Contacts of the helix formed by residues 45 - 71 (chain D) 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 HIS 45 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE 4.6 1.3 - - - -
38D ASP* 3.4 44.2 + - - -
43D ALA* 3.3 15.3 + - + -
44D LEU* 1.3 69.2 - - - +
46D ASN* 1.3 64.6 + - - +
48D ALA* 3.5 7.1 - - - +
49D GLU* 3.1 30.5 + - + +
167D ASP* 3.6 3.2 + - - +
67H LYS* 5.0 4.7 + - - -
142X LYS* 4.0 2.9 - - - -
146X ASP* 3.0 34.0 + - + -
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Residues in contact with ASN 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D HIS* 1.3 77.3 - - - +
47D VAL* 1.3 66.3 + - - +
49D GLU* 3.3 8.8 + - - +
50D PHE 3.0 17.7 + - - -
167D ASP* 3.0 46.9 + - - +
168D LYS* 4.4 10.1 - - - +
171D VAL* 3.2 27.7 - - + +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.9 20.2 - - + -
44D LEU* 3.5 18.6 - - + +
46D ASN* 1.3 76.4 - - - +
48D ALA* 1.3 62.0 + - - +
50D PHE* 3.2 9.0 + - - +
51D PHE* 3.2 46.0 + - + -
92D THR* 4.1 26.0 - - + +
96D MET* 4.6 4.5 - - + -
163D GLU 5.8 0.2 - - - +
166D PHE* 4.3 13.9 - - + -
167D ASP* 3.1 22.9 + - + +
171D VAL* 4.6 4.5 - - + -
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.2 41.3 - - + +
37D PHE* 3.7 23.8 - - + +
38D ASP* 4.1 4.7 - - + +
44D LEU 3.0 14.5 + - - +
45D HIS* 3.5 14.8 - - - +
47D VAL* 1.3 77.4 - - - +
49D GLU* 1.3 58.1 + - - +
51D PHE* 3.4 1.7 + - - -
52D LYS 3.0 21.1 + - - -
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Residues in contact with GLU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.6 23.2 + - - -
45D HIS* 3.1 18.7 + - + +
46D ASN* 3.3 11.2 + - - +
48D ALA* 1.3 75.0 - - - +
50D PHE* 1.3 60.7 + - - +
52D LYS* 3.6 25.6 + - - +
53D GLU* 2.9 40.2 + - - +
67H LYS* 5.8 1.6 - - - -
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 5.9 0.2 - + - -
46D ASN 3.0 13.2 + - - +
47D VAL* 3.2 10.7 + - - +
49D GLU* 1.3 77.1 - - - +
51D PHE* 1.3 93.1 + + - +
53D GLU* 3.5 8.5 + - + +
54D HIS* 3.2 54.8 + + - -
96D MET* 4.0 21.3 - - + -
143D ARG* 3.9 17.7 - - - -
144D ILE* 4.5 12.3 - - + -
147D PHE* 3.7 27.8 - + - -
171D VAL* 3.7 20.2 - - + +
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Residues in contact with PHE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.6 50.6 - + + +
33D MET* 3.8 30.5 - - + -
34D TYR 4.0 4.5 - - - +
37D PHE* 3.7 23.1 - + - -
47D VAL* 3.2 36.6 + - + -
48D ALA 3.9 4.9 - - - +
50D PHE* 1.3 97.5 - + - +
52D LYS* 1.3 59.3 + - - +
54D HIS* 3.2 5.1 + - + +
55D SER* 2.9 24.3 + - - -
95D ALA* 4.1 11.9 - - + -
96D MET* 3.7 23.1 - - + -
99D ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 3.7 38.8 + - + +
48D ALA 3.0 18.0 + - - +
49D GLU* 3.6 31.8 + - - +
50D PHE 3.3 0.2 - - - -
51D PHE* 1.3 76.5 - - - +
53D GLU* 1.3 63.8 + - + +
55D SER* 3.2 21.7 + - - +
56D HIS* 3.3 29.6 + - + +
63H GLU* 3.6 25.0 + - - +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 2.9 26.1 + - + +
50D PHE* 3.6 9.2 - - + +
52D LYS* 1.3 78.1 - - + +
54D HIS* 1.3 63.0 - - + +
56D HIS* 3.3 10.2 + - - +
57D GLU* 3.1 35.5 + - - +
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Residues in contact with HIS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.9 23.0 - + + -
50D PHE* 3.2 40.6 + + - +
51D PHE* 3.4 10.8 - - - +
53D GLU* 1.3 82.5 - - + +
55D SER* 1.3 64.0 + - - +
57D GLU* 3.4 17.8 + - - +
58D GLU* 3.2 32.2 + - - +
103D GLU* 3.6 18.4 + - - -
140D ASP* 3.7 26.2 - - + -
143D ARG* 3.2 26.7 + - - -
144D ILE* 4.9 4.5 - - + -
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Residues in contact with SER 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D SER* 2.9 47.6 + - - +
30D TYR* 3.7 14.5 - - - +
31D SER* 3.8 14.1 + - - -
51D PHE 2.9 10.2 + - - -
52D LYS* 3.2 15.9 + - - +
53D GLU 3.3 0.4 - - - -
54D HIS* 1.3 74.7 - - - +
56D HIS* 1.3 76.9 + - - +
58D GLU 3.4 0.9 + - - -
59D ARG* 3.1 12.2 + - - +
63H GLU* 4.4 5.5 + - - -
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Residues in contact with HIS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LYS* 3.3 34.9 + - + +
53D GLU* 3.3 12.1 + - - +
54D HIS 3.2 0.4 - - - -
55D SER* 1.3 91.2 + - - +
57D GLU* 1.3 56.4 + - - +
59D ARG* 3.5 7.8 + - + +
60D GLU* 3.1 26.0 + - - +
59H ARG* 6.0 2.7 - - + +
63H GLU* 3.1 28.9 + - - -
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU* 3.1 21.4 + - - +
54D HIS* 3.6 25.7 + - - +
55D SER 3.2 0.2 - - - -
56D HIS* 1.3 76.1 - - - +
58D GLU* 1.3 64.1 + - + +
60D GLU* 3.2 7.4 + - + +
61D HIS* 2.9 46.7 + - + +
140D ASP* 4.1 17.3 - - - +
143D ARG* 5.8 1.4 + - - -
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU* 2.7 30.2 - - - +
26D ALA* 4.2 9.4 - - + +
27D SER* 3.8 13.7 - - - +
30D TYR* 4.0 17.3 - - + -
54D HIS* 3.2 20.8 + - - +
55D SER 3.4 0.2 + - - -
57D GLU* 1.3 80.7 - - - +
59D ARG* 1.3 56.8 + - - +
61D HIS* 3.1 11.1 + - - +
62D ALA* 3.0 26.2 + - - +
103D GLU* 3.4 15.2 - - - +
106D VAL* 4.9 1.0 - - - +
176D MG 2.0 32.0 - - - -
177D MG 2.6 24.5 - - - -
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Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 4.9 12.3 - - + +
27D SER* 3.6 13.6 + - - +
55D SER 3.1 18.3 + - - +
56D HIS* 3.6 10.1 - - + +
58D GLU* 1.3 74.4 - - - +
60D GLU* 1.3 63.9 + - - +
62D ALA* 3.2 8.1 + - - +
63D GLU* 3.1 35.6 + - + +
56H HIS* 6.0 2.7 - - + +
59H ARG* 5.7 9.4 - - + -
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D HIS 3.1 14.7 + - - +
57D GLU* 3.2 11.0 + - - +
59D ARG* 1.3 77.2 - - - +
61D HIS* 1.3 60.6 + - + +
63D GLU* 3.5 12.1 + - - +
64D LYS* 3.1 32.1 + - - +
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Residues in contact with HIS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU* 3.4 16.4 + - - +
57D GLU* 2.9 32.0 + - + +
58D GLU* 3.1 17.3 + - - +
59D ARG 3.2 0.2 - - - -
60D GLU* 1.3 77.5 - - + +
62D ALA* 1.3 65.3 + - - +
64D LYS* 3.4 18.2 + - - -
65D PHE* 3.3 12.9 + - - -
132D GLU 4.6 6.6 + - - -
133D TYR* 3.0 40.2 + + + -
136D GLU* 5.1 13.7 - - + +
137D GLN* 5.1 1.3 - - - -
140D ASP* 5.6 0.4 - - - -
176D MG 2.7 24.1 - - - -
177D MG 4.3 10.5 - - - -
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.7 17.3 - - + +
23D GLU* 3.8 10.5 - - + +
24D LEU* 3.7 35.0 - - + -
58D GLU 3.0 12.5 + - - +
59D ARG 3.2 8.9 + - - +
61D HIS* 1.3 75.7 - - - +
63D GLU* 1.3 63.8 + - + +
65D PHE* 3.3 9.4 + - - +
66D MET* 3.1 25.8 + - + +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 6.4 0.2 - - + -
59D ARG* 3.1 23.7 + - + +
60D GLU* 3.8 12.2 - - - +
62D ALA* 1.3 76.1 - - + +
64D LYS* 1.3 64.1 + - - +
66D MET* 3.2 24.7 + - + +
67D LYS* 3.1 25.2 + - - +
31H SER* 4.9 5.7 + - - +
34H TYR* 5.1 10.8 - - + -
52H LYS* 3.6 21.0 - - - +
55H SER* 4.4 5.5 + - - -
56H HIS* 3.0 36.0 + - - -
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Residues in contact with LYS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLU* 3.1 19.7 + - - +
61D HIS* 3.6 18.6 + - - +
62D ALA 3.3 0.4 - - - -
63D GLU* 1.3 76.3 - - - +
65D PHE* 1.3 58.3 + - - +
67D LYS* 3.5 7.3 + - - +
68D TYR* 2.9 27.0 + - - +
128D PHE* 3.7 9.8 - - + -
132D GLU* 2.9 52.1 + - + +
133D TYR* 3.2 21.8 - - + +
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Residues in contact with PHE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D VAL* 3.9 29.2 - - + +
19D MET* 3.4 33.0 - - + -
20D LEU* 4.2 19.9 - - + +
23D GLU* 4.1 15.0 - - + -
61D HIS 3.3 16.4 + - - -
62D ALA 3.3 8.0 + - - +
63D GLU 3.2 0.4 - - - -
64D LYS* 1.3 78.7 - - - +
66D MET* 1.3 64.8 + - - +
68D TYR* 3.5 2.4 - - + +
69D GLN* 3.0 24.3 + - - +
110D LEU* 4.0 10.5 - - + -
113D LEU* 4.5 7.9 - - + -
125D LEU* 5.3 0.2 - - + -
128D PHE* 3.5 26.0 - + - -
129D LEU* 4.0 12.1 - - + -
133D TYR* 3.4 30.3 - + - -
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Residues in contact with MET 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.8 31.0 - - + -
24D LEU* 5.1 7.9 - - + -
62D ALA* 3.1 20.7 + - + +
63D GLU* 3.2 23.5 + - + +
65D PHE* 1.3 75.9 - - - +
67D LYS* 1.3 61.4 + - - +
69D GLN* 3.4 4.4 - - - +
70D ASN* 3.3 27.2 + - - -
76D VAL* 3.9 21.5 - - + +
78D LEU* 4.7 7.2 - - + -
28H TYR* 5.6 0.4 - - + -
31H SER* 3.3 40.4 - - - +
34H TYR* 4.5 15.5 - - + -
35H ALA* 4.3 13.2 - - + -
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D GLU 3.1 10.4 + - - +
64D LYS* 3.6 10.8 - - - +
65D PHE 3.3 0.2 - - - -
66D MET* 1.3 79.6 - - - +
68D TYR* 1.3 57.4 + - - +
70D ASN* 3.5 3.3 + - - +
71D LYS* 3.0 44.4 + - + +
34H TYR* 3.4 29.1 + - - +
38H ASP* 3.1 33.0 + - - +
45H HIS* 5.0 5.3 + - - -
49H GLU* 5.8 1.8 - - - -
142I LYS* 6.0 0.2 - - - +
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Residues in contact with TYR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 3.9 18.4 - + - -
16D VAL* 4.6 8.1 - - + -
64D LYS 2.9 18.4 + - - +
65D PHE* 3.5 6.5 - - - +
66D MET 3.2 0.2 - - - -
67D LYS* 1.3 74.3 - - - +
69D GLN* 1.3 67.7 + - - +
71D LYS* 3.1 16.9 + - + +
72D ARG* 2.8 52.1 + - + +
124D HIS* 2.8 42.0 + + - -
125D LEU* 3.2 36.6 - - + -
128D PHE* 3.6 42.6 - + + -
135I GLU* 5.6 0.2 - - - -
----------------------------------------------------------
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Residues in contact with GLN 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 3.0 36.0 + - - -
13D GLU* 3.2 27.6 + - - +
16D VAL* 3.5 13.9 - - + +
17D ASN* 3.4 19.6 + - - -
20D LEU* 5.8 0.9 - - + +
65D PHE 3.0 14.4 + - - +
66D MET 3.4 6.5 - - - +
68D TYR* 1.3 82.9 - - - +
70D ASN* 1.3 61.1 + - - +
72D ARG* 3.2 4.5 + - - +
73D GLY 3.1 3.5 + - - -
74D GLY* 2.9 43.7 + - - -
75D ARG 4.0 6.7 - - - -
76D VAL* 3.7 24.7 - - + +
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Residues in contact with ASN 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 4.5 0.5 - - - +
66D MET 3.3 13.5 + - - -
67D LYS 3.9 3.4 - - - +
69D GLN* 1.3 77.2 - - - +
71D LYS* 1.3 64.7 + - - +
73D GLY* 3.2 10.4 + - - -
74D GLY 3.9 12.4 - - - +
75D ARG* 4.0 1.2 + - - +
76D VAL* 4.6 9.5 + - - +
35H ALA* 3.0 30.1 + - - +
38H ASP* 3.2 38.6 + - - +
39H ARG* 3.3 27.6 - - - +
40H ASP* 4.9 3.3 + - - +
142I LYS* 3.2 18.7 - - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 3.4 17.5 - - - +
67D LYS* 3.0 29.4 + - + +
68D TYR* 3.1 22.3 + - + +
70D ASN* 1.3 76.8 - - - +
72D ARG* 1.3 64.8 + - + +
128D PHE* 6.2 2.4 - - - -
135I GLU* 2.8 35.2 + - - +
138I VAL* 4.3 24.1 - - + +
139I LYS* 4.5 11.6 - - - +
142I LYS* 4.1 26.8 - - + +
----------------------------------------------------------
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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