Contacts of the helix formed by residues 47 - 78 (chain A) in PDB entry 5DHG
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 PRO 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 1.3 66.9 + - - +
49A GLY 3.5 3.6 - - - +
50A LEU* 3.7 34.1 - - + +
51A LYS* 3.1 34.5 + - - +
295A GLU* 5.1 20.0 - - + +
299A ALA* 6.0 1.3 - - + -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 1.3 76.2 - - - +
49A GLY* 1.3 59.1 + - - +
51A LYS* 3.2 16.8 - - - +
52A VAL* 3.0 33.3 + - + +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.5 2.0 - - - +
48A LEU* 1.3 76.6 - - - +
50A LEU* 1.3 59.6 + - - +
52A VAL* 3.2 11.6 + - - +
53A THR* 3.0 28.6 + - - -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.6 33.8 + - + +
48A LEU 3.4 0.4 - - - -
49A GLY* 1.3 77.1 - - - +
51A LYS* 1.3 57.3 + - - +
53A THR* 3.1 16.4 - - + +
54A ILE* 3.1 27.0 + - + +
299A ALA* 4.1 24.9 - - + -
303A PHE* 4.2 24.4 - - + -
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.1 24.8 + - - +
48A LEU* 3.2 24.9 - - - +
50A LEU* 1.3 73.5 - - - +
52A VAL* 1.3 60.5 + - - +
54A ILE* 3.2 9.7 + - - +
55A VAL* 2.9 33.8 + - - +
111A ILE* 3.3 35.9 + - + +
112A LEU* 3.3 36.3 + - + +
113A LEU 5.4 0.2 - - - -
114A GLY* 5.2 3.0 - - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU 3.0 22.3 + - - +
49A GLY* 3.2 13.9 + - - +
51A LYS* 1.3 76.3 - - - +
53A THR* 1.3 57.0 + - - +
55A VAL* 3.9 0.9 - - - +
56A GLY* 2.9 27.4 + - - -
112A LEU* 4.4 14.4 - - + -
1124B ALA* 4.9 19.1 - - + +
1127B VAL* 4.5 23.9 - - + +
1128B GLY* 5.4 2.5 - - - +
1131B LEU* 5.8 3.8 - - + -
1504B OLA 5.1 18.4 - - + -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 3.0 13.4 + - - -
50A LEU* 3.1 19.8 - - + +
52A VAL* 1.3 78.7 - - - +
54A ILE* 1.3 63.6 + - - +
56A GLY* 3.4 1.3 + - - -
57A LEU* 2.9 25.8 + - + +
303A PHE* 4.3 22.4 - - + -
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.1 15.4 + - + +
51A LYS* 3.2 13.9 + - + +
53A THR* 1.3 75.5 - - - +
55A VAL* 1.3 59.2 + - - +
57A LEU* 3.1 10.1 + - + +
58A TYR* 2.9 42.4 + - + +
111A ILE* 3.6 32.1 - - + -
302A ARG* 4.2 26.9 - - + +
303A PHE* 3.5 45.5 - - + -
306A ALA* 4.7 4.7 - - + -
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS 2.9 20.9 + - - +
52A VAL 4.0 2.7 - - - +
54A ILE* 1.3 76.7 - - + +
56A GLY* 1.3 58.9 + - - +
58A TYR* 3.0 10.0 + - + +
59A LEU* 2.9 36.4 + - + +
108A GLY* 3.4 36.8 - - - +
111A ILE* 4.2 11.2 - - + -
112A LEU* 3.7 21.3 - - + -
1127B VAL* 3.8 24.9 - - + -
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL 2.9 16.4 + - - -
53A THR 3.8 0.9 - - - -
55A VAL* 1.3 76.2 - - - +
57A LEU* 1.3 61.9 + - - +
59A LEU* 3.2 7.7 + - - +
60A ALA* 3.0 23.6 + - - +
1123B LEU* 4.2 20.7 - - - +
1127B VAL* 3.9 16.2 - - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A THR* 2.9 16.9 + - + +
54A ILE* 3.1 11.9 + - - +
56A GLY* 1.3 76.2 - - - +
58A TYR* 1.3 63.6 + - + +
60A ALA* 3.3 9.1 + - + +
61A VAL* 2.9 42.5 + - + +
303A PHE* 4.9 17.3 - - + -
306A ALA* 3.8 27.4 - - + -
307A LEU 5.6 0.2 - - - +
310A VAL* 4.6 13.5 - - + -
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 2.9 23.7 + - + +
55A VAL* 3.0 11.9 + - + +
57A LEU* 1.3 79.9 - - + +
59A LEU* 1.3 53.8 + - + +
61A VAL* 3.2 4.7 + - + +
62A CYS* 2.7 37.8 + - - +
104A LEU* 3.7 45.2 - - + +
105A PRO* 6.0 0.2 - - + -
107A GLN* 4.3 17.7 + - + -
108A GLY* 4.1 11.0 - - - -
111A ILE* 3.7 28.2 - - + +
302A ARG* 4.6 2.3 + - - -
305A THR* 4.3 6.1 - - - +
306A ALA* 3.8 36.6 + - + +
309A TYR* 3.7 26.4 - + + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 2.9 21.6 + - + +
56A GLY* 3.6 7.2 - - - +
58A TYR* 1.3 75.2 - - + +
60A ALA* 1.3 62.7 + - - +
62A CYS* 3.2 5.3 + - + +
63A VAL* 2.9 33.2 + - + +
105A PRO* 5.2 21.1 - - + -
1123B LEU* 4.6 13.7 - - + +
1126B CYS* 4.2 22.9 - - + -
1127B VAL* 3.5 31.2 - - + -
1130B LEU* 6.0 2.2 - - + -
1169B PRO* 5.2 10.1 - - + -
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY 3.0 12.5 + - - +
57A LEU* 3.6 13.9 - - + +
59A LEU* 1.3 78.2 - - - +
61A VAL* 1.3 63.7 + - + +
62A CYS 3.2 0.2 + - - -
63A VAL* 4.1 3.4 - - - +
64A GLY* 3.0 23.2 + - - -
1123B LEU* 4.4 20.3 - - + +
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 2.9 30.0 + - + +
58A TYR* 3.7 6.5 - - + +
60A ALA* 1.3 76.3 - - + +
62A CYS* 1.3 56.9 + - - +
65A GLY* 2.8 24.6 + - - -
101A LEU* 3.3 11.5 - - + +
104A LEU* 3.7 17.9 - - + -
306A ALA 5.5 0.2 - - - +
309A TYR* 3.3 27.8 - - + +
310A VAL* 3.7 29.6 - - + +
313A CYS* 3.7 22.4 - - + +
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Residues in contact with CYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR 2.7 21.8 + - - +
59A LEU* 3.4 9.6 - - + +
60A ALA 3.1 0.2 - - - -
61A VAL* 1.3 70.7 - - - +
63A VAL* 1.3 70.3 + - + +
66A LEU* 3.0 45.3 + - - +
101A LEU* 3.6 31.1 - - - +
102A LEU* 5.3 0.7 - - - -
104A LEU* 4.2 6.5 - - + +
105A PRO* 3.9 22.9 - - + -
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 2.9 18.2 + - + +
60A ALA* 4.1 3.1 - - - +
62A CYS* 1.3 78.0 - - + +
64A GLY* 1.3 65.3 + - - +
66A LEU* 4.0 3.6 - - - +
67A LEU* 3.0 28.0 + - + +
1169B PRO* 4.2 25.8 - - + +
1170B PHE* 5.7 9.2 - - + -
1173B THR* 3.9 27.1 - - + -
1182B PHE* 4.6 17.5 - - + -
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA 3.0 14.6 + - - -
63A VAL* 1.3 78.5 - - - +
65A GLY* 1.3 56.5 + - - +
67A LEU* 3.5 8.9 + - - +
68A GLY* 2.9 26.2 + - - -
313A CYS* 4.4 7.6 - - - +
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL 2.8 23.9 + - - -
64A GLY* 1.3 71.0 - - - +
66A LEU* 1.3 60.1 + - - +
68A GLY* 3.9 0.6 - - - -
69A ASN* 2.9 36.3 + - - +
101A LEU* 3.3 14.6 - - - -
313A CYS* 3.4 23.3 - - - +
316A PRO* 5.7 0.2 - - - -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A CYS* 3.0 37.5 + - - +
63A VAL* 4.0 3.4 - - - +
65A GLY* 1.3 74.4 - - - +
67A LEU* 1.3 63.8 + - - +
69A ASN* 5.0 1.1 - - - -
70A CYS* 2.9 38.0 + - - +
98A THR* 3.8 39.7 - - + +
101A LEU* 3.5 15.6 - - + +
102A LEU* 3.9 23.3 - - + -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 3.0 23.0 + - + +
64A GLY* 3.7 8.7 - - - +
66A LEU* 1.3 77.3 - - - +
68A GLY* 1.3 62.2 + - - +
70A CYS* 4.0 2.6 - - - +
71A LEU* 3.0 27.4 + - + +
1173B THR* 6.0 2.7 - - - +
1177B LEU* 4.9 11.0 - - + -
1181B PRO* 4.6 33.4 - - + +
1182B PHE* 5.0 16.8 - - + -
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY 2.9 15.6 + - - -
67A LEU* 1.3 78.9 - - - +
69A ASN* 1.3 57.2 + - - +
71A LEU* 3.1 11.3 + - - +
72A VAL* 2.9 30.5 + - - +
316A PRO* 3.4 24.6 - - - +
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY* 2.9 28.9 + - - +
66A LEU* 4.5 0.7 - - - +
68A GLY* 1.3 69.3 - - - -
70A CYS* 1.3 61.2 + - - +
72A VAL* 3.2 6.2 + - - +
73A MET* 2.9 35.2 + - - +
94A ALA* 3.5 23.1 - - + +
97A ASP* 3.5 24.7 - - - +
98A THR* 3.8 17.7 - - - +
101A LEU* 3.6 8.0 - - + +
312A SER 3.2 22.4 + - - -
315A ASN* 4.5 2.8 - - - +
316A PRO* 3.5 16.7 - - - +
319A TYR* 5.4 1.9 - - - -
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Residues in contact with CYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 2.9 34.5 + - - +
67A LEU* 4.0 3.1 - - + +
69A ASN* 1.3 75.9 - - - +
71A LEU* 1.3 62.5 + - - +
73A MET* 3.5 10.3 + - - +
74A TYR* 3.0 25.1 + - - +
98A THR* 4.8 15.7 + - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.0 19.0 + - + +
68A GLY* 3.1 13.7 + - - +
70A CYS* 1.3 76.0 - - - +
72A VAL* 1.3 66.3 + - + +
74A TYR* 3.2 12.8 + - + +
75A VAL* 2.9 42.3 + - + +
316A PRO* 6.3 0.7 - - + -
329A CYS 5.8 3.4 - - - +
330A PHE* 4.2 32.5 - - + -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 2.9 15.9 + - - +
69A ASN* 3.2 8.0 + - - +
71A LEU* 1.3 78.6 - - + +
73A MET* 1.3 65.1 + - - +
75A VAL* 3.1 3.5 + - - +
76A ILE* 3.0 37.0 + - + +
90A ILE* 3.9 16.8 - - + -
94A ALA* 4.7 8.5 - - + -
316A PRO* 3.9 22.7 - - + +
319A TYR* 4.0 15.5 - - + -
326A PHE* 3.7 29.4 - - + -
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Residues in contact with MET 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN 2.9 19.2 + - - +
70A CYS* 3.9 8.5 - - - +
72A VAL* 1.3 75.7 - - - +
74A TYR* 1.3 58.4 + - - +
76A ILE 3.5 0.2 + - - -
77A LEU* 2.9 36.3 + - + +
91A PHE* 3.6 45.2 - - + +
94A ALA* 3.7 14.8 - - + -
95A LEU* 3.8 35.4 - - + -
98A THR* 3.8 24.5 - - + -
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Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A CYS 3.0 19.0 + - - +
71A LEU* 3.5 11.7 - - + +
73A MET* 1.3 76.6 - - - +
75A VAL* 1.3 73.4 + - + +
77A LEU* 4.6 2.9 - - - -
78A ARG* 3.2 61.4 + - + +
79A HIS* 3.4 35.2 + + + +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 2.9 36.0 + - + +
72A VAL* 3.1 9.6 + - - +
74A TYR* 1.3 78.1 - - + +
76A ILE* 1.3 63.5 + - - +
79A HIS* 3.4 33.2 - - + +
80A THR* 3.4 11.2 + - - +
82A MET* 3.6 26.1 - - - +
326A PHE* 4.3 14.8 - - + -
329A CYS* 3.8 33.0 - - + +
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 3.0 26.8 + - + +
73A MET 4.1 1.8 - - - +
75A VAL* 1.3 77.1 - - + +
77A LEU* 1.3 67.2 + - - +
80A THR 3.4 14.0 - - - +
82A MET* 4.4 10.0 - - + +
83A LYS* 3.7 14.4 - - + +
87A ASN* 3.3 44.6 - - + +
88A ILE* 4.3 16.8 - - + -
90A ILE* 4.0 7.2 - - + -
91A PHE* 4.1 18.4 - - + +
326A PHE* 3.8 29.6 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 2.9 21.4 + - + +
74A TYR* 3.3 2.4 + - - +
76A ILE* 1.3 76.3 - - - +
78A ARG* 1.3 100.7 + - + +
83A LYS* 3.1 34.8 + - - +
91A PHE* 4.1 24.9 - - + -
----------------------------------------------------------
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 3.2 45.3 + - + +
77A LEU* 1.3 112.7 - - + +
79A HIS* 1.3 69.5 + - - +
80A THR* 3.0 7.1 + - - +
83A LYS* 5.3 0.7 + - - -
----------------------------------------------------------
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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