* 2.9 26.6 + - - +
102G LEU* 5.4 1.6 - - + -
105G THR* 4.4 16.4 - - + +
106G VAL* 3.9 30.7 - - + +
109G ALA* 3.7 31.0 - - + -
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Residues in contact with GLU 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G MET* 2.9 20.4 + - + +
20G LEU 3.4 9.2 - - - +
22G LEU* 1.3 76.9 - - - +
24G LEU* 1.3 58.1 + - - +
26G ALA* 3.3 5.9 + - - +
27G SER* 2.9 27.7 + - - -
58G GLU* 2.7 27.9 - - - +
61G HIS* 3.4 18.2 - - + +
62G ALA* 3.8 7.6 - - + -
65G PHE* 4.1 18.7 - - + -
106G VAL* 4.0 15.6 - - - +
110G LEU* 4.9 2.6 - - - +
133G TYR* 3.7 14.9 - - - -
176G MG 2.4 30.8 - - - -
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Residues in contact with LEU 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.6 38.6 - - + +
20G LEU* 3.1 31.9 + - + +
21G ASN* 3.1 8.9 + - - +
23G GLU* 1.3 75.5 - - - +
25G TYR* 1.3 57.0 + - - +
27G SER* 3.5 6.1 - - - +
28G TYR* 3.0 27.4 + - - +
59G ARG* 4.9 17.0 - - + -
62G ALA* 3.7 18.2 - - + -
63G GLU* 6.4 0.4 - - + -
66G MET* 5.1 6.7 - - + -
81G ILE* 3.7 24.8 - - + +
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Residues in contact with TYR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASN* 2.8 17.2 + - - +
22G LEU* 3.4 27.4 - - + +
23G GLU 3.2 0.2 - - - -
24G LEU* 1.3 72.8 - - - +
26G ALA* 1.3 64.1 + - - +
28G TYR* 3.2 4.0 + - - +
29G THR* 2.9 48.6 + - + -
81G ILE* 4.0 9.6 - - + +
82G LYS* 3.4 38.1 - - + +
83G LYS 3.8 11.6 + - - -
84G PRO* 4.1 1.8 - - + -
85G GLU* 3.8 25.3 + - - +
102G LEU* 4.1 16.8 - - + -
105G THR* 6.5 0.4 - - + -
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Residues in contact with ALA 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU 2.9 13.8 + - - +
23G GLU* 3.5 9.9 - - - +
25G TYR* 1.3 76.0 - - - +
27G SER* 1.3 62.2 + - - +
29G THR* 3.3 3.3 + - - -
30G TYR* 3.1 31.8 + - + -
58G GLU* 4.2 15.7 - - + -
102G LEU* 4.0 26.0 - - + -
103G GLU* 6.5 0.4 - - - -
106G VAL* 4.2 19.3 - - + -
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Residues in contact with SER 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLU 2.9 16.6 + - - -
24G LEU* 3.5 11.6 - - - +
26G ALA* 1.3 76.7 - - - +
28G TYR* 1.3 61.8 + - - +
30G TYR 3.1 2.8 + - - -
31G SER* 3.0 18.8 + - - -
55G SER* 2.9 39.7 + - - +
58G GLU* 3.8 12.4 - - - +
59G ARG* 3.6 16.7 - - - +
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Residues in contact with TYR 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 4.4 3.1 + - - +
24A LEU* 3.6 27.6 - - + +
66A MET* 5.5 0.4 - - + -
78A LEU* 3.4 37.3 - - + +
79A GLN 3.0 29.7 + - - -
81A ILE* 3.7 22.6 - - + +
24G LEU 3.0 18.8 + - - +
25G TYR* 3.2 6.0 + - - +
27G SER* 1.3 76.8 + - - +
29G THR* 1.3 60.7 + - - +
31G SER* 3.2 16.3 - - - -
32G SER* 3.2 18.5 + - - -
81G ILE* 4.0 13.2 - - + -
82G LYS 3.6 18.2 - - - +
83G LYS* 4.0 3.4 - - - -
84G PRO* 3.7 17.1 - - + +
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Residues in contact with THR 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TYR* 2.9 30.2 + - + -
26G ALA 3.6 8.5 - - - -
27G SER 3.2 0.2 - - - -
28G TYR* 1.3 76.3 - - - +
30G TYR* 1.3 60.6 + - - +
32G SER* 3.2 6.8 + - - -
33G MET* 3.2 39.4 + - + +
84G PRO* 3.4 22.1 - - + +
85G GLU* 5.8 0.4 - - - +
89G TRP* 4.0 15.0 - - + -
102G LEU* 3.7 25.6 - - + -
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Residues in contact with TYR 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ALA* 3.1 24.5 + - + -
27G SER 3.1 6.3 + - - +
29G THR* 1.3 73.1 - - - +
31G SER* 1.3 59.8 + - - +
33G MET* 3.2 12.8 + - + +
34G TYR* 2.8 29.3 + - - +
50G PHE* 5.9 0.4 - + - -
51G PHE* 3.6 46.6 - + - +
54G HIS* 3.9 28.5 + + + -
55G SER* 3.7 7.4 - - - -
58G GLU* 4.0 12.8 - - + -
99G ALA* 3.9 24.9 + - + +
102G LEU* 3.9 17.0 - - + +
103G GLU* 2.8 40.8 + - - +
144G ILE* 4.3 3.0 - - + +
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Residues in contact with SER 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 6.1 0.5 - - - +
63A GLU* 4.8 6.2 + - - +
66A MET* 3.3 30.5 - - - +
78A LEU* 4.9 1.1 - - - -
27G SER 3.0 11.9 + - - -
28G TYR* 3.2 24.8 - - - -
30G TYR* 1.3 76.0 - - - +
32G SER* 1.3 61.7 + - - +
34G TYR* 3.4 11.8 + - - +
35G ALA* 3.1 23.2 + - - +
55G SER* 3.8 12.2 + - - -
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Residues in contact with SER 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.4 17.9 - - - +
28G TYR 3.2 5.7 + - - -
29G THR 3.2 12.0 + - - -
30G TYR 3.2 0.2 - - - -
31G SER* 1.3 73.7 - - - +
33G MET* 1.3 61.3 + - - +
35G ALA* 3.2 7.8 + - - +
36G PHE* 2.9 28.4 + - - +
84G PRO* 3.2 29.4 - - - +
86G ARG 4.0 6.4 + - - -
87G ASP* 5.1 7.8 + - - +
89G TRP* 3.4 17.0 + - - -
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Residues in contact with MET 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G THR* 3.2 34.0 + - + +
30G TYR* 3.5 16.4 - - + +
32G SER* 1.3 76.8 - - - +
34G TYR* 1.3 64.8 + - - +
36G PHE* 3.3 0.9 + - - +
37G PHE* 3.0 33.1 + - + -
51G PHE* 3.8 41.3 - - + -
89G TRP* 3.7 44.0 - - + -
95G ALA* 3.8 22.7 - - + +
98G ALA* 4.0 7.6 - - + -
99G ALA* 4.2 9.6 - - - +
102G LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 5.1 11.4 + - + -
66A MET* 4.6 22.4 - - + -
67A LYS* 3.3 38.1 - - + +
30G TYR 2.8 13.3 + - - +
31G SER* 3.4 14.8 - - - +
33G MET* 1.3 77.9 - - - +
35G ALA* 1.3 72.3 + - - +
37G PHE 3.4 0.3 + - - -
38G ASP* 3.2 30.0 + - + +
48G ALA* 3.2 38.0 - - + +
49G GLU* 3.6 19.9 + - - -
51G PHE* 4.0 2.2 - - - +
52G LYS* 3.7 41.7 + - + +
55G SER* 5.8 0.2 - - - +
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Residues in contact with ALA 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 4.3 14.4 - - + -
70A ASN* 3.1 27.9 + - - +
76A VAL* 4.2 32.0 - - + +
31G SER 3.1 11.1 + - - +
32G SER* 3.6 8.7 - - - +
34G TYR* 1.3 86.3 - - + +
36G PHE* 1.3 63.1 + - - +
38G ASP* 4.4 0.9 - - - -
39G ARG* 3.5 9.9 + - - +
----------------------------------------------------------
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Residues in contact with PHE 36 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G SER 2.9 16.8 + - - +
33G MET 3.5 4.9 - - - +
34G TYR 3.1 0.4 - - - -
35G ALA* 1.3 77.5 - - - +
37G PHE* 1.3 84.8 + + - +
39G ARG* 3.3 52.1 - - - +
42G VAL* 3.3 37.2 - - + +
87G ASP 4.5 3.8 - - - +
88G GLU* 3.8 12.6 - - + -
89G TRP* 3.6 32.5 - - + -
90G GLY* 3.5 42.0 - - - -
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Residues in contact with PHE 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G MET* 3.0 27.4 + - + +
34G TYR 3.4 0.8 + - - -
36G PHE* 1.3 90.1 - + - +
38G ASP* 1.3 60.8 + - - +
39G ARG 3.2 0.7 - - - -
42G VAL* 3.5 23.3 - - + -
43G ALA* 3.5 7.6 + - - -
44G LEU* 3.2 49.4 + - + +
45G HIS* 4.3 0.7 + - - -
47G VAL* 3.9 11.7 - - + -
48G ALA* 3.7 14.1 - - + -
51G PHE* 3.7 20.0 - + - -
89G TRP* 4.8 0.4 - - + -
91G ASN* 3.5 24.5 - - - -
92G THR* 3.6 27.4 - - - -
95G ALA* 3.7 22.2 - - + -
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Residues in contact with ASP 38 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 3.1 44.3 + - - +
70A ASN* 3.2 30.9 + - - +
34G TYR* 3.2 27.8 + - + +
35G ALA* 4.3 1.3 - - - -
36G PHE 3.2 0.4 - - - -
37G PHE* 1.3 74.9 - - - +
39G ARG* 1.3 61.6 + - - +
45G HIS* 3.4 23.9 + - - -
48G ALA* 4.1 3.0 - - + +
142H LYS* 2.9 31.8 + - - -
----------------------------------------------------------
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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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