Contacts of the helix formed by residues 10 - 38 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5U ARG* 4.0 4.5 + - - +
8U TYR 3.7 1.8 + - - -
9U HIS* 1.3 83.4 + - - +
11U ASP* 1.3 65.0 + - - +
13U GLU* 3.4 18.2 + - - +
14U ALA* 3.1 22.9 + - - +
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Residues in contact with ASP 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U HIS* 2.8 23.7 + - + +
10U SER* 1.3 73.8 - - - +
12U CYS* 1.3 63.2 + - - +
14U ALA* 3.4 7.1 + - - +
15U ALA* 2.9 29.5 + - - +
18U ARG* 4.6 2.1 + - - -
116U LEU* 3.6 20.8 - - + +
120U LYS* 3.1 22.1 + - - +
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Residues in contact with CYS 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8U TYR* 4.1 9.9 - - + -
9U HIS* 3.1 25.3 + - + +
11U ASP* 1.3 79.9 - - - +
13U GLU* 1.3 57.5 + - - +
15U ALA* 3.1 3.3 + - - +
16U VAL* 2.9 35.5 + - - +
113U LEU* 4.3 0.8 - - - +
116U LEU* 4.0 25.1 - - - -
117U ALA* 4.3 8.1 - - - -
120U LYS* 4.1 15.9 - - - -
122U ASP* 5.0 4.9 - - - -
125U LEU* 4.0 26.7 - - + -
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Residues in contact with GLU 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5U ARG* 2.7 34.5 + - - -
8U TYR* 3.7 21.0 + - + -
9U HIS 3.1 8.1 + - - +
10U SER* 3.5 18.6 + - - +
12U CYS* 1.3 79.4 - - - +
14U ALA* 1.3 62.1 + - - +
16U VAL 3.3 0.5 + - - -
17U ASN* 3.1 22.5 + - - +
69U GLN* 3.2 27.8 + - - +
74U GLY* 3.8 2.0 - - - -
75U ARG* 2.9 32.8 + - - +
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Residues in contact with ALA 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U SER 3.1 17.8 + - - +
11U ASP* 3.7 7.6 - - - +
13U GLU* 1.3 77.8 - - - +
15U ALA* 1.3 60.9 + - - +
17U ASN* 3.5 10.0 + - - +
18U ARG* 3.1 39.4 + - - +
79U GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11U ASP 2.9 17.7 + - - +
12U CYS 3.1 1.3 + - - +
14U ALA* 1.3 74.7 - - - +
16U VAL* 1.3 60.6 - - - +
18U ARG* 3.3 24.0 + - - +
19U MET* 2.9 29.3 + - - +
113U LEU* 3.5 27.6 - - + +
116U LEU* 3.7 11.0 - - + -
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Residues in contact with VAL 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8U TYR* 3.6 14.4 - - - +
12U CYS 2.9 20.4 + - - +
13U GLU 3.6 4.7 - - - +
15U ALA* 1.3 76.3 - - - +
17U ASN* 1.3 56.7 + - - +
19U MET* 3.2 7.5 + - - +
20U LEU* 2.9 29.4 + - + +
65U PHE* 3.9 33.2 - - + +
68U TYR* 4.6 5.4 - - + -
69U GLN* 3.5 22.9 - - + +
113U LEU* 4.3 12.1 - - + -
125U LEU* 4.3 23.3 - - + -
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Residues in contact with ASN 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U GLU* 3.1 16.0 + - - +
14U ALA* 3.6 12.0 - - - +
15U ALA 3.3 0.2 - - - -
16U VAL* 1.3 75.3 - - - +
18U ARG* 1.3 62.3 + - - +
20U LEU* 3.5 17.4 - - - +
21U ASN* 3.4 19.8 + - - +
69U GLN* 3.4 12.7 + - - +
75U ARG 3.2 18.6 + - - -
76U VAL* 3.3 10.4 - - - -
77U VAL* 3.1 46.5 + - + +
79U GLN* 4.6 9.4 + - - +
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Residues in contact with ARG 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11U ASP 4.6 2.6 + - - -
14U ALA* 3.1 21.3 + - - +
15U ALA* 3.4 34.2 - - - +
16U VAL 3.1 0.4 - - - -
17U ASN* 1.3 80.3 - - - +
19U MET* 1.3 64.3 + - - +
21U ASN* 3.4 7.1 + - - +
22U LEU* 3.1 20.8 + - - +
79U GLN* 4.8 16.6 - - - +
116U LEU* 5.4 2.0 - - - +
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Residues in contact with MET 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U ALA 2.9 16.2 + - - +
16U VAL* 3.5 6.7 - - - +
18U ARG* 1.3 76.4 - - - +
20U LEU* 1.3 64.6 + - - +
22U LEU* 3.2 12.9 + - - +
23U GLU* 2.9 27.8 + - + +
65U PHE* 3.4 30.1 - - + -
106U VAL* 4.6 3.1 - - - +
109U ALA* 3.1 50.5 - - + +
110U LEU* 3.5 20.6 - - + +
113U LEU* 3.7 20.2 - - + -
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Residues in contact with LEU 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16U VAL* 2.9 16.6 + - + +
17U ASN* 3.5 19.5 - - - +
19U MET* 1.3 76.5 - - - +
21U ASN* 1.3 61.8 + - + +
23U GLU* 3.4 9.2 + - - +
24U LEU* 3.1 41.7 + - + +
62U ALA* 3.7 17.2 - - + +
65U PHE* 4.2 13.8 - - + +
66U MET* 3.8 36.6 - - + +
69U GLN* 5.8 0.4 - - + +
76U VAL* 4.0 17.9 - - + -
77U VAL 5.6 0.4 - - - +
78U LEU* 3.7 17.9 - - + -
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Residues in contact with ASN 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q TYR* 4.4 4.8 + - - +
17U ASN 3.4 7.4 + - - +
18U ARG 3.6 8.3 - - - +
19U MET 3.2 0.4 - - - -
20U LEU* 1.3 82.9 - - + +
22U LEU* 1.3 61.7 + - - +
24U LEU* 3.1 8.2 + - - +
25U TYR* 2.8 29.8 + - - +
79U GLN* 3.5 45.5 + - - +
80U ASP 3.2 27.5 + - - +
81U ILE* 4.3 7.2 - - - +
82U LYS 5.6 0.9 + - - -
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Residues in contact with LEU 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U ARG 3.1 14.1 + - - +
19U MET* 3.2 15.5 + - - +
21U ASN* 1.3 77.8 + - - +
23U GLU* 1.3 57.4 + - - +
25U TYR* 3.2 24.1 + - + +
26U ALA* 2.9 27.1 + - - +
102U LEU* 5.4 1.8 - - + -
105U THR* 4.4 16.2 - - + +
106U VAL* 3.9 31.1 - - + +
109U ALA* 3.7 31.0 - - + -
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Residues in contact with GLU 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U MET* 2.9 19.9 + - + +
20U LEU 3.4 9.4 - - - +
22U LEU* 1.3 75.9 - - - +
24U LEU* 1.3 58.7 + - - +
26U ALA* 3.3 5.4 + - - +
27U SER* 2.9 28.2 + - - -
58U GLU* 2.7 20.8 - - - +
61U HIS* 3.4 19.0 - - + +
62U ALA* 3.8 13.7 - - + -
65U PHE* 4.1 20.0 - - + -
106U VAL* 4.0 15.7 - - - +
110U LEU* 4.9 2.4 - - - +
133U TYR* 3.7 14.7 - - - -
176U MG 2.4 30.8 - - - -
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Residues in contact with LEU 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q TYR* 3.5 39.5 - - + +
20U LEU* 3.1 31.1 + - + +
21U ASN* 3.1 9.2 + - - +
23U GLU* 1.3 75.1 - - - +
25U TYR* 1.3 57.6 + - - +
27U SER* 3.5 6.7 - - - +
28U TYR* 3.0 27.5 + - - +
59U ARG* 4.9 17.3 - - + +
62U ALA* 3.7 18.4 - - + -
63U GLU* 6.4 0.2 - - + -
66U MET* 5.1 6.7 - - + -
81U ILE* 3.7 23.5 - - + +
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Residues in contact with TYR 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21U ASN* 2.8 17.4 + - - +
22U LEU* 3.4 28.0 - - + +
24U LEU* 1.3 73.6 - - - +
26U ALA* 1.3 62.6 + - - +
28U TYR* 3.2 4.4 + - + +
29U THR* 2.9 48.2 + - + +
81U ILE* 4.0 9.6 - - + +
82U LYS* 3.4 38.1 - - + +
83U LYS 3.8 11.6 + - - -
84U PRO* 4.1 1.6 - - + -
85U GLU* 3.8 25.8 + - - +
102U LEU* 4.1 16.8 - - + -
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Residues in contact with ALA 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22U LEU 2.9 14.0 + - - +
23U GLU* 3.3 9.6 + - - +
25U TYR* 1.3 76.7 - - - +
27U SER* 1.3 62.7 + - - +
29U THR* 3.3 2.8 + - - -
30U TYR* 3.1 31.5 + - + -
58U GLU* 4.2 15.3 - - + -
102U LEU* 4.0 26.7 - - + -
103U GLU* 6.5 0.4 - - - -
106U VAL* 4.2 19.5 - - + -
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Residues in contact with SER 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U GLU 2.9 16.4 + - - -
24U LEU* 3.5 11.1 - - - +
26U ALA* 1.3 75.6 - - - +
28U TYR* 1.3 62.5 + - - +
30U TYR 3.1 2.9 + - - -
31U SER* 3.0 19.3 + - - -
55U SER* 2.9 39.5 + - - +
58U GLU* 3.8 13.4 - - - +
59U ARG* 3.6 16.9 - - - +
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Residues in contact with TYR 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Q ASN* 4.4 3.1 + - - +
24Q LEU* 3.6 29.0 - - + +
66Q MET* 5.6 0.2 - - + -
78Q LEU* 3.4 37.0 - - + +
79Q GLN 2.9 30.3 + - - -
81Q ILE* 3.7 23.5 - - + +
24U LEU 3.0 18.6 + - - +
25U TYR* 3.2 5.6 + - - +
27U SER* 1.3 78.0 + - - +
29U THR* 1.3 60.4 + - - +
31U SER* 3.2 16.1 - - - -
32U SER* 3.2 19.2 + - - -
81U ILE* 4.0 13.0 - - + -
82U LYS 3.6 18.2 - - - +
83U LYS* 4.0 3.4 - - - -
84U PRO* 3.7 17.8 - - + +
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Residues in contact with THR 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U TYR* 2.9 30.3 + - + -
26U ALA 3.6 8.3 - - - -
27U SER 3.2 0.2 - - - -
28U TYR* 1.3 75.5 - - - +
30U TYR* 1.3 61.5 + - - +
32U SER* 3.2 6.8 + - - -
33U MET* 3.2 39.8 + - + +
84U PRO* 3.4 21.8 - - - +
85U GLU 5.8 0.2 - - - +
89U TRP* 4.0 15.5 - - + -
102U LEU* 3.7 26.0 - - + -
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Residues in contact with TYR 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U ALA* 3.1 23.0 + - + -
27U SER 3.1 6.7 + - - +
29U THR* 1.3 73.2 - - - +
31U SER* 1.3 60.8 + - - +
33U MET* 3.2 12.0 + - + +
34U TYR* 2.8 28.9 + - - +
50U PHE* 5.9 0.2 - + - -
51U PHE* 3.6 47.0 - + - +
54U HIS* 3.9 30.8 + + + -
55U SER* 3.7 7.9 - - - -
58U GLU* 4.0 12.8 - - + -
99U ALA* 3.9 25.4 + - + +
102U LEU* 3.9 17.6 - - + +
103U GLU* 2.8 41.5 + - - +
144U ILE* 4.3 2.9 - - + +
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Residues in contact with SER 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q LEU* 6.1 0.3 - - - +
63Q GLU* 4.9 6.2 + - - +
66Q MET* 3.3 29.6 - - - +
78Q LEU* 4.8 2.5 - - - -
27U SER 3.0 12.3 + - - -
28U TYR* 3.2 25.1 - - - -
30U TYR* 1.3 74.9 - - - +
32U SER* 1.3 61.4 + - - +
34U TYR* 3.4 11.3 + - - +
35U ALA* 3.1 22.5 + - - +
55U SER* 3.8 12.4 + - - -
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Residues in contact with SER 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Q VAL* 6.4 0.2 - - - -
78Q LEU* 3.3 16.8 - - - +
28U TYR 3.2 5.8 + - - -
29U THR 3.2 10.9 + - - -
30U TYR 3.2 0.2 - - - -
31U SER* 1.3 73.7 - - - +
33U MET* 1.3 60.9 + - - +
35U ALA* 3.2 7.3 + - - +
36U PHE* 2.9 27.7 + - - +
84U PRO* 3.2 29.5 - - - +
86U ARG 4.0 6.2 + - - -
87U ASP* 5.1 7.0 + - - +
89U TRP* 3.4 17.1 + - - -
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Residues in contact with MET 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U THR* 3.2 34.0 + - + +
30U TYR* 3.5 15.9 - - + +
32U SER* 1.3 76.8 - - - +
34U TYR* 1.3 65.4 + - - +
36U PHE* 3.3 0.9 + - - +
37U PHE* 3.0 33.7 + - + -
51U PHE* 3.8 42.6 - - + -
89U TRP* 3.7 44.2 - - + +
95U ALA* 3.8 24.5 - - + +
98U ALA* 4.0 7.9 - - + +
99U ALA* 4.2 9.0 - - - +
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Residues in contact with TYR 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q GLU* 5.1 13.1 - - + +
66Q MET* 4.5 23.8 - - + -
67Q LYS* 3.4 36.6 - - + +
30U TYR 2.8 13.3 + - - +
31U SER* 3.4 14.8 - - - +
33U MET* 1.3 78.2 - - - +
35U ALA* 1.3 71.5 + - - +
36U PHE 3.3 0.2 + - - -
37U PHE 3.4 0.7 + - - -
38U ASP* 3.2 29.5 + - + +
48U ALA* 3.2 38.1 - - + +
49U GLU* 3.6 20.1 + - - -
51U PHE* 4.0 2.6 - - - +
52U LYS* 3.7 42.9 + - + +
55U SER* 5.8 0.2 - - - +
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Residues in contact with ALA 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q MET* 4.3 15.0 - - + -
70Q ASN* 3.1 27.4 + - - +
76Q VAL* 4.2 32.3 - - + +
78Q LEU* 6.3 0.2 - - + -
31U SER 3.1 10.7 + - - +
32U SER* 3.2 8.9 + - - +
34U TYR* 1.3 85.4 - - - +
36U PHE* 1.3 62.3 + - - +
38U ASP* 4.4 0.7 - - - -
39U ARG* 3.5 9.9 + - - +
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Residues in contact with PHE 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32U SER 2.9 16.4 + - - +
33U MET 3.5 4.9 - - - +
34U TYR 3.1 0.2 - - - -
35U ALA* 1.3 79.2 - - - +
37U PHE* 1.3 87.6 + + - +
39U ARG* 3.3 52.1 - - - +
42U VAL* 3.3 35.4 - - + +
87U ASP 4.5 3.4 - - - +
88U GLU* 3.8 12.1 - - + -
89U TRP* 3.6 33.2 - - + -
90U GLY* 3.5 41.1 - - - -
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Residues in contact with PHE 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U MET* 3.0 26.7 + - + +
34U TYR 4.0 0.2 - - - -
36U PHE* 1.3 90.5 - + - +
38U ASP* 1.3 60.7 + - - +
39U ARG 3.2 0.4 - - - -
42U VAL* 3.5 23.8 - - + -
43U ALA* 3.5 7.7 + - - -
44U LEU* 3.2 49.0 + - + +
45U HIS* 4.3 0.7 + - - -
47U VAL* 3.9 12.3 - - + -
48U ALA* 3.7 14.5 - - + +
51U PHE* 3.7 20.4 - + - -
89U TRP* 4.8 0.7 - - + -
91U ASN* 3.5 23.6 - - - -
92U THR* 3.6 27.8 - - - -
95U ALA* 3.7 22.0 - - + -
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Residues in contact with ASP 38 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142N LYS* 3.0 31.0 + - - -
67Q LYS* 3.1 45.5 + - - +
70Q ASN* 3.1 31.1 + - - +
34U TYR* 3.2 29.0 + - + +
35U ALA* 4.3 1.3 - - - -
36U PHE 3.2 0.4 - - - -
37U PHE* 1.3 75.9 - - - +
39U ARG* 1.3 60.5 + - - +
45U HIS* 3.4 23.0 + - - -
48U ALA* 4.1 3.0 - - + +
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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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