Contacts of the helix formed by residues 10 - 38 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M ARG* 4.0 4.0 + - - +
8M TYR 3.7 1.6 + - - -
9M HIS* 1.3 84.0 + - - +
11M ASP* 1.3 63.7 + - - +
13M GLU* 3.4 18.7 + - - +
14M ALA* 3.1 23.2 + - - +
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Residues in contact with ASP 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M HIS* 2.8 23.8 + - + +
10M SER* 1.3 74.2 - - - +
12M CYS* 1.3 61.8 + - - +
14M ALA* 3.4 6.9 + - - +
15M ALA* 2.9 28.6 + - - +
18M ARG* 4.6 2.1 + - - -
116M LEU* 3.6 20.7 - - + +
120M LYS* 3.1 22.3 + - + +
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Residues in contact with CYS 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M TYR* 4.1 10.1 - - + -
9M HIS* 3.1 25.0 + - + +
11M ASP* 1.3 78.8 - - - +
13M GLU* 1.3 58.2 + - - +
15M ALA* 3.1 3.6 + - - +
16M VAL* 2.9 35.6 + - - +
113M LEU* 4.3 1.0 - - - +
116M LEU* 4.0 24.2 - - - -
117M ALA* 4.3 7.4 - - - -
120M LYS* 4.1 16.2 - - - -
122M ASP* 5.0 5.2 - - - -
125M LEU* 4.0 26.5 - - + -
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Residues in contact with GLU 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M ARG* 2.7 34.6 + - - -
8M TYR* 3.7 20.3 + - + -
9M HIS 3.1 8.3 + - - +
10M SER* 3.5 17.6 + - - +
12M CYS* 1.3 79.7 - - - +
14M ALA* 1.3 62.3 + - - +
16M VAL 3.3 0.5 + - - -
17M ASN* 3.1 22.6 + - - +
69M GLN* 3.2 26.7 + - - +
74M GLY* 3.8 2.7 - - - -
75M ARG* 2.9 32.6 + - - +
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Residues in contact with ALA 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M SER 3.1 16.7 + - - +
11M ASP* 3.7 7.2 - - - +
13M GLU* 1.3 78.4 - - - +
15M ALA* 1.3 61.7 + - - +
17M ASN* 3.5 10.9 + - - +
18M ARG* 3.1 38.9 + - - +
79M GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M ASP 2.9 16.9 + - - +
12M CYS 3.1 1.8 + - - +
14M ALA* 1.3 75.7 - - - +
16M VAL* 1.3 60.9 + - - +
18M ARG* 3.3 23.6 + - - +
19M MET* 2.9 29.3 + - - +
113M LEU* 3.5 27.6 - - + +
116M LEU* 3.7 11.2 - - + -
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Residues in contact with VAL 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M TYR* 3.6 14.4 - - - +
12M CYS 2.9 21.3 + - - +
13M GLU 3.6 5.2 - - - +
15M ALA* 1.3 76.2 - - - +
17M ASN* 1.3 57.0 + - - +
19M MET* 3.2 7.0 + - - +
20M LEU* 2.9 29.4 + - + +
65M PHE* 3.9 34.2 - - + +
68M TYR* 4.6 5.2 - - + -
69M GLN* 3.5 21.5 - - + +
113M LEU* 4.3 12.1 - - + -
125M LEU* 4.3 23.6 - - + -
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Residues in contact with ASN 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M GLU* 3.1 15.5 + - - +
14M ALA* 3.6 12.2 - - - +
15M ALA 3.3 0.2 - - - -
16M VAL* 1.3 75.8 - - - +
18M ARG* 1.3 60.9 + - - +
20M LEU* 3.5 17.3 - - - +
21M ASN* 3.4 20.1 + - - +
69M GLN* 3.4 12.1 + - - -
75M ARG 3.2 18.8 + - - -
76M VAL* 3.3 10.6 - - - -
77M VAL* 3.1 46.0 + - + +
79M GLN* 4.6 9.2 + - - +
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Residues in contact with ARG 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M ASP 4.6 2.8 + - - -
14M ALA* 3.1 20.7 + - - +
15M ALA* 3.4 34.7 - - - +
16M VAL 3.1 0.2 - - - -
17M ASN* 1.3 79.5 - - - +
19M MET* 1.3 63.7 + - - +
21M ASN* 3.4 7.7 + - - +
22M LEU* 3.1 20.8 + - - +
79M GLN* 4.8 17.0 - - - +
116M LEU* 5.4 1.8 - - - +
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Residues in contact with MET 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M ALA 2.9 15.8 + - - +
16M VAL* 3.2 6.5 + - - +
18M ARG* 1.3 75.0 - - - +
20M LEU* 1.3 64.4 + - - +
22M LEU* 3.2 13.1 + - - +
23M GLU* 2.9 27.9 + - - +
65M PHE* 3.4 30.3 - - + -
106M VAL* 4.6 3.1 - - - +
109M ALA* 3.1 50.9 - - + +
110M LEU* 3.5 21.8 - - + +
113M LEU* 3.7 20.0 - - + -
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Residues in contact with LEU 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M VAL* 2.9 16.0 + - + +
17M ASN* 3.5 18.8 - - - +
19M MET* 1.3 77.4 - - - +
21M ASN* 1.3 62.2 + - + +
23M GLU* 3.3 8.9 + - - +
24M LEU* 3.1 42.3 + - + +
62M ALA* 3.7 16.8 - - + +
65M PHE* 4.2 14.5 - - + +
66M MET* 3.8 35.4 - - + +
69M GLN* 5.8 0.7 - - + +
76M VAL* 4.0 18.8 - - + -
77M VAL 5.6 0.9 - - - +
78M LEU* 3.7 17.5 - - + -
28S TYR* 5.2 0.2 - - - +
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Residues in contact with ASN 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ASN 3.4 7.4 + - - +
18M ARG 3.6 8.5 - - - +
19M MET 3.2 0.6 - - - -
20M LEU* 1.3 82.5 - - + +
22M LEU* 1.3 61.0 + - - +
24M LEU* 3.1 8.1 + - - +
25M TYR* 2.8 30.1 + - - +
79M GLN* 3.5 44.7 + - - +
80M ASP 3.2 27.3 + - - +
81M ILE* 4.3 8.0 - - - +
82M LYS 5.6 0.9 + - - -
28S TYR* 4.4 4.6 + - - +
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Residues in contact with LEU 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M ARG 3.1 13.0 + - - +
19M MET* 3.2 15.7 + - - +
21M ASN* 1.3 78.3 + - - +
23M GLU* 1.3 56.9 + - - +
25M TYR* 3.2 23.2 + - + -
26M ALA* 2.9 27.0 + - - +
102M LEU* 5.4 2.0 - - + -
105M THR* 4.4 17.0 - - + +
106M VAL* 3.9 30.2 - - + +
109M ALA* 3.7 30.7 - - + -
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Residues in contact with GLU 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M MET* 2.9 19.3 + - + +
20M LEU 3.4 9.2 - - - +
22M LEU* 1.3 76.7 - - - +
24M LEU* 1.3 56.8 + - - +
26M ALA* 3.3 5.9 + - - +
27M SER* 2.9 27.7 + - - -
58M GLU* 2.7 21.7 - - - +
61M HIS* 3.4 17.8 - - + +
62M ALA* 3.8 13.0 - - + -
65M PHE* 4.1 20.0 - - + -
106M VAL* 4.0 14.8 - - - +
110M LEU* 4.9 2.9 - - - +
133M TYR* 3.7 15.4 - - - -
176M MG 2.4 30.9 - - - -
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Residues in contact with LEU 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M LEU* 3.1 31.2 + - + +
21M ASN* 3.5 9.6 - - - +
23M GLU* 1.3 75.3 - - - +
25M TYR* 1.3 58.7 + - - +
27M SER* 3.5 6.2 - - - +
28M TYR* 3.0 27.0 + - - +
59M ARG* 4.9 18.4 - - + -
62M ALA* 3.7 17.7 - - + -
63M GLU* 6.4 0.4 - - + -
66M MET* 5.1 6.3 - - + -
78M LEU* 4.8 0.2 - - + -
81M ILE* 3.7 24.5 - - + +
28S TYR* 3.6 38.6 - - + +
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Residues in contact with TYR 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ASN* 2.8 17.8 + - - +
22M LEU* 3.4 28.0 - - + +
23M GLU 3.2 0.2 - - - -
24M LEU* 1.3 71.9 - - - +
26M ALA* 1.3 63.9 + - - +
28M TYR* 3.2 3.9 + - + +
29M THR* 2.9 48.2 + - + -
81M ILE* 4.0 10.5 - - + +
82M LYS* 3.4 38.4 - - + +
83M LYS 3.8 11.4 + - - -
84M PRO* 4.1 2.0 - - + -
85M GLU* 3.8 25.6 + - - +
102M LEU* 4.1 17.3 - - + -
105M THR* 6.5 0.7 - - + -
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Residues in contact with ALA 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M LEU 2.9 13.8 + - - +
23M GLU* 3.5 9.6 - - - +
25M TYR* 1.3 78.6 - - - +
27M SER* 1.3 60.9 + - - +
29M THR* 3.3 2.9 + - - -
30M TYR* 3.1 31.6 + - + -
58M GLU* 4.2 15.7 - - + -
102M LEU* 4.0 25.1 - - + -
103M GLU* 6.5 0.4 - - - -
106M VAL* 4.2 19.7 - - + -
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Residues in contact with SER 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M GLU 2.9 17.5 + - - -
24M LEU* 3.5 11.5 - - - +
26M ALA* 1.3 76.7 - - - +
28M TYR* 1.3 62.3 + - - +
30M TYR 3.1 2.8 + - - -
31M SER* 3.0 19.2 + - - -
55M SER* 2.9 40.2 + - - +
58M GLU* 3.8 12.9 - - - +
59M ARG* 3.6 16.6 - - - +
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Residues in contact with TYR 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M LEU 3.0 19.0 + - - +
25M TYR* 3.2 6.3 + - - +
27M SER* 1.3 76.8 - - - +
29M THR* 1.3 60.5 + - - +
31M SER* 3.2 16.0 - - - -
32M SER* 3.2 18.4 + - - -
81M ILE* 4.0 13.0 - - + -
82M LYS 3.6 18.8 - - - +
83M LYS* 4.0 3.1 - - - -
84M PRO* 3.7 17.6 - - + +
21S ASN* 4.4 2.8 + - - +
24S LEU* 3.6 28.6 - - + +
66S MET* 5.5 0.4 - - + -
78S LEU* 3.4 37.3 - - + +
79S GLN 3.0 30.0 + - - -
81S ILE* 3.7 22.6 - - + +
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Residues in contact with THR 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M TYR* 2.9 30.9 + - + -
26M ALA* 3.6 8.7 - - - -
27M SER 3.2 0.2 - - - -
28M TYR* 1.3 75.9 - - - +
30M TYR* 1.3 62.9 + - - +
32M SER* 3.2 7.1 + - - -
33M MET* 3.2 39.0 + - + +
84M PRO* 3.4 21.9 - - + +
85M GLU* 6.1 0.2 - - - +
89M TRP* 4.0 15.9 - - + -
102M LEU* 3.7 25.6 - - + -
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Residues in contact with TYR 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M ALA* 3.1 23.5 + - + -
27M SER 3.1 6.0 + - - +
29M THR* 1.3 73.6 - - - +
31M SER* 1.3 59.6 + - - +
33M MET* 3.2 13.4 + - + +
34M TYR* 2.8 29.1 + - - +
50M PHE* 5.9 0.7 - + - -
51M PHE* 3.6 47.5 - + - +
54M HIS* 3.9 29.2 - + + -
55M SER* 3.7 7.9 - - - -
58M GLU* 4.0 13.0 - - + -
99M ALA* 3.9 24.9 + - + +
102M LEU* 3.9 17.5 - - + +
103M GLU* 2.8 41.3 + - - +
144M ILE* 4.3 2.9 - - - +
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Residues in contact with SER 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M SER 3.0 12.1 + - - -
28M TYR* 3.2 23.9 - - - -
30M TYR* 1.3 75.7 - - - +
32M SER* 1.3 61.5 + - - +
34M TYR* 3.4 12.0 + - - +
35M ALA* 3.1 23.2 + - - +
55M SER* 3.8 12.4 + - - -
24S LEU* 6.1 0.5 - - - +
63S GLU* 4.8 6.2 + - - +
66S MET* 3.3 31.6 - - - +
78S LEU* 4.9 1.6 - - - -
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Residues in contact with SER 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M TYR 3.2 5.4 + - - -
29M THR 3.2 12.0 + - - -
30M TYR 3.2 0.4 - - - -
31M SER* 1.3 74.5 - - - +
33M MET* 1.3 60.5 + - - +
35M ALA* 3.2 7.0 + - - +
36M PHE* 2.9 28.2 + - - +
84M PRO* 3.2 28.7 - - - +
86M ARG 4.0 6.6 + - - -
87M ASP* 5.1 7.6 + - - +
89M TRP* 3.4 16.6 + - - -
76S VAL* 6.4 0.2 - - - -
78S LEU* 3.3 16.9 - - - +
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Residues in contact with MET 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M THR* 3.2 33.3 + - + +
30M TYR* 3.5 16.4 - - + +
32M SER* 1.3 76.6 - - - +
34M TYR* 1.3 65.7 + - - +
36M PHE* 3.3 0.9 + - - +
37M PHE* 3.0 33.2 + - + -
51M PHE* 3.8 42.6 - - + -
89M TRP* 3.7 43.5 - - + +
95M ALA* 3.8 23.3 - - + +
98M ALA* 4.0 8.1 - - + +
99M ALA* 4.2 9.2 - - - +
102M LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M TYR 2.8 13.8 + - - +
31M SER* 3.4 15.0 - - - +
33M MET* 1.3 77.2 - - - +
35M ALA* 1.3 72.6 + - - +
37M PHE 3.4 0.3 + - - -
38M ASP* 3.2 29.9 + - + +
48M ALA* 3.2 39.2 - - + +
49M GLU* 3.6 19.9 + - - -
51M PHE* 4.0 2.6 - - - +
52M LYS* 3.7 42.0 + - + +
63S GLU* 5.1 12.8 + - + +
66S MET* 4.5 23.1 - - + -
67S LYS* 3.3 36.5 - - + +
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Residues in contact with ALA 35 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M SER 3.1 10.4 + - - +
32M SER* 3.6 9.0 - - - +
34M TYR* 1.3 84.9 - - - +
36M PHE* 1.3 63.2 + - - +
38M ASP* 4.4 0.9 - - - -
39M ARG* 3.5 9.6 + - - +
66S MET* 4.3 14.8 - - + -
70S ASN* 3.0 28.2 + - - +
76S VAL* 4.1 32.1 - - + -
----------------------------------------------------------
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Residues in contact with PHE 36 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M SER 2.9 16.8 + - - +
33M MET 3.5 4.9 - - - +
34M TYR 3.1 0.2 - - - -
35M ALA* 1.3 78.1 - - - +
37M PHE* 1.3 85.4 + + - +
39M ARG* 3.3 52.7 - - - +
42M VAL* 3.3 35.6 - - + +
87M ASP 4.5 3.6 - - - +
88M GLU* 3.8 12.6 - - + -
89M TRP* 3.6 32.8 - - + -
90M GLY* 3.5 42.2 - - - -
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Residues in contact with PHE 37 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M MET* 3.0 27.4 + - + +
34M TYR 4.0 0.2 - - - -
36M PHE* 1.3 90.5 - + - +
38M ASP* 1.3 60.8 + - - +
39M ARG 3.2 0.7 - - - -
42M VAL* 3.5 22.2 - - + -
43M ALA* 3.5 6.9 + - - -
44M LEU* 3.2 50.5 + - + +
45M HIS* 4.3 0.9 + - - -
47M VAL* 3.9 11.7 - - + -
48M ALA* 3.7 14.4 - - + -
51M PHE* 3.7 19.7 - + - -
89M TRP* 4.8 0.2 - - + -
91M ASN* 3.5 24.0 - - - -
92M THR* 3.6 28.0 - - - -
95M ALA* 3.7 22.7 - - + -
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Residues in contact with ASP 38 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LYS* 3.0 31.6 + - - -
34M TYR* 3.2 28.1 + - + +
35M ALA* 4.3 1.8 - - - -
36M PHE 3.2 0.4 - - - -
37M PHE* 1.3 74.7 - - - +
39M ARG* 1.3 60.4 + - - +
45M HIS* 3.4 22.5 + - - -
48M ALA* 4.1 3.4 - - + +
67S LYS* 3.1 45.3 + - - +
70S ASN* 3.2 32.3 + - - +
----------------------------------------------------------
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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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