Contacts of the helix formed by residues 10 - 38 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P ARG* 4.0 3.9 + - - +
8P TYR 3.7 1.4 + - - -
9P HIS* 1.3 83.1 + - - +
11P ASP* 1.3 65.7 + - - +
13P GLU* 3.4 18.7 + - - +
14P ALA* 3.1 22.7 + - - +
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Residues in contact with ASP 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P HIS* 2.8 23.7 + - + +
10P SER* 1.3 73.9 - - - +
12P CYS* 1.3 61.7 + - - +
14P ALA* 3.4 7.1 + - - +
15P ALA* 2.9 29.1 + - - +
18P ARG* 4.6 1.9 + - - -
116P LEU* 3.6 21.7 - - + +
120P LYS* 3.1 21.9 + - - +
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Residues in contact with CYS 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P TYR* 4.1 9.9 - - + -
9P HIS* 3.1 24.8 + - + +
11P ASP* 1.3 79.9 - - - +
13P GLU* 1.3 57.5 + - - +
15P ALA* 3.1 3.1 + - - +
16P VAL* 2.9 35.5 + - - +
113P LEU* 4.3 0.8 - - - +
116P LEU* 4.0 24.7 - - - -
117P ALA* 4.3 8.3 - - - -
120P LYS* 4.1 16.4 - - - -
122P ASP* 5.0 5.2 - - - -
125P LEU* 4.0 26.7 - - + -
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Residues in contact with GLU 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P ARG* 2.7 34.3 + - - -
8P TYR* 3.7 20.7 + - + -
9P HIS 3.1 8.1 + - - +
10P SER* 3.5 17.9 + - - +
12P CYS* 1.3 80.3 - - - +
14P ALA* 1.3 62.0 + - - +
16P VAL 3.3 0.7 + - - -
17P ASN* 3.1 22.2 + - - +
69P GLN* 3.2 26.9 + - - +
74P GLY* 3.8 2.0 - - - -
75P ARG* 2.9 31.9 + - - +
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Residues in contact with ALA 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P SER 3.1 16.7 + - - +
11P ASP* 3.7 7.4 - - - +
12P CYS 3.3 0.2 - - - -
13P GLU* 1.3 78.4 - - - +
15P ALA* 1.3 63.0 + - - +
17P ASN* 3.5 10.8 + - - +
18P ARG* 3.1 38.0 + - - +
79P GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P ASP 2.9 17.5 + - - +
12P CYS 3.5 1.3 - - - +
14P ALA* 1.3 75.1 - - - +
16P VAL* 1.3 61.1 + - - +
18P ARG* 3.3 24.6 + - - +
19P MET* 2.9 28.6 + - - +
113P LEU* 3.5 27.0 - - + +
116P LEU* 3.7 11.2 - - + -
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Residues in contact with VAL 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P TYR* 3.6 15.0 - - - +
12P CYS 2.9 19.1 + - - +
13P GLU 3.6 5.4 - - - +
15P ALA* 1.3 76.8 - - - +
17P ASN* 1.3 56.9 + - - +
19P MET* 3.2 7.4 + - - +
20P LEU* 2.9 29.4 + - + +
65P PHE* 3.9 32.9 - - + +
68P TYR* 4.6 5.4 - - + -
69P GLN* 3.5 21.8 - - + +
113P LEU* 4.3 12.6 - - + -
125P LEU* 4.3 23.6 - - + -
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Residues in contact with ASN 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P GLU* 3.1 15.2 + - - +
14P ALA* 3.6 11.7 - - - +
15P ALA 3.3 0.2 - - - -
16P VAL* 1.3 75.8 - - - +
18P ARG* 1.3 62.6 + - - +
20P LEU* 3.5 17.2 - - - +
21P ASN* 3.4 19.8 + - - +
69P GLN* 3.4 13.0 + - - +
75P ARG 3.2 19.0 + - - -
76P VAL* 3.3 10.4 - - - -
77P VAL* 3.1 46.8 + - - +
79P GLN* 4.6 9.0 + - - +
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Residues in contact with ARG 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P ASP 4.6 2.4 + - - -
14P ALA* 3.1 22.3 + - - +
15P ALA* 3.4 34.0 - - - +
17P ASN* 1.3 79.5 - - - +
19P MET* 1.3 64.5 + - - +
21P ASN* 3.4 6.8 + - - +
22P LEU* 3.1 21.0 + - - +
79P GLN* 4.8 16.4 - - - +
116P LEU* 5.4 2.0 - - - +
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Residues in contact with MET 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P ALA 2.9 16.4 + - - +
16P VAL* 3.5 6.3 - - - +
18P ARG* 1.3 75.8 - - - +
20P LEU* 1.3 63.7 + - - +
22P LEU* 3.2 13.5 + - - +
23P GLU* 2.9 27.8 + - + +
65P PHE* 3.4 31.0 - - + -
106P VAL* 4.6 3.4 - - - +
109P ALA* 3.1 50.7 - - + +
110P LEU* 3.5 22.2 - - + +
113P LEU* 3.7 20.0 - - + -
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Residues in contact with LEU 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P VAL* 2.9 15.8 + - + +
17P ASN* 3.5 20.4 - - - +
19P MET* 1.3 77.6 - - - +
21P ASN* 1.3 63.6 + - - +
23P GLU* 3.3 8.9 + - - +
24P LEU* 3.1 41.1 + - + +
62P ALA* 3.7 17.1 - - - +
65P PHE* 4.2 14.1 - - + +
66P MET* 3.8 36.1 - - + +
69P GLN* 5.8 0.7 - - + +
76P VAL* 4.0 18.6 - - + -
77P VAL 5.6 0.7 - - - +
78P LEU* 3.7 17.5 - - + -
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Residues in contact with ASN 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ASN 3.4 8.1 + - - +
18P ARG 3.6 8.0 - - - +
19P MET 3.2 0.6 - - - -
20P LEU* 1.3 82.9 - - + +
22P LEU* 1.3 62.0 + - - +
24P LEU* 3.1 8.5 + - - +
25P TYR* 2.8 30.1 + - - +
79P GLN* 3.5 44.4 + - - +
80P ASP 3.2 26.6 + - - +
81P ILE* 4.3 7.7 - - - +
82P LYS 5.6 0.9 + - - -
28T TYR* 4.4 4.8 + - - +
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Residues in contact with LEU 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P ARG 3.1 12.9 + - - +
19P MET* 3.2 15.9 + - - +
21P ASN* 1.3 78.9 + - - +
23P GLU* 1.3 56.7 + - - +
25P TYR* 3.2 23.0 + - + +
26P ALA* 2.9 26.5 + - - +
102P LEU* 5.4 1.3 - - + -
105P THR* 4.4 17.0 - - + +
106P VAL* 3.9 30.9 - - + +
109P ALA* 3.7 30.5 - - + -
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Residues in contact with GLU 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P MET* 2.9 20.3 + - + +
20P LEU 3.4 9.2 - - - +
21P ASN 3.2 0.2 - - - -
22P LEU* 1.3 77.0 - - - +
24P LEU* 1.3 57.6 + - - +
26P ALA* 3.3 5.1 + - - +
27P SER* 2.9 27.7 + - - -
58P GLU* 2.7 21.5 - - - +
61P HIS* 3.4 18.6 + - + +
62P ALA* 3.8 13.5 - - + -
65P PHE* 4.1 19.0 - - + -
106P VAL* 4.0 14.8 - - - +
110P LEU* 4.9 2.6 - - - +
133P TYR* 3.7 15.4 - - - -
176P MG 2.4 30.6 - - - -
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Residues in contact with LEU 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P LEU* 3.1 30.4 + - + +
21P ASN* 3.5 9.2 - - - +
23P GLU* 1.3 76.8 - - - +
25P TYR* 1.3 57.0 + - - +
27P SER* 3.5 6.9 - - - -
28P TYR* 3.0 27.5 + - - +
59P ARG* 4.9 17.7 - - + -
62P ALA* 3.7 18.4 - - + -
63P GLU* 6.4 0.4 - - + -
66P MET* 5.1 6.3 - - + -
78P LEU* 4.8 0.2 - - + -
81P ILE* 3.7 24.1 - - + +
28T TYR* 3.6 39.0 - - + +
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Residues in contact with TYR 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P ASN* 2.8 17.9 + - - +
22P LEU* 3.4 27.4 - - + +
24P LEU* 1.3 74.2 - - - +
26P ALA* 1.3 63.8 + - - +
28P TYR* 3.2 3.8 + - - +
29P THR* 2.9 48.1 + - - -
81P ILE* 4.0 9.6 - - + +
82P LYS* 3.4 38.8 - - + +
83P LYS 3.8 11.2 + - - -
84P PRO* 4.1 2.0 - - + -
85P GLU* 3.8 25.3 + - - +
102P LEU* 4.1 17.7 - - + -
105P THR* 6.5 0.2 - - + -
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Residues in contact with ALA 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P LEU 2.9 13.6 + - - +
23P GLU* 3.3 10.1 + - - +
25P TYR* 1.3 76.0 - - - +
27P SER* 1.3 63.1 + - - +
29P THR* 3.3 2.9 + - - -
30P TYR* 3.1 32.1 + - + -
58P GLU* 4.2 15.5 - - + -
102P LEU* 4.0 25.4 - - + -
103P GLU* 6.5 0.2 - - - -
106P VAL* 4.2 19.3 - - + -
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Residues in contact with SER 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P GLU 2.9 16.5 + - - -
24P LEU* 3.5 10.9 - - - +
25P TYR 3.2 0.2 - - - -
26P ALA* 1.3 76.9 - - - +
28P TYR* 1.3 61.7 + - - +
30P TYR 3.1 2.6 + - - -
31P SER* 3.0 19.3 + - - -
55P SER* 2.9 39.7 + - - +
58P GLU* 3.8 12.7 - - - +
59P ARG* 3.6 17.5 - - - +
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Residues in contact with TYR 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P LEU 3.0 19.4 + - - +
25P TYR* 3.5 6.1 - - - +
27P SER* 1.3 78.3 + - - +
29P THR* 1.3 61.2 + - - +
31P SER* 3.2 16.0 - - - -
32P SER* 3.2 18.5 + - - -
81P ILE* 4.0 12.8 - - + -
82P LYS 3.6 17.7 - - - -
83P LYS* 4.0 3.6 - - - -
84P PRO* 3.7 18.1 - - + +
20T LEU* 5.1 0.2 - - - +
21T ASN* 4.4 3.1 + - - +
24T LEU* 3.6 27.9 - - + +
66T MET* 5.5 0.4 - - + -
78T LEU* 3.4 37.3 - - + +
79T GLN 3.0 30.4 + - - -
81T ILE* 3.7 22.7 - - + +
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Residues in contact with THR 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P TYR* 2.9 30.7 + - + +
26P ALA 3.6 8.1 - - - -
27P SER 3.2 0.4 - - - -
28P TYR* 1.3 76.5 - - - +
30P TYR* 1.3 61.4 + - - +
32P SER* 3.2 6.9 + - - -
33P MET* 3.2 39.6 + - + +
84P PRO* 3.4 21.0 - - - +
85P GLU 5.0 0.4 + - - +
89P TRP* 4.0 15.3 - - + -
102P LEU* 3.7 25.8 - - + -
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Residues in contact with TYR 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ALA* 3.1 23.8 + - + -
27P SER 3.1 6.5 + - - +
29P THR* 1.3 73.9 - - - +
31P SER* 1.3 59.7 + - - +
33P MET* 3.2 11.5 + - + +
34P TYR* 2.8 29.1 + - - +
50P PHE* 5.9 0.2 - + - -
51P PHE* 3.6 47.2 - + - +
54P HIS* 3.9 29.8 - + + -
55P SER* 3.7 7.0 - - - -
58P GLU* 4.0 12.8 - - + -
99P ALA* 3.9 25.1 + - + +
102P LEU* 3.9 18.1 - - + +
103P GLU* 2.8 41.5 + - - +
144P ILE* 4.3 3.7 - - + +
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Residues in contact with SER 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P SER 3.0 12.0 + - - -
28P TYR* 3.2 24.6 - - - -
30P TYR* 1.3 75.8 - - - +
32P SER* 1.3 61.1 + - - +
34P TYR* 3.4 13.3 + - - +
35P ALA* 3.1 22.5 + - - +
55P SER* 3.8 12.7 + - - -
24T LEU* 6.1 0.5 - - - +
63T GLU* 4.8 6.6 + - - +
66T MET* 3.3 30.7 - - - +
78T LEU* 4.8 1.3 - - - -
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Residues in contact with SER 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P TYR 3.2 5.5 + - - -
29P THR 3.2 10.9 + - - -
30P TYR 3.2 0.2 - - - -
31P SER* 1.3 73.3 - - - +
33P MET* 1.3 60.4 + - - +
35P ALA* 3.2 7.2 + - - +
36P PHE* 2.9 28.9 + - - +
84P PRO* 3.2 29.6 - - - +
86P ARG 4.0 6.4 + - - -
87P ASP* 5.1 7.4 + - - +
89P TRP* 3.4 17.7 + - - -
76T VAL* 6.4 0.2 - - - -
78T LEU* 3.3 18.2 - - - +
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Residues in contact with MET 33 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P THR* 3.2 34.2 + - + +
30P TYR* 3.2 15.5 + - + +
32P SER* 1.3 75.7 - - - +
34P TYR* 1.3 65.6 + - - +
36P PHE* 3.3 0.9 + - - +
37P PHE* 3.0 32.8 + - + -
51P PHE* 3.8 43.5 - - + -
89P TRP* 3.7 44.2 - - + +
95P ALA* 3.8 23.3 - - + +
98P ALA* 4.0 8.1 - - + -
99P ALA* 4.2 9.0 - - - +
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Residues in contact with TYR 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TYR 2.8 14.2 + - - +
31P SER* 3.4 15.3 - - - +
33P MET* 1.3 77.0 - - - +
35P ALA* 1.3 73.5 + - - +
36P PHE 3.3 0.3 + - - -
37P PHE 3.4 0.3 + - - -
38P ASP* 3.2 29.7 + - + +
48P ALA* 3.2 37.8 - - + +
49P GLU* 3.6 19.7 + - - -
51P PHE* 4.0 2.4 - - - +
52P LYS* 3.7 41.4 + - + +
63T GLU* 5.1 13.2 + - + -
66T MET* 4.5 21.5 - - + -
67T LYS* 3.3 36.0 - - + +
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Residues in contact with ALA 35 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P SER 3.1 10.6 + - - +
32P SER* 3.2 8.9 + - - +
34P TYR* 1.3 85.1 - - - +
36P PHE* 1.3 63.4 + - - +
38P ASP* 4.4 0.9 - - - -
39P ARG* 3.5 10.0 + - - +
66T MET* 4.3 15.3 - - + -
70T ASN* 3.0 28.3 + - - +
76T VAL* 4.2 31.2 - - + -
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Residues in contact with PHE 36 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P SER 2.9 16.6 + - - +
33P MET 3.5 4.5 - - - +
34P TYR 3.1 0.2 - - - -
35P ALA* 1.3 77.2 - - - +
37P PHE* 1.3 84.5 + + - +
39P ARG* 3.3 53.1 - - - +
42P VAL* 3.3 35.4 - - + +
87P ASP 4.5 3.4 - - - +
88P GLU* 3.8 11.4 - - + -
89P TRP* 3.6 33.7 - - + -
90P GLY* 3.5 42.0 - - - -
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Residues in contact with PHE 37 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET* 3.0 28.1 + - + +
34P TYR 3.4 0.2 + - - -
36P PHE* 1.3 90.1 - + - +
38P ASP* 1.3 60.6 + - - +
39P ARG 3.2 0.4 - - - -
42P VAL* 3.5 22.0 - - + -
43P ALA* 3.5 7.3 + - - -
44P LEU* 3.2 50.7 + - + +
45P HIS* 4.3 0.9 + - - -
47P VAL* 3.9 11.4 - - + -
48P ALA* 3.7 14.4 - - + -
51P PHE* 3.7 19.3 - + - -
89P TRP* 4.8 0.4 - - + -
91P ASN* 3.5 24.9 - - - -
92P THR* 3.6 27.6 - - - -
95P ALA* 3.7 21.8 - - + -
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Residues in contact with ASP 38 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L LYS* 2.9 31.4 + - - -
34P TYR* 3.2 28.9 + - + +
35P ALA* 4.3 1.6 - - - -
36P PHE 3.2 0.4 - - - -
37P PHE* 1.3 74.8 - - - +
39P ARG* 1.3 61.5 + - - +
45P HIS* 3.4 24.0 + - - -
48P ALA* 4.5 2.1 - - + +
67T LYS* 3.1 44.4 + - - +
70T ASN* 3.2 31.1 + - - +
----------------------------------------------------------
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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