Contacts of the helix formed by residues 10 - 38 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 4.0 3.5 + - - +
8C TYR 3.7 2.0 + - - -
9C HIS* 1.3 82.9 + - - +
11C ASP* 1.3 64.1 + - - +
13C GLU* 3.4 19.3 + - - +
14C ALA* 3.1 22.9 + - - +
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Residues in contact with ASP 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C HIS* 2.8 23.7 + - - +
10C SER* 1.3 74.1 - - - +
12C CYS* 1.3 62.9 + - - +
14C ALA* 3.4 6.7 + - - +
15C ALA* 2.9 29.5 + - - +
18C ARG* 4.6 2.3 + - - -
116C LEU* 3.6 20.7 - - + +
120C LYS* 3.1 22.2 + - - +
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Residues in contact with CYS 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C TYR* 4.1 10.5 - - + -
9C HIS* 3.1 26.3 + - + +
11C ASP* 1.3 79.0 - - - +
13C GLU* 1.3 58.6 + - - +
15C ALA* 3.1 3.0 + - - +
16C VAL* 2.9 35.9 + - - +
113C LEU* 4.3 1.0 - - - +
116C LEU* 4.0 25.4 - - - -
117C ALA* 4.3 7.6 - - - -
120C LYS* 4.1 15.0 - - - -
122C ASP* 5.0 4.9 - - - -
125C LEU* 4.0 26.2 - - + -
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Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 2.7 33.3 + - - -
8C TYR* 3.7 20.5 + - + -
9C HIS 3.1 8.3 + - - +
10C SER* 3.5 18.0 + - - +
12C CYS* 1.3 79.6 - - - +
14C ALA* 1.3 63.1 + - - +
16C VAL 3.3 0.5 + - - -
17C ASN* 3.1 22.0 + - - +
69C GLN* 3.2 27.8 + - - +
74C GLY* 3.8 2.5 - - - -
75C ARG* 2.9 32.8 + - - +
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Residues in contact with ALA 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C SER 3.1 17.2 + - - +
11C ASP* 3.7 7.6 - - - +
13C GLU* 1.3 79.1 - - - +
15C ALA* 1.3 61.7 + - - +
17C ASN* 3.5 10.6 + - - +
18C ARG* 3.1 38.5 + - - +
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Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP 2.9 16.5 + - - +
12C CYS 3.1 1.5 + - - +
14C ALA* 1.3 76.1 - - - +
16C VAL* 1.3 60.7 + - - +
18C ARG* 3.3 23.9 + - - +
19C MET* 2.9 29.3 + - - +
113C LEU* 3.5 28.4 - - + +
116C LEU* 3.7 11.2 - - + -
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Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C TYR* 3.6 14.4 - - - +
12C CYS 2.9 20.2 + - - +
13C GLU 3.6 4.9 - - - +
14C ALA 3.3 0.2 - - - -
15C ALA* 1.3 75.7 - - - +
17C ASN* 1.3 57.3 + - - +
19C MET* 3.2 7.3 + - - +
20C LEU* 2.9 30.1 + - + +
65C PHE* 3.9 33.8 - - + +
68C TYR* 4.6 4.9 - - + -
69C GLN* 3.5 22.4 - - + +
113C LEU* 4.3 11.9 - - + -
125C LEU* 4.3 23.3 - - + -
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Residues in contact with ASN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU* 3.1 15.6 + - - +
14C ALA* 3.6 12.4 - - - +
15C ALA 3.3 0.2 - - - -
16C VAL* 1.3 75.8 - - - +
18C ARG* 1.3 61.6 + - - +
20C LEU* 3.5 17.8 - - - +
21C ASN* 3.4 19.4 + - - +
69C GLN* 3.4 12.0 + - - +
75C ARG 3.2 19.0 + - - -
76C VAL* 3.3 10.0 - - - -
77C VAL* 3.1 48.9 + - - +
79C GLN* 4.6 9.0 + - - +
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Residues in contact with ARG 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP 4.6 3.0 + - - -
14C ALA* 3.1 21.2 + - - +
15C ALA* 3.4 34.3 - - - +
16C VAL 3.1 0.2 - - - -
17C ASN* 1.3 79.9 - - - +
19C MET* 1.3 64.3 + - - +
21C ASN* 3.4 7.0 + - + +
22C LEU* 3.1 20.8 + - - +
79C GLN* 4.8 17.0 - - - +
116C LEU* 5.4 2.4 - - - +
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Residues in contact with MET 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA 2.9 17.5 + - - +
16C VAL* 3.2 6.0 + - - +
18C ARG* 1.3 75.4 - - - +
20C LEU* 1.3 64.1 + - - +
22C LEU* 3.2 13.0 + - - +
23C GLU* 2.9 27.8 + - + +
65C PHE* 3.4 30.7 - - + -
106C VAL* 4.6 3.1 - - - +
109C ALA* 3.1 51.1 - - + +
110C LEU* 3.5 20.6 - - + +
113C LEU* 3.7 19.3 - - + -
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL* 2.9 17.7 + - + +
17C ASN* 3.5 19.3 - - - +
19C MET* 1.3 78.0 - - - +
21C ASN* 1.3 63.3 + - + +
23C GLU* 3.4 8.3 + - - +
24C LEU* 3.1 42.1 + - + +
62C ALA* 3.7 17.0 - - - +
65C PHE* 4.2 13.9 - - + +
66C MET* 3.8 35.4 - - + +
69C GLN* 5.8 0.2 - - - +
76C VAL* 4.0 18.6 - - + -
77C VAL 5.6 0.7 - - - +
78C LEU* 3.7 17.0 - - + -
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Residues in contact with ASN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASN 3.4 7.8 + - - +
18C ARG 3.6 8.5 - - - +
19C MET 3.2 0.4 - - - -
20C LEU* 1.3 82.3 - - + +
22C LEU* 1.3 60.6 + - - +
24C LEU* 3.1 8.4 + - - +
25C TYR* 2.8 30.0 + - - +
79C GLN* 3.5 43.5 + - - +
80C ASP 3.2 27.7 + - - +
81C ILE* 4.3 9.6 - - - +
82C LYS 5.6 0.7 + - - -
28O TYR* 4.4 2.2 + - - +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG 3.1 13.3 + - - +
19C MET* 3.2 15.0 + - - +
21C ASN* 1.3 78.2 + - - +
23C GLU* 1.3 58.0 + - - +
25C TYR* 3.2 24.3 + - + -
26C ALA* 2.9 26.7 + - - +
102C LEU* 5.4 1.1 - - + -
105C THR* 4.4 16.8 - - + +
106C VAL* 3.9 30.7 - - + +
109C ALA* 3.7 30.5 - - + -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C MET* 2.9 20.4 + - + +
20C LEU 3.4 9.0 - - - +
22C LEU* 1.3 76.7 - - - +
24C LEU* 1.3 58.2 + - - +
26C ALA* 3.3 5.2 + - - +
27C SER* 2.9 27.9 + - - -
58C GLU* 2.7 20.7 - - - +
61C HIS* 3.4 18.1 - - + +
62C ALA* 3.8 13.9 - - + +
65C PHE* 4.1 19.0 - - + -
106C VAL* 4.0 14.5 - - + +
110C LEU* 4.9 2.9 - - - +
133C TYR* 3.7 15.2 - - - -
176C MG 2.4 29.8 - - - -
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.1 33.5 + - + +
21C ASN* 3.1 10.1 + - - +
23C GLU* 1.3 75.3 - - - +
25C TYR* 1.3 56.0 + - - +
27C SER* 3.5 6.8 - - - -
28C TYR* 3.0 27.7 + - - +
59C ARG* 4.9 16.8 - - + -
62C ALA* 3.7 19.1 - - + -
63C GLU* 6.4 0.4 - - + -
66C MET* 5.1 6.3 - - + -
81C ILE* 3.7 25.1 - - + +
28O TYR* 3.6 37.5 - - + +
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Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASN* 2.8 17.9 + - - +
22C LEU* 3.4 28.0 - - + +
23C GLU 3.2 0.2 - - - -
24C LEU* 1.3 73.0 - - - +
26C ALA* 1.3 62.9 - - - +
28C TYR* 3.2 4.2 + - + +
29C THR* 2.9 47.9 + - + -
81C ILE* 4.0 10.7 - - + +
82C LYS* 3.4 37.0 - - + +
83C LYS 3.8 12.1 + - - -
84C PRO* 4.1 2.0 - - + -
85C GLU* 3.8 25.6 + - - +
102C LEU* 4.1 16.8 - - + -
105C THR* 6.5 0.4 - - + -
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU 2.9 14.0 + - - +
23C GLU* 3.3 9.8 + - - +
25C TYR* 1.3 77.1 - - - +
27C SER* 1.3 62.0 + - - +
29C THR* 3.3 2.4 + - - -
30C TYR* 3.1 31.2 + - + -
58C GLU* 4.2 15.3 - - + -
102C LEU* 4.0 26.0 - - + -
103C GLU* 6.5 0.7 - - - -
106C VAL* 4.2 19.3 - - + -
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Residues in contact with SER 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLU 2.9 17.1 + - - -
24C LEU* 3.5 11.6 - - - +
26C ALA* 1.3 75.8 - - - +
28C TYR* 1.3 61.8 + - - +
30C TYR 3.1 2.8 + - - -
31C SER* 3.0 19.2 + - - -
55C SER* 2.9 39.4 + - - +
58C GLU* 3.8 12.3 - - - +
59C ARG* 3.6 17.7 - - - +
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Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU 3.0 18.6 + - - +
25C TYR* 3.2 6.0 + - - +
27C SER* 1.3 76.4 - - - +
29C THR* 1.3 59.9 + - - +
31C SER* 3.2 16.1 - - - -
32C SER* 3.2 18.4 + - - -
81C ILE* 4.0 12.3 - - + -
82C LYS 3.6 18.6 - - - +
83C LYS* 4.0 3.6 - - - -
84C PRO* 3.7 17.7 - - + +
20O LEU* 5.2 0.2 - - - +
21O ASN* 4.4 3.1 + - - +
24O LEU* 3.6 28.0 - - + +
66O MET* 5.5 0.4 - - + -
78O LEU* 3.3 37.8 - - + +
79O GLN 3.0 30.2 + - - -
81O ILE* 3.8 22.2 - - + +
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Residues in contact with THR 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 2.9 31.1 + - + +
26C ALA 3.6 8.3 - - - -
27C SER 3.2 0.2 - - - -
28C TYR* 1.3 76.1 - - - +
30C TYR* 1.3 61.9 + - - +
32C SER* 3.2 6.4 + - - -
33C MET* 3.2 39.7 + - + +
84C PRO* 3.4 21.5 - - + +
85C GLU* 5.0 0.6 + - - +
89C TRP* 4.0 15.9 - - + -
102C LEU* 3.7 25.1 - - + -
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Residues in contact with TYR 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA* 3.1 24.5 + - + -
27C SER 3.5 6.1 - - - +
29C THR* 1.3 72.5 - - - +
31C SER* 1.3 60.6 + - - +
33C MET* 3.2 13.2 + - + +
34C TYR* 2.8 28.9 + - - +
50C PHE* 5.9 0.2 - + - -
51C PHE* 3.6 47.5 - + - +
54C HIS* 3.9 28.3 - + + -
55C SER* 3.7 7.6 - - - -
58C GLU* 4.0 12.8 - - + -
99C ALA* 3.9 24.9 + - + +
102C LEU* 3.9 17.2 - - + +
103C GLU* 2.8 41.0 + - - +
144C ILE* 4.3 3.4 - - + +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C SER 3.0 11.6 + - - -
28C TYR* 3.2 23.5 - - - -
30C TYR* 1.3 75.7 - - - +
32C SER* 1.3 61.7 + - - +
34C TYR* 3.4 12.2 + - - +
35C ALA* 3.1 22.7 + - - +
55C SER* 3.8 13.9 + - - -
24O LEU* 6.1 0.2 - - - +
63O GLU* 4.9 6.1 + - - +
66O MET* 3.4 29.5 - - - +
78O LEU* 4.9 2.7 - - - -
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR 3.2 5.3 + - - -
29C THR 3.2 11.6 + - - -
30C TYR 3.2 0.2 - - - -
31C SER* 1.3 74.1 - - - +
33C MET* 1.3 60.3 + - - -
35C ALA* 3.2 7.0 + - - +
36C PHE* 2.9 28.6 + - - +
84C PRO* 3.2 29.0 - - - +
86C ARG 4.0 6.2 + - - -
87C ASP* 5.1 7.7 + - - +
89C TRP* 3.4 17.0 + - - -
78O LEU* 3.4 17.3 - - - +
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Residues in contact with MET 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C THR* 3.2 33.5 + - + +
30C TYR* 3.2 16.1 + - + +
32C SER* 1.3 77.1 - - - +
34C TYR* 1.3 65.1 + - - +
36C PHE* 3.3 0.7 + - - +
37C PHE* 3.0 33.5 + - + -
51C PHE* 3.8 42.8 - - + -
89C TRP* 3.7 42.6 - - + +
95C ALA* 3.8 23.6 - - + +
98C ALA* 4.0 7.9 - - + -
99C ALA* 4.2 9.0 - - - +
102C LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR 2.8 13.3 + - - +
31C SER* 3.4 15.5 - - - +
32C SER 3.2 0.2 - - - -
33C MET* 1.3 77.1 - - - +
35C ALA* 1.3 73.1 + - - +
37C PHE 3.4 0.5 + - - -
38C ASP* 3.2 30.2 + - + +
48C ALA* 3.2 37.7 - - + +
49C GLU* 3.6 19.9 + - - -
51C PHE* 4.0 2.6 - - - +
52C LYS* 3.7 42.0 + - + +
63O GLU* 5.2 11.8 + - + -
66O MET* 4.6 23.3 - - + -
67O LYS* 3.3 38.1 - - + +
70O ASN* 6.3 0.2 - - - -
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Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER 3.1 10.6 + - - +
32C SER* 3.6 9.6 - - - +
34C TYR* 1.3 85.2 - - + +
36C PHE* 1.3 62.9 + - - +
38C ASP* 4.4 1.1 - - - -
39C ARG* 3.5 10.3 + - - +
66O MET* 4.4 13.9 - - + -
70O ASN* 3.1 27.9 + - - +
76O VAL* 4.2 31.8 - - + +
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Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C SER 2.9 16.7 + - - +
33C MET 3.5 4.9 - - - +
34C TYR 3.1 0.4 - - - -
35C ALA* 1.3 78.4 - - - +
37C PHE* 1.3 84.6 + + - +
39C ARG* 3.3 52.5 - - - +
42C VAL* 3.3 35.4 - - + +
87C ASP 4.5 3.4 - - - +
88C GLU* 3.8 11.4 - - + -
89C TRP* 3.6 33.7 - - + -
90C GLY* 3.5 42.4 - - - -
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Residues in contact with PHE 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C MET* 3.0 27.6 + - + +
34C TYR 3.4 0.4 + - - -
36C PHE* 1.3 91.8 - + - +
38C ASP* 1.3 60.7 + - - +
39C ARG 3.2 0.7 - - - -
42C VAL* 3.5 22.9 - - + -
43C ALA* 3.5 6.8 + - - -
44C LEU* 3.2 50.2 + - + +
45C HIS* 4.3 0.9 + - - -
47C VAL* 3.9 10.8 - - + -
48C ALA* 3.7 14.4 - - + -
51C PHE* 3.7 19.7 - + - -
89C TRP* 4.8 0.4 - - + -
91C ASN* 3.5 23.8 - - - -
92C THR* 3.6 28.5 - - - -
95C ALA* 3.7 21.5 - - + -
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR* 3.2 28.5 + - + +
35C ALA* 4.3 1.6 - - - -
36C PHE 3.2 0.6 - - - -
37C PHE* 1.3 74.0 - - - +
39C ARG* 1.3 61.8 + - - +
45C HIS* 3.4 23.2 + - - -
48C ALA* 4.1 2.7 - - + +
142F LYS* 2.9 32.1 + - - -
67O LYS* 3.2 44.1 + - - +
70O ASN* 3.1 31.4 + - - +
----------------------------------------------------------
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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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