Contacts of the helix formed by residues 10 - 38 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L ARG* 4.0 3.8 + - - +
8L TYR 3.7 1.8 + - - -
9L HIS* 1.3 83.8 + - - +
11L ASP* 1.3 65.1 + - - +
13L GLU* 3.4 19.4 + - - +
14L ALA* 3.1 22.3 + - - +
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Residues in contact with ASP 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L HIS* 2.8 23.6 + - - +
10L SER* 1.3 73.3 - - - +
12L CYS* 1.3 62.3 + - - +
14L ALA* 3.4 7.5 + - - +
15L ALA* 2.9 29.3 + - - +
18L ARG* 4.6 1.9 + - - -
116L LEU* 3.6 21.3 - - + +
120L LYS* 3.1 22.8 + - - +
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Residues in contact with CYS 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L TYR* 4.1 9.6 - - + -
9L HIS* 3.1 25.9 + - + +
11L ASP* 1.3 79.6 - - - +
13L GLU* 1.3 57.6 + - - +
15L ALA* 3.1 3.6 + - - +
16L VAL* 2.9 35.6 + - - +
113L LEU* 4.3 1.4 - - - +
116L LEU* 4.0 25.1 - - - -
117L ALA* 4.3 7.6 - - - -
120L LYS* 4.1 15.7 - - - -
122L ASP* 5.0 5.2 - - - -
125L LEU* 4.0 25.6 - - + -
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Residues in contact with GLU 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L ARG* 2.7 34.0 + - - -
8L TYR* 3.7 21.2 + - + -
9L HIS 3.1 7.4 + - - +
10L SER* 3.5 17.1 + - - +
12L CYS* 1.3 80.1 - - - +
14L ALA* 1.3 61.8 + - - +
16L VAL 3.3 0.7 + - - -
17L ASN* 3.1 22.6 + - - +
69L GLN* 3.2 26.7 + - - +
74L GLY* 3.8 2.2 - - - -
75L ARG* 2.9 32.6 + - - +
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Residues in contact with ALA 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L SER 3.1 17.1 + - - +
11L ASP* 3.7 7.4 - - - +
12L CYS 3.3 0.2 - - - -
13L GLU* 1.3 77.4 - - - +
15L ALA* 1.3 61.8 - - - +
17L ASN* 3.5 10.0 + - - +
18L ARG* 3.1 39.5 + - - +
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Residues in contact with ALA 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L ASP 2.9 17.5 + - - +
12L CYS 3.5 1.3 - - - +
14L ALA* 1.3 75.1 - - - +
16L VAL* 1.3 61.7 + - - +
18L ARG* 3.3 25.2 + - - +
19L MET* 2.9 29.5 + - - +
113L LEU* 3.5 27.7 - - + +
116L LEU* 3.7 11.2 - - + -
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Residues in contact with VAL 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L TYR* 3.6 14.6 - - - +
12L CYS 2.9 19.8 + - - +
13L GLU 3.6 5.2 - - - +
14L ALA 3.3 0.2 - - - -
15L ALA* 1.3 76.3 - - - +
17L ASN* 1.3 56.7 + - - +
19L MET* 3.2 7.9 + - - +
20L LEU* 2.9 29.5 + - + +
65L PHE* 3.9 33.4 - - + +
68L TYR* 4.6 4.7 - - + -
69L GLN* 3.5 22.4 - - + +
113L LEU* 4.3 12.1 - - + -
125L LEU* 4.3 23.6 - - + -
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Residues in contact with ASN 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L GLU* 3.1 15.8 + - - +
14L ALA* 3.6 11.8 - - - +
16L VAL* 1.3 77.1 - - - +
18L ARG* 1.3 61.6 + - - +
20L LEU* 3.5 16.0 - - - +
21L ASN* 3.4 20.4 + - - +
69L GLN* 3.4 12.9 + - - +
75L ARG 3.2 19.2 + - - -
76L VAL* 3.3 10.6 - - - -
77L VAL* 3.1 46.6 + - - +
79L GLN* 4.6 9.6 + - - +
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Residues in contact with ARG 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L ASP 4.6 2.8 + - - -
14L ALA* 3.1 21.5 + - - +
15L ALA* 3.4 33.4 - - - +
16L VAL 3.1 0.4 - - - -
17L ASN* 1.3 79.7 - - - +
19L MET* 1.3 64.1 + - - +
21L ASN* 3.4 6.8 + - - +
22L LEU* 3.1 20.8 + - - +
79L GLN* 4.8 16.6 - - - +
116L LEU* 5.4 2.0 - - - +
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Residues in contact with MET 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L ALA 2.9 16.5 + - - +
16L VAL* 3.5 6.1 - - - +
18L ARG* 1.3 75.8 - - - +
20L LEU* 1.3 63.7 + - - +
22L LEU* 3.2 13.7 + - - +
23L GLU* 2.9 28.0 + - + +
65L PHE* 3.4 30.3 - - + -
106L VAL* 4.6 3.6 - - - +
109L ALA* 3.1 49.6 - - + +
110L LEU* 3.5 21.5 - - + +
113L LEU* 3.7 19.5 - - + -
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Residues in contact with LEU 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L VAL* 2.9 15.4 + - + +
17L ASN* 3.5 20.9 - - - +
19L MET* 1.3 77.4 - - - +
21L ASN* 1.3 62.7 + - + +
23L GLU* 3.4 8.5 + - - +
24L LEU* 3.1 42.9 + - + +
62L ALA* 3.7 16.4 - - + +
65L PHE* 4.2 13.9 - - + +
66L MET* 3.8 35.9 - - + +
69L GLN* 5.8 0.7 - - + +
76L VAL* 4.0 17.9 - - + -
77L VAL 5.6 0.7 - - - +
78L LEU* 3.7 16.8 - - + -
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Residues in contact with ASN 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L ASN 3.4 7.6 + - - +
18L ARG* 3.6 8.5 - - + +
19L MET 3.2 0.4 - - - -
20L LEU* 1.3 81.8 - - + +
22L LEU* 1.3 60.7 + - - +
24L LEU* 3.1 8.5 + - - +
25L TYR* 2.8 30.1 + - - +
79L GLN* 3.5 44.3 + - - +
80L ASP 3.2 26.1 + - - +
81L ILE* 4.3 8.1 - - - +
82L LYS 5.6 0.9 + - - -
28V TYR* 4.4 4.6 + - - +
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Residues in contact with LEU 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ARG 3.1 13.5 + - - +
19L MET* 3.2 16.1 + - - +
21L ASN* 1.3 77.6 + - - +
23L GLU* 1.3 57.6 + - - +
25L TYR* 3.2 22.7 + - + -
26L ALA* 2.9 26.7 + - - +
102L LEU* 5.4 2.0 - - + -
105L THR* 4.4 17.5 - - + +
106L VAL* 3.9 31.1 - - + +
109L ALA* 3.7 30.1 - - + -
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Residues in contact with GLU 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L MET* 2.9 19.9 + - + +
20L LEU 3.4 9.2 - - - +
22L LEU* 1.3 77.0 - - - +
24L LEU* 1.3 57.6 + - - +
26L ALA* 3.3 5.6 + - - +
27L SER* 2.9 28.1 + - - -
58L GLU* 2.7 26.9 - - - +
61L HIS* 3.4 18.2 - - + +
62L ALA* 3.8 7.2 - - + +
65L PHE* 4.1 18.7 - - + -
106L VAL* 4.0 15.5 - - - +
110L LEU* 4.9 2.4 - - - +
133L TYR* 3.7 14.9 - - - -
176L MG 2.4 30.0 - - - -
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Residues in contact with LEU 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L LEU* 3.1 31.3 + - + +
21L ASN* 3.5 10.1 - - - +
23L GLU* 1.3 75.3 - - - +
25L TYR* 1.3 56.8 + - - +
27L SER* 3.5 6.8 - - - -
28L TYR* 3.0 27.2 + - - +
59L ARG* 4.9 17.7 - - + +
62L ALA* 3.7 18.2 - - + -
63L GLU* 6.4 0.4 - - + -
66L MET* 5.1 6.5 - - + -
78L LEU* 4.8 0.2 - - + -
81L ILE* 3.7 24.3 - - + +
28V TYR* 3.7 36.3 - - + +
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Residues in contact with TYR 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L ASN* 2.8 17.4 + - - +
22L LEU* 3.4 27.6 - - + +
23L GLU 3.2 0.2 - - - -
24L LEU* 1.3 73.0 - - - +
26L ALA* 1.3 63.7 + - - +
28L TYR* 3.2 3.9 + - + +
29L THR* 2.9 48.3 + - - +
81L ILE* 4.0 9.8 - - + +
82L LYS* 3.4 37.7 - - + +
83L LYS 3.8 11.4 + - - -
84L PRO* 4.1 1.1 - - + -
85L GLU* 3.8 25.3 + - - +
102L LEU* 4.1 17.5 - - + -
105L THR* 6.5 0.7 - - + -
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Residues in contact with ALA 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L LEU 2.9 12.6 + - - +
23L GLU* 3.3 9.8 + - - +
25L TYR* 1.3 77.3 - - - +
27L SER* 1.3 63.7 + - - +
29L THR* 3.3 2.8 + - - -
30L TYR* 3.1 31.2 + - + -
58L GLU* 4.2 15.7 - - + -
102L LEU* 3.9 26.4 - - + +
103L GLU* 6.2 0.4 - - - +
106L VAL* 4.2 19.1 - - + -
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Residues in contact with SER 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L GLU 2.9 16.8 + - - -
24L LEU* 3.5 11.2 - - - +
26L ALA* 1.3 76.1 - - - +
28L TYR* 1.3 62.5 + - - +
30L TYR 3.1 2.6 + - - -
31L SER* 3.0 19.3 + - - -
55L SER* 2.9 39.3 + - - +
58L GLU* 3.8 13.4 - - - +
59L ARG* 3.6 17.0 - - - +
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Residues in contact with TYR 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L LEU 3.0 18.2 + - - +
25L TYR* 3.5 6.1 - - - +
27L SER* 1.3 77.6 + - - +
29L THR* 1.3 61.1 + - - +
31L SER* 3.2 17.1 - - - -
32L SER* 3.2 18.2 + - - -
81L ILE* 4.0 12.6 - - + -
82L LYS 3.6 18.6 - - - +
83L LYS* 4.0 3.8 - - - -
84L PRO* 3.7 18.2 - - + +
20V LEU* 5.1 0.2 - - - +
21V ASN* 4.5 2.8 + - - +
24V LEU* 3.6 28.1 - - + +
66V MET* 5.5 0.7 - - + -
78V LEU* 3.4 38.7 - - + +
79V GLN 3.0 30.4 + - - -
81V ILE* 3.7 21.7 - - + +
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Residues in contact with THR 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L TYR* 2.9 30.4 + - + -
26L ALA* 3.6 8.7 - - - -
27L SER 3.2 0.2 - - - -
28L TYR* 1.3 75.7 - - - +
30L TYR* 1.3 62.5 + - - +
32L SER* 3.2 6.6 + - - -
33L MET* 3.2 38.2 + - + +
84L PRO* 3.4 21.0 - - + +
85L GLU 5.0 0.2 + - - -
89L TRP* 4.0 15.3 - - + -
102L LEU* 3.7 24.9 - - + -
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Residues in contact with TYR 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L ALA* 3.1 23.2 + - + -
27L SER 3.1 6.7 + - - +
29L THR* 1.3 74.7 - - - +
31L SER* 1.3 60.4 + - - +
33L MET* 3.2 11.4 + - + +
34L TYR* 2.8 29.8 + - - +
50L PHE* 5.9 0.2 - + - -
51L PHE* 3.6 46.2 - + - +
54L HIS* 3.9 29.4 - + + -
55L SER* 3.7 7.6 - - - -
58L GLU* 4.0 13.9 - - + -
99L ALA* 3.9 24.9 + - + +
102L LEU* 3.9 17.2 - - + +
103L GLU* 2.8 40.9 + - - +
144L ILE* 4.3 4.0 - - + +
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Residues in contact with SER 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L SER 3.0 12.0 + - - -
28L TYR* 3.2 23.7 - - - -
30L TYR* 1.3 75.0 - - - +
32L SER* 1.3 61.7 + - - +
34L TYR* 3.4 12.3 + - - +
35L ALA* 3.1 22.7 + - - +
55L SER* 3.8 13.1 + - - -
24V LEU* 6.1 0.2 - - - +
63V GLU* 4.8 6.8 + - - +
66V MET* 3.3 30.4 - - - +
78V LEU* 4.9 0.9 - - - -
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Residues in contact with SER 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L TYR 3.2 5.4 + - - -
29L THR 3.2 10.9 + - - -
30L TYR 3.2 0.4 - - - -
31L SER* 1.3 74.3 - - - +
33L MET* 1.3 59.6 - - - +
35L ALA* 3.2 7.1 + - - +
36L PHE* 2.9 28.9 + - - +
84L PRO* 3.2 29.6 - - - +
86L ARG 4.0 6.4 + - - -
87L ASP* 5.1 7.6 + - - +
89L TRP* 3.4 17.5 + - - -
78V LEU* 3.4 17.0 - - - +
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Residues in contact with MET 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L THR* 3.2 33.4 + - + +
30L TYR* 3.5 15.5 - - + +
32L SER* 1.3 76.8 - - - +
34L TYR* 1.3 66.1 + - - +
36L PHE* 3.3 0.7 + - - +
37L PHE* 3.0 33.0 + - + -
51L PHE* 3.8 42.8 - - + -
89L TRP* 3.7 43.7 - - + +
95L ALA* 3.8 23.3 - - + +
98L ALA* 4.0 7.4 - - + +
99L ALA* 4.2 9.0 - - - +
102L LEU* 5.2 0.4 - - + -
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Residues in contact with TYR 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR 2.8 13.7 + - - +
31L SER* 3.4 15.5 - - - +
33L MET* 1.3 77.6 - - - +
35L ALA* 1.3 73.1 + - - +
36L PHE 3.3 0.2 + - - -
37L PHE 3.4 0.3 + - - -
38L ASP* 3.2 30.0 + - + +
48L ALA* 3.2 38.1 - - + +
49L GLU* 3.6 20.1 + - - -
51L PHE* 4.0 2.6 - - - +
52L LYS* 3.7 41.8 + - + +
63V GLU* 5.1 11.8 + - + -
66V MET* 4.6 22.7 - - + -
67V LYS* 3.3 38.0 - - + +
70V ASN* 6.3 0.2 - - - -
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Residues in contact with ALA 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L SER 3.1 10.0 + - - +
32L SER* 3.6 9.2 - - - +
34L TYR* 1.3 84.5 - - - +
36L PHE* 1.3 63.0 + - - +
38L ASP* 4.4 1.1 - - - -
39L ARG* 3.5 9.9 + - - +
66V MET* 4.3 15.3 - - + -
70V ASN* 3.0 28.9 + - - +
76V VAL* 4.2 31.4 - - + +
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Residues in contact with PHE 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L SER 2.9 16.4 + - - +
33L MET 3.5 5.2 - - - +
34L TYR 3.1 0.6 - - - -
35L ALA* 1.3 77.9 - - - +
37L PHE* 1.3 84.4 + + - +
39L ARG* 3.3 52.9 - - - +
42L VAL* 3.3 35.4 - - + +
87L ASP 4.5 3.4 - - - +
88L GLU* 3.8 11.7 - - + -
89L TRP* 3.6 33.9 - - + -
90L GLY* 3.5 40.8 - - - -
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Residues in contact with PHE 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L MET* 3.0 26.6 + - + +
34L TYR 4.0 0.2 - - - -
36L PHE* 1.3 91.1 - + - +
38L ASP* 1.3 60.5 + - - +
39L ARG 3.2 0.4 - - - -
42L VAL* 3.5 22.4 - - + -
43L ALA* 3.5 7.8 + - - -
44L LEU* 3.2 49.5 + - + +
45L HIS* 4.3 0.5 + - - -
47L VAL* 3.9 12.1 - - + -
48L ALA* 3.7 14.3 - - + +
51L PHE* 3.7 20.4 - + - -
89L TRP* 4.8 0.2 - - + -
91L ASN* 3.5 24.2 - - - -
92L THR* 3.6 27.6 - - - -
95L ALA* 3.7 22.0 - - + -
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Residues in contact with ASP 38 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LYS* 2.9 31.4 + - - -
34L TYR* 3.2 28.2 + - + +
35L ALA* 4.3 1.8 - - - -
36L PHE 3.2 0.4 - - - -
37L PHE* 1.3 76.7 - - - +
39L ARG* 1.3 60.8 + - - +
45L HIS* 3.4 22.9 + - - -
48L ALA* 4.1 2.7 - - + +
67V LYS* 3.1 45.4 + - - +
70V ASN* 3.2 30.9 + - - +
----------------------------------------------------------
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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