Contacts of the helix formed by residues 10 - 38 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ARG* 4.0 3.9 + - - +
8K TYR 3.7 1.8 + - - -
9K HIS* 1.3 82.9 + - - +
11K ASP* 1.3 65.5 + - - +
13K GLU* 3.4 19.5 + - - +
14K ALA* 3.1 22.2 + - - +
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Residues in contact with ASP 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K HIS* 2.8 23.5 + - + +
10K SER* 1.3 73.7 - - - +
12K CYS* 1.3 62.9 + - - +
14K ALA* 3.4 7.0 + - - +
15K ALA* 2.9 28.8 + - - +
18K ARG* 4.6 2.1 + - - -
116K LEU* 3.6 22.1 - - + +
120K LYS* 3.1 23.0 + - - +
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Residues in contact with CYS 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K TYR* 4.1 9.9 - - + -
9K HIS* 3.1 25.7 + - + +
11K ASP* 1.3 80.0 - - - +
13K GLU* 1.3 58.2 + - - +
15K ALA* 3.1 3.3 + - - +
16K VAL* 2.9 36.4 + - - +
113K LEU* 4.3 1.0 - - - +
116K LEU* 4.0 25.1 - - - -
117K ALA* 4.3 7.6 - - - -
120K LYS* 4.1 15.5 - - - -
122K ASP* 5.0 4.9 - - - -
125K LEU* 4.0 26.5 - - + -
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Residues in contact with GLU 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ARG* 2.7 34.3 + - - -
8K TYR* 3.7 21.0 + - + -
9K HIS 3.1 8.3 + - - +
10K SER* 3.5 17.6 + - - +
12K CYS* 1.3 79.5 - - - +
14K ALA* 1.3 62.0 + - - +
16K VAL 3.3 0.9 + - - -
17K ASN* 3.1 22.6 + - - +
69K GLN* 3.2 26.8 + - - +
74K GLY* 3.8 2.5 - - - -
75K ARG* 2.9 33.0 + - - +
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Residues in contact with ALA 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K SER 3.1 16.7 + - - +
11K ASP* 3.7 7.2 - - - +
12K CYS 3.3 0.2 - - - -
13K GLU* 1.3 78.2 - - - +
15K ALA* 1.3 62.0 + - - +
17K ASN* 3.5 10.6 + - - +
18K ARG* 3.2 38.7 + - - +
79K GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K ASP 2.9 17.3 + - - +
12K CYS 3.1 1.5 + - - +
14K ALA* 1.3 75.3 - - - +
16K VAL* 1.3 60.5 + - - +
18K ARG* 3.3 24.2 + - - +
19K MET* 2.9 28.6 + - - +
113K LEU* 3.5 27.2 - - + +
116K LEU* 3.7 11.0 - - + -
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Residues in contact with VAL 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K TYR* 3.6 13.7 - - - +
12K CYS 2.9 19.8 + - - +
13K GLU 3.6 4.9 - - - +
14K ALA 3.3 0.2 - - - -
15K ALA* 1.3 76.1 - - - +
17K ASN* 1.3 56.4 + - - +
19K MET* 3.2 7.5 + - - +
20K LEU* 2.9 29.6 + - + +
65K PHE* 3.9 33.8 - - + +
68K TYR* 4.6 5.6 - - + -
69K GLN* 3.5 22.4 - - + +
113K LEU* 4.3 12.8 - - + -
125K LEU* 4.3 23.3 - - + -
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Residues in contact with ASN 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K GLU* 3.1 16.0 + - - +
14K ALA* 3.6 12.2 - - - +
15K ALA 3.3 0.2 - - - -
16K VAL* 1.3 76.9 - - - +
18K ARG* 1.3 60.4 + - - +
20K LEU* 3.5 16.4 - - - +
21K ASN* 3.4 19.8 + - - +
69K GLN* 3.4 12.3 + - - +
75K ARG 3.2 19.0 + - - -
76K VAL* 3.3 10.7 - - - -
77K VAL* 3.1 46.2 + - + +
79K GLN* 4.6 10.0 + - - +
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Residues in contact with ARG 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ASP 4.6 2.8 + - - -
14K ALA* 3.2 20.9 + - - +
15K ALA* 3.4 33.9 - - - +
16K VAL 3.1 0.2 - - - -
17K ASN* 1.3 79.3 - - - +
19K MET* 1.3 64.3 + - - +
21K ASN* 3.4 7.6 + - - +
22K LEU* 3.1 20.6 + - - +
79K GLN* 4.8 16.6 - - - +
116K LEU* 5.4 2.2 - - - +
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Residues in contact with MET 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K ALA 2.9 16.8 + - - +
16K VAL* 3.5 5.8 - - - +
18K ARG* 1.3 74.8 - - - +
20K LEU* 1.3 64.4 + - - +
22K LEU* 3.2 14.0 + - - +
23K GLU* 2.9 27.4 + - - +
65K PHE* 3.4 30.3 - - + -
106K VAL* 4.6 3.8 - - - +
109K ALA* 3.1 50.0 - - + +
110K LEU* 3.5 21.5 - - + +
113K LEU* 3.7 20.2 - - + -
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Residues in contact with LEU 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K VAL* 2.9 16.2 + - + +
17K ASN* 3.5 19.7 - - - +
19K MET* 1.3 77.1 - - - +
21K ASN* 1.3 63.5 + - + +
23K GLU* 3.4 9.1 + - - +
24K LEU* 3.1 42.0 + - + +
62K ALA* 3.7 16.4 - - - +
65K PHE* 4.2 14.3 - - + +
66K MET* 3.8 35.9 - - + +
69K GLN* 5.8 0.4 - - - +
76K VAL* 4.0 19.5 - - + -
77K VAL 5.6 0.7 - - - +
78K LEU* 3.7 17.0 - - + -
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Residues in contact with ASN 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K ASN 3.4 7.6 + - - +
18K ARG 3.6 8.3 - - - +
19K MET 3.2 0.4 - - - -
20K LEU* 1.3 81.8 - - + +
22K LEU* 1.3 61.0 + - - +
24K LEU* 3.1 8.8 + - - +
25K TYR* 2.8 30.3 + - - +
79K GLN* 3.5 43.4 + - - +
80K ASP 3.2 27.7 + - - +
81K ILE* 4.3 6.8 - - - +
82K LYS 5.6 0.9 + - - -
28W TYR* 4.4 5.0 + - - +
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Residues in contact with LEU 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ARG 3.1 13.3 + - - +
19K MET* 3.2 16.8 + - - +
21K ASN* 1.3 77.8 + - - +
23K GLU* 1.3 56.9 + - - +
25K TYR* 3.2 24.9 + - + +
26K ALA* 2.9 26.3 + - - +
102K LEU* 5.4 1.1 - - + -
105K THR* 4.4 17.0 - - + +
106K VAL* 3.9 31.1 - - + +
109K ALA* 3.7 30.1 - - + -
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Residues in contact with GLU 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K MET* 2.9 19.7 + - + +
20K LEU 3.4 8.7 - - - +
21K ASN 3.2 0.2 - - - -
22K LEU* 1.3 77.3 - - - +
24K LEU* 1.3 58.2 + - - +
26K ALA* 3.3 5.0 + - - +
27K SER* 2.9 28.2 + - - -
58K GLU* 2.7 20.5 - - - +
61K HIS* 3.4 18.0 - - + +
62K ALA* 3.8 14.6 - - + +
65K PHE* 4.1 18.5 - - + -
106K VAL* 4.0 15.4 - - + +
110K LEU* 4.9 2.8 - - - +
133K TYR* 3.7 15.2 - - - -
176K MG 2.4 30.8 - - - -
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Residues in contact with LEU 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 3.1 30.6 + - + +
21K ASN* 3.1 9.8 + - - +
23K GLU* 1.3 75.6 - - - +
25K TYR* 1.3 56.8 + - - +
27K SER* 3.5 6.8 - - - +
28K TYR* 3.0 27.5 + - - +
59K ARG* 4.9 17.3 - - + +
62K ALA* 3.7 18.6 - - + -
63K GLU* 6.4 0.4 - - + -
66K MET* 5.1 6.7 - - + -
81K ILE* 3.7 24.0 - - + +
28W TYR* 3.6 37.9 - - + +
31W SER* 6.0 0.7 - - - +
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Residues in contact with TYR 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ASN* 2.8 17.8 + - - +
22K LEU* 3.4 27.6 - - + +
24K LEU* 1.3 73.0 - - - +
26K ALA* 1.3 63.8 + - - +
28K TYR* 3.2 3.9 + - - +
29K THR* 2.9 48.4 + - + +
81K ILE* 4.0 9.6 - - + +
82K LYS* 3.4 38.1 - - + +
83K LYS 3.8 11.8 + - - -
84K PRO* 4.1 1.6 - - + -
85K GLU* 3.8 25.8 + - - +
102K LEU* 4.1 16.8 - - + -
105K THR* 6.5 0.7 - - + -
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Residues in contact with ALA 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K LEU 2.9 14.2 + - - +
23K GLU* 3.3 9.6 + - - +
25K TYR* 1.3 76.6 - - - +
27K SER* 1.3 62.8 + - - +
29K THR* 3.3 2.8 + - - -
30K TYR* 3.1 32.0 + - + -
58K GLU* 4.2 15.7 - - + -
102K LEU* 4.0 25.4 - - + -
103K GLU* 6.5 0.2 - - - -
106K VAL* 4.2 19.1 - - + -
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Residues in contact with SER 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLU 2.9 16.4 + - - -
24K LEU* 3.5 11.8 - - - +
26K ALA* 1.3 76.3 - - - +
28K TYR* 1.3 62.1 + - - +
30K TYR 3.1 2.9 + - - -
31K SER* 3.0 19.3 + - - -
55K SER* 2.9 40.0 + - - +
58K GLU* 3.8 12.1 - - - +
59K ARG* 3.6 16.9 - - - +
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Residues in contact with TYR 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K LEU 3.0 18.3 + - - +
25K TYR* 3.2 6.7 + - - +
27K SER* 1.3 77.2 + - - +
29K THR* 1.3 60.3 + - - +
31K SER* 3.2 16.4 - - - -
32K SER* 3.2 19.1 + - - -
81K ILE* 4.0 13.0 - - + -
82K LYS 3.6 17.9 - - - +
83K LYS* 4.0 3.6 - - - -
84K PRO* 3.7 17.2 - - + +
21W ASN* 4.4 2.9 + - - +
24W LEU* 3.6 27.9 - - + +
66W MET* 5.6 0.2 - - + -
78W LEU* 3.4 36.5 - - + +
79W GLN 2.9 30.5 + - - -
81W ILE* 3.7 23.0 - - + +
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Residues in contact with THR 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TYR* 2.9 30.9 + - + +
26K ALA 3.6 8.5 - - - -
27K SER 3.2 0.2 - - - -
28K TYR* 1.3 75.7 - - - +
30K TYR* 1.3 63.1 + - - +
32K SER* 3.2 6.8 + - - -
33K MET* 3.2 38.5 + - + +
84K PRO* 3.4 21.5 - - + +
85K GLU* 5.0 0.8 + - - +
89K TRP* 4.0 15.3 - - + -
102K LEU* 3.7 25.6 - - + -
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Residues in contact with TYR 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K ALA* 3.1 22.8 + - + -
27K SER 3.1 6.7 + - - +
29K THR* 1.3 72.8 - - - +
31K SER* 1.3 60.3 + - - +
33K MET* 3.2 12.9 + - + +
34K TYR* 2.8 29.5 + - - +
50K PHE* 5.9 0.2 - + - -
51K PHE* 3.6 45.8 - + - +
54K HIS* 3.9 29.1 + + + -
55K SER* 3.7 7.4 - - - -
58K GLU* 4.0 12.3 - - + -
99K ALA* 3.9 24.5 + - + +
102K LEU* 3.9 17.5 - - + +
103K GLU* 2.8 40.6 + - - +
144K ILE* 4.3 4.1 - - + +
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Residues in contact with SER 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K SER 3.0 12.2 + - - -
28K TYR* 3.2 24.5 - - - -
30K TYR* 1.3 75.1 - - - +
32K SER* 1.3 62.4 + - - +
34K TYR* 3.4 12.5 + - - +
35K ALA* 3.1 22.9 + - - +
55K SER* 3.8 12.7 + - - -
24W LEU* 6.0 0.5 - - - +
63W GLU* 4.8 6.2 + - - +
66W MET* 3.4 30.1 - - - +
78W LEU* 4.8 2.7 - - - -
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Residues in contact with SER 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K TYR 3.2 5.5 + - - -
29K THR 3.2 11.8 + - - -
30K TYR 3.2 0.6 - - - -
31K SER* 1.3 73.5 - - - +
33K MET* 1.3 60.2 + - - +
35K ALA* 3.2 7.2 + - - +
36K PHE* 2.9 28.1 + - - +
84K PRO* 3.2 29.7 - - - +
86K ARG 4.0 6.4 + - - -
87K ASP* 5.1 7.4 + - - +
89K TRP* 3.4 17.3 + - - -
78W LEU* 3.3 17.2 - - - +
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Residues in contact with MET 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K THR* 3.2 34.0 + - + +
30K TYR* 3.2 16.1 + - + +
32K SER* 1.3 76.6 - - - +
34K TYR* 1.3 65.5 + - - +
36K PHE* 3.3 1.1 + - - +
37K PHE* 3.0 33.0 + - + -
51K PHE* 3.8 42.0 - - + -
89K TRP* 3.7 44.0 - - + +
95K ALA* 3.8 24.0 - - + +
98K ALA* 4.0 7.2 - - + -
99K ALA* 4.2 9.4 - - - +
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Residues in contact with TYR 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K TYR 2.8 12.7 + - - +
31K SER* 3.4 15.7 - - - +
32K SER 3.2 0.2 - - - -
33K MET* 1.3 78.6 - - - +
35K ALA* 1.3 72.1 + - - +
36K PHE 3.3 0.2 + - - -
37K PHE 3.4 0.7 + - - -
38K ASP* 3.2 30.2 + - + +
48K ALA* 3.2 38.1 - - + +
49K GLU* 3.6 19.8 + - - -
51K PHE* 4.0 2.4 - - - +
52K LYS* 3.7 41.6 + - + +
63W GLU* 5.1 13.1 + - + +
66W MET* 4.5 22.9 - - + -
67W LYS* 3.4 35.6 - - + +
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Residues in contact with ALA 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K SER 3.1 10.6 + - - +
32K SER* 3.6 9.4 - - - +
34K TYR* 1.3 85.4 - - + +
36K PHE* 1.3 64.0 + - - +
38K ASP* 4.4 1.1 - - - -
39K ARG* 3.5 9.6 + - - +
66W MET* 4.2 15.5 - - + -
70W ASN* 3.1 28.3 + - - +
76W VAL* 4.2 32.0 - - + +
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Residues in contact with PHE 36 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K SER 2.9 16.5 + - - +
33K MET 3.5 4.9 - - - +
34K TYR 3.1 0.4 - - - -
35K ALA* 1.3 79.2 - - - +
37K PHE* 1.3 85.2 + + - +
39K ARG* 3.3 52.3 - - - +
42K VAL* 3.3 36.2 - - + +
87K ASP 4.5 3.4 - - - +
88K GLU* 3.8 12.3 - - + -
89K TRP* 3.6 33.4 - - + -
90K GLY* 3.5 41.5 - - - -
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Residues in contact with PHE 37 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K MET* 3.0 25.9 + - + +
34K TYR 3.4 0.2 + - - -
36K PHE* 1.3 92.4 - + - +
38K ASP* 1.3 60.0 + - - +
39K ARG 3.2 0.4 - - - -
42K VAL* 3.5 22.4 - - + -
43K ALA* 3.5 7.1 + - - -
44K LEU* 3.2 49.9 + - + +
45K HIS* 4.3 0.9 + - - -
47K VAL* 3.9 11.7 - - + -
48K ALA* 3.7 14.4 - - + -
51K PHE* 3.7 20.0 - + - -
89K TRP* 4.8 0.7 - - + -
91K ASN* 3.5 24.0 - - - -
92K THR* 3.6 28.5 - - - -
95K ALA* 3.7 22.4 - - + -
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Residues in contact with ASP 38 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LYS* 2.9 32.0 + - - -
34K TYR* 3.2 29.8 + - + +
35K ALA* 4.3 1.3 - - - -
36K PHE 3.2 0.4 - - - -
37K PHE* 1.3 75.7 - - - +
39K ARG* 1.3 60.8 + - - +
45K HIS* 3.4 23.5 + - - -
48K ALA* 4.5 2.1 - - + +
67W LYS* 3.1 45.3 + - - +
70W ASN* 3.1 30.5 + - - +
----------------------------------------------------------
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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