Contacts of the helix formed by residues 10 - 38 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ARG* 4.0 3.9 + - - +
8H TYR 3.7 1.6 + - - -
9H HIS* 1.3 82.4 + - - +
11H ASP* 1.3 65.2 + - - +
13H GLU* 3.4 19.4 + - - +
14H ALA* 3.1 22.5 + - - +
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Residues in contact with ASP 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H HIS* 2.8 23.5 + - - +
10H SER* 1.3 73.5 - - - +
12H CYS* 1.3 62.3 + - - +
14H ALA* 3.4 6.7 + - - +
15H ALA* 2.9 29.5 + - - +
18H ARG* 4.6 1.7 + - - -
116H LEU* 3.6 22.1 - - + +
120H LYS* 3.1 21.0 + - - -
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Residues in contact with CYS 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H TYR* 4.1 10.1 - - + -
9H HIS* 3.1 26.1 + - + +
11H ASP* 1.3 79.8 - - - +
13H GLU* 1.3 56.7 + - - +
15H ALA* 3.1 3.0 + - - +
16H VAL* 2.9 35.9 + - - +
113H LEU* 4.3 0.8 - - - +
116H LEU* 4.0 25.4 - - - -
117H ALA* 4.3 8.5 - - - -
120H LYS* 4.1 14.8 - - - -
122H ASP* 5.0 5.6 - - - -
125H LEU* 4.0 25.8 - - + -
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Residues in contact with GLU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ARG* 2.7 35.3 + - - -
8H TYR* 3.7 21.2 + - + -
9H HIS 3.1 8.5 + - - +
10H SER* 3.5 17.7 + - - +
12H CYS* 1.3 78.8 - - - +
14H ALA* 1.3 62.4 + - - +
16H VAL 3.3 0.7 + - - -
17H ASN* 3.1 22.7 + - - +
69H GLN* 3.2 26.9 + - - +
74H GLY* 3.8 2.0 - - - -
75H ARG* 2.9 32.4 + - - +
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Residues in contact with ALA 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H SER 3.1 16.9 + - - +
11H ASP* 3.7 7.4 - - - +
12H CYS 3.3 0.2 - - - -
13H GLU* 1.3 78.2 - - - +
15H ALA* 1.3 62.5 + - - +
17H ASN* 3.5 10.4 + - - +
18H ARG* 3.1 39.6 + - - +
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Residues in contact with ALA 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASP 2.9 17.1 + - - +
12H CYS 3.1 2.0 + - - +
14H ALA* 1.3 75.5 - - - +
16H VAL* 1.3 60.8 + - - +
18H ARG* 3.3 24.3 + - - +
19H MET* 2.9 28.4 + - - +
113H LEU* 3.5 27.5 - - + +
116H LEU* 3.7 11.9 - - + -
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Residues in contact with VAL 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H TYR* 3.6 14.4 - - - +
12H CYS 2.9 20.0 + - - +
13H GLU 3.6 5.4 - - - +
14H ALA 3.3 0.2 - - - -
15H ALA* 1.3 76.8 - - - +
17H ASN* 1.3 57.5 + - - +
19H MET* 3.2 7.3 + - - +
20H LEU* 2.9 29.9 + - + +
65H PHE* 3.9 33.2 - - + +
68H TYR* 4.6 5.4 - - + -
69H GLN* 3.5 22.0 - - + +
113H LEU* 4.3 12.8 - - + -
125H LEU* 4.3 24.0 - - + -
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Residues in contact with ASN 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H GLU* 3.1 15.6 + - - +
14H ALA* 3.6 12.0 - - - +
16H VAL* 1.3 77.3 - - - +
18H ARG* 1.3 61.5 + - - +
20H LEU* 3.5 16.5 - - - +
21H ASN* 3.4 19.8 + - - +
69H GLN* 3.4 12.4 + - - +
75H ARG 3.2 18.6 + - - -
76H VAL* 3.3 10.6 - - - -
77H VAL* 3.1 47.1 + - - +
79H GLN* 4.6 9.0 + - - +
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Residues in contact with ARG 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ASP 4.6 3.0 + - - -
14H ALA* 3.1 21.5 + - - +
15H ALA* 3.4 33.5 - - - +
16H VAL 3.1 0.2 - - - -
17H ASN* 1.3 79.8 - - - +
19H MET* 1.3 63.9 + - - +
21H ASN* 3.4 7.4 + - + +
22H LEU* 3.1 20.8 + - - +
79H GLN* 4.8 16.4 - - - +
116H LEU* 5.4 2.4 - - - +
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Residues in contact with MET 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H ALA 2.9 15.3 + - - +
16H VAL* 3.5 6.1 - - - +
18H ARG* 1.3 76.3 - - - +
20H LEU* 1.3 63.7 + - - +
22H LEU* 3.2 12.9 + - - +
23H GLU* 2.9 28.3 + - + +
65H PHE* 3.4 29.8 - - + -
106H VAL* 4.6 3.8 - - - +
109H ALA* 3.1 50.7 - - + +
110H LEU* 3.5 22.0 - - + +
113H LEU* 3.7 18.6 - - + -
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TYR* 5.1 0.2 - - - +
16H VAL* 2.9 16.2 + - + +
17H ASN* 3.5 19.5 - - - +
19H MET* 1.3 76.6 - - - +
21H ASN* 1.3 64.3 + - + +
23H GLU* 3.4 8.5 + - - +
24H LEU* 3.1 42.4 + - + +
62H ALA* 3.7 17.0 - - - +
65H PHE* 4.2 14.1 - - + +
66H MET* 3.8 35.2 - - + +
69H GLN* 5.8 0.9 - - + +
76H VAL* 4.0 19.1 - - + -
77H VAL 5.6 0.7 - - - +
78H LEU* 3.7 16.8 - - + -
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Residues in contact with ASN 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TYR* 4.4 2.8 + - - +
17H ASN 3.4 7.6 + - - +
18H ARG* 3.6 8.7 - - + +
19H MET 3.2 0.6 - - - -
20H LEU* 1.3 82.1 - - + +
22H LEU* 1.3 61.5 + - - +
24H LEU* 3.1 7.8 + - - +
25H TYR* 2.8 30.3 + - - +
79H GLN* 3.5 43.9 + - - +
80H ASP 3.2 27.2 + - - +
81H ILE* 4.3 10.1 - - - +
82H LYS 5.6 0.7 + - - -
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Residues in contact with LEU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ARG 3.1 13.5 + - - +
19H MET* 3.2 15.7 + - - +
21H ASN* 1.3 78.5 + - - +
23H GLU* 1.3 57.1 + - - +
25H TYR* 3.2 23.9 + - + -
26H ALA* 2.9 26.7 + - - +
102H LEU* 5.4 1.1 - - + -
105H THR* 4.4 16.8 - - + +
106H VAL* 3.9 30.7 - - + +
109H ALA* 3.7 30.3 - - + -
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Residues in contact with GLU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H MET* 2.9 20.8 + - + +
20H LEU 3.4 9.2 - - - +
21H ASN 3.2 0.2 - - - -
22H LEU* 1.3 76.3 - - - +
24H LEU* 1.3 57.4 + - - +
26H ALA* 3.3 5.5 + - - +
27H SER* 2.9 27.9 + - - -
58H GLU* 2.7 20.8 - - - +
61H HIS* 3.4 17.9 - - + +
62H ALA* 3.8 13.5 - - + -
65H PHE* 4.1 18.7 - - + -
106H VAL* 4.0 14.9 - - - +
110H LEU* 4.9 2.8 - - - +
133H TYR* 3.7 15.1 - - - -
176H MG 2.4 31.1 - - - -
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Residues in contact with LEU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TYR* 3.6 38.4 - - + +
20H LEU* 3.1 30.6 + - + +
21H ASN* 3.1 9.6 + - - +
23H GLU* 1.3 75.3 - - - +
25H TYR* 1.3 57.3 + - - +
27H SER* 3.5 6.6 - - - -
28H TYR* 3.0 27.2 + - - +
59H ARG* 4.9 17.7 - - + -
62H ALA* 3.7 17.9 - - + -
63H GLU* 6.4 0.4 - - + -
66H MET* 5.1 7.0 - - + -
78H LEU* 4.8 0.2 - - + -
81H ILE* 3.7 24.3 - - + +
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Residues in contact with TYR 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ASN* 2.8 17.8 + - - +
22H LEU* 3.4 28.3 - - + +
23H GLU 3.2 0.2 - - - -
24H LEU* 1.3 72.9 - - - +
26H ALA* 1.3 64.0 + - - +
28H TYR* 3.2 3.9 + - - +
29H THR* 2.9 49.0 + - - +
81H ILE* 4.0 9.6 - - + +
82H LYS* 3.4 39.0 - - + +
83H LYS 3.8 11.7 - - - -
84H PRO* 4.1 1.3 - - + -
85H GLU* 3.8 25.5 + - - +
102H LEU* 4.1 17.5 - - + -
105H THR* 6.5 0.7 - - + -
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Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LEU 2.9 13.8 + - - +
23H GLU* 3.5 9.9 - - - +
25H TYR* 1.3 77.8 - - - +
27H SER* 1.3 61.2 + - - +
29H THR* 3.3 3.5 + - - -
30H TYR* 3.1 31.2 + - + -
58H GLU* 4.2 15.5 - - + -
102H LEU* 4.0 26.9 - - + -
103H GLU* 6.2 0.7 - - - +
106H VAL* 4.2 18.8 - - + -
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Residues in contact with SER 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H GLU 2.9 17.3 + - - -
24H LEU* 3.5 11.6 - - - +
26H ALA* 1.3 77.1 - - - +
28H TYR* 1.3 62.4 + - - +
30H TYR 3.1 2.8 + - - -
31H SER* 3.0 19.2 + - - -
55H SER* 2.9 39.1 + - - +
58H GLU* 3.8 12.7 - - - +
59H ARG* 3.6 16.9 - - - +
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Residues in contact with TYR 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASN* 4.4 2.9 + - - +
24D LEU* 3.6 27.0 - - + +
66D MET* 5.6 0.2 - - + -
78D LEU* 3.4 37.5 - - + +
79D GLN 2.9 30.5 + - - -
81D ILE* 3.7 22.3 - - + +
24H LEU 3.0 19.8 + - - +
25H TYR* 3.5 6.1 - - - +
27H SER* 1.3 76.6 - - - +
29H THR* 1.3 59.8 + - - +
31H SER* 3.2 16.0 - - - -
32H SER* 3.2 19.1 + - - -
81H ILE* 4.0 13.0 - - + -
82H LYS 3.6 18.6 - - - +
83H LYS* 4.0 3.4 - - - -
84H PRO* 3.7 17.6 - - + +
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Residues in contact with THR 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H TYR* 2.9 30.4 + - - +
26H ALA 3.6 8.5 - - - -
27H SER 3.2 0.2 - - - -
28H TYR* 1.3 75.7 - - - +
30H TYR* 1.3 62.4 + - - +
32H SER* 3.2 6.6 + - - -
33H MET* 3.2 39.4 + - + +
84H PRO* 3.4 22.5 - - + +
85H GLU* 5.0 0.4 + - - +
89H TRP* 4.0 15.7 - - + -
102H LEU* 3.7 25.1 - - + -
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Residues in contact with TYR 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA* 3.1 22.8 + - + -
27H SER 3.5 6.7 - - - +
29H THR* 1.3 74.7 - - - +
31H SER* 1.3 60.7 + - - +
33H MET* 3.2 12.6 + - + +
34H TYR* 2.8 28.9 + - - +
50H PHE* 5.9 0.2 - + - -
51H PHE* 3.6 46.4 - + - +
54H HIS* 3.9 30.0 + + + -
55H SER* 3.7 6.7 - - - -
58H GLU* 4.0 13.5 - - + -
99H ALA* 3.9 24.7 + - + +
102H LEU* 3.9 18.1 - - + +
103H GLU* 2.8 40.1 + - - +
144H ILE* 4.3 3.6 - - + +
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Residues in contact with SER 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 6.1 0.5 - - - +
63D GLU* 4.9 6.1 + - - +
66D MET* 3.3 30.7 - - - +
78D LEU* 4.8 1.6 - - - -
27H SER 3.0 12.5 + - - -
28H TYR* 3.2 24.8 - - - -
30H TYR* 1.3 75.1 - - - +
32H SER* 1.3 62.4 + - - +
34H TYR* 3.4 12.2 + - - +
35H ALA* 3.1 22.7 + - - +
55H SER* 3.8 13.3 + - - -
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Residues in contact with SER 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 6.4 0.2 - - - -
78D LEU* 3.4 17.4 - - - +
28H TYR 3.2 5.1 + - - -
29H THR 3.2 12.0 + - - -
30H TYR 3.2 0.2 - - - -
31H SER* 1.3 73.5 - - - +
33H MET* 1.3 61.0 + - - +
35H ALA* 3.2 6.6 + - - +
36H PHE* 2.9 28.6 + - - +
84H PRO* 3.2 29.0 - - - +
86H ARG 4.0 6.6 + - - -
87H ASP* 5.1 7.6 + - - +
89H TRP* 3.4 17.1 + - - -
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Residues in contact with MET 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H THR* 3.2 34.4 + - + +
30H TYR* 3.2 15.2 + - + +
32H SER* 1.3 76.6 - - - +
34H TYR* 1.3 65.1 + - - +
36H PHE* 3.3 0.9 + - - +
37H PHE* 3.0 33.7 + - + -
51H PHE* 3.8 42.2 - - + -
89H TRP* 3.7 42.8 - - + +
95H ALA* 3.8 22.7 - - + +
98H ALA* 4.0 7.6 - - + -
99H ALA* 4.2 9.0 - - - +
102H LEU* 5.2 0.4 - - + -
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Residues in contact with TYR 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D GLU* 5.1 12.3 + - + -
66D MET* 4.5 23.6 - - + -
67D LYS* 3.4 36.2 - - + +
30H TYR 2.8 13.4 + - - +
31H SER* 3.4 14.8 - - - +
32H SER 3.2 0.2 - - - -
33H MET* 1.3 77.9 - - - +
35H ALA* 1.3 71.7 + - - +
36H PHE 3.3 0.2 + - - -
37H PHE 3.4 0.5 + - - -
38H ASP* 3.2 30.0 + - + +
48H ALA* 3.2 38.5 - - + +
49H GLU* 3.6 20.1 + - - -
51H PHE* 4.0 2.4 - - - +
52H LYS* 3.7 41.3 + - + +
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Residues in contact with ALA 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D MET* 4.3 14.8 - - + -
70D ASN* 3.0 28.3 + - - +
76D VAL* 4.2 31.6 - - + -
31H SER 3.1 10.2 + - - +
32H SER* 3.6 9.0 - - - +
34H TYR* 1.3 84.3 - - - +
36H PHE* 1.3 62.9 + - - +
38H ASP* 4.4 1.1 - - - -
39H ARG* 3.5 9.9 + - - +
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Residues in contact with PHE 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H SER 2.9 16.5 + - - +
33H MET 3.5 4.9 - - - +
34H TYR 3.1 0.4 - - - -
35H ALA* 1.3 77.5 - - - +
37H PHE* 1.3 84.6 + + - +
39H ARG* 3.3 52.9 - - - +
42H VAL* 3.3 35.4 - - + +
87H ASP 4.5 3.8 - - - +
88H GLU* 3.8 11.4 - - + -
89H TRP* 3.6 33.2 - - + -
90H GLY* 3.5 42.4 - - - -
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Residues in contact with PHE 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H MET* 3.0 26.8 + - + -
34H TYR 3.4 0.2 + - - -
36H PHE* 1.3 90.5 - + - +
38H ASP* 1.3 60.4 + - - +
39H ARG 3.2 0.4 - - - -
42H VAL* 3.5 23.3 - - + -
43H ALA* 3.5 7.1 + - - -
44H LEU* 3.2 50.5 + - + +
45H HIS* 4.3 0.7 + - - -
47H VAL* 3.9 11.4 - - + -
48H ALA* 3.7 14.1 - - + -
51H PHE* 3.7 19.3 - + - -
89H TRP* 4.8 0.7 - - + -
91H ASN* 3.5 23.6 - - - -
92H THR* 3.6 28.3 - - - -
95H ALA* 3.7 22.0 - - + -
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Residues in contact with ASP 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS* 3.1 44.3 + - - +
70D ASN* 3.2 30.9 + - - +
34H TYR* 3.2 29.6 + - + +
35H ALA* 4.4 1.3 - - - -
36H PHE 3.2 0.4 - - - -
37H PHE* 1.3 74.1 - - - +
39H ARG* 1.3 61.2 + - - +
45H HIS* 3.4 24.0 + - - -
48H ALA* 4.1 2.7 - - + +
142I LYS* 2.9 31.3 + - - -
----------------------------------------------------------
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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