Contacts of the helix formed by residues 56 - 85 (chain T) in PDB entry 6Y5D
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 56 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78S ARG* 3.8 11.0 - - - +
79S ILE 2.8 13.7 + - - -
80S ILE* 3.6 19.1 - - - -
81S PRO* 3.7 4.8 - - - +
55T ILE* 1.3 76.6 - - - +
57T SER* 1.3 60.2 + - - +
58T LYS* 3.6 5.2 + - - -
59T ALA* 3.0 24.1 + - - +
60T MET* 3.0 27.7 + - - +
23V C 4.2 10.5 - - - -
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Residues in contact with SER 57 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56T SER* 1.3 73.8 - - - +
58T LYS* 1.3 65.2 + - - +
60T MET* 3.5 7.9 + - - +
61T GLY* 3.0 21.8 + - - -
23V C 3.4 31.1 + - - -
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Residues in contact with LYS 58 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N GLY* 5.1 0.9 - - - -
81S PRO* 3.4 27.8 - - + -
105S GLN* 4.9 18.4 - - + +
56T SER* 3.6 5.6 + - - +
57T SER* 1.3 85.5 + - - +
59T ALA* 1.3 66.1 + - - +
60T MET 3.1 1.6 - - - -
61T GLY* 3.0 3.2 + - - -
62T ILE* 3.0 26.5 + - + +
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Residues in contact with ALA 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S ILE* 3.4 17.7 - - + +
80S ILE* 3.9 8.7 - - - -
81S PRO* 4.0 1.7 - - - +
84S LEU* 3.5 20.8 - - + +
55T ILE* 3.5 17.3 - - + -
56T SER* 3.0 18.0 + - - +
58T LYS* 1.3 78.9 - - - +
60T MET* 1.3 56.9 + - - +
62T ILE* 3.3 7.1 + - - +
63T MET* 2.9 31.4 + - - +
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Residues in contact with MET 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T SER* 3.0 56.5 - - - +
42T VAL* 3.6 22.4 - - + -
43T TYR* 3.9 17.3 - - + +
55T ILE* 3.7 28.6 - - + +
56T SER 3.0 16.0 + - - +
57T SER* 3.6 9.0 - - - +
58T LYS 3.1 0.2 - - - -
59T ALA* 1.3 74.9 - - - +
61T GLY* 1.3 60.0 + - - +
63T MET* 3.1 3.8 + - - +
64T ASN* 2.8 33.8 + - - +
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Residues in contact with GLY 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N GLY* 4.0 13.3 + - - -
102N GLY* 4.9 2.1 + - - +
57T SER 3.0 11.3 + - - -
58T LYS* 3.0 7.8 + - - -
60T MET* 1.3 75.3 - - - +
62T ILE* 1.3 61.6 + - - +
64T ASN* 3.3 12.3 + - - +
65T SER* 3.1 25.3 + - - -
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Residues in contact with ILE 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99N TYR* 3.6 24.1 - - + +
100N GLY* 3.6 24.0 - - - +
81S PRO* 3.5 25.4 - - + -
84S LEU* 3.6 15.3 - - + -
103S ILE* 3.5 21.3 - - + -
104S ALA* 3.4 26.0 - - + +
58T LYS* 3.0 15.6 + - + +
59T ALA 3.4 6.3 - - - +
61T GLY* 1.3 78.2 - - - +
63T MET* 1.3 60.6 + - - +
65T SER* 3.2 5.2 + - - -
66T PHE* 2.9 25.6 + - - +
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Residues in contact with MET 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S THR* 3.9 25.8 - - + -
63S ILE* 4.0 21.8 - - + -
64S LEU* 4.2 11.9 - - + -
84S LEU* 3.7 30.5 - - + -
88S ILE* 6.2 0.7 - - - -
42T VAL* 3.6 26.0 - - + -
55T ILE* 4.5 1.8 - - + -
59T ALA 2.9 21.7 + - - +
60T MET* 3.6 4.9 - - - +
62T ILE* 1.3 78.6 - - - +
64T ASN* 1.3 58.0 + - - +
66T PHE* 3.2 33.9 + - + +
67T VAL* 2.9 33.5 + - - +
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Residues in contact with ASN 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N GLY 6.5 0.9 - - - -
103N GLY* 4.7 2.2 - - - +
37T SER* 4.2 9.1 + - - -
38T TYR* 3.4 17.8 + - + +
39T SER* 2.8 47.9 + - - -
42T VAL* 4.2 2.6 - - - +
60T MET* 2.8 22.9 + - - +
61T GLY* 3.5 10.0 - - - +
63T MET* 1.3 75.7 - - - +
65T SER* 1.3 64.4 + - - +
67T VAL* 3.3 6.1 + - - +
68T ASN* 3.2 32.5 + - - +
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Residues in contact with SER 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N LEU 4.5 1.3 - - - -
99N TYR* 3.6 27.9 - - - -
100N GLY* 3.1 15.1 + - - -
102N GLY 2.5 30.2 + - - -
103N GLY* 4.4 11.3 - - - -
61T GLY 3.1 8.2 + - - -
62T ILE 3.4 8.3 - - - -
64T ASN* 1.3 77.5 - - - +
66T PHE* 1.3 62.9 + - - +
68T ASN* 3.4 2.4 + - - +
69T ASP* 3.0 24.1 + - - +
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Residues in contact with PHE 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99N TYR* 3.5 32.7 - + + -
56S LEU* 4.8 2.2 - - + -
59S LEU* 3.8 19.7 - - + -
60S THR* 3.8 24.0 - - - -
63S ILE* 3.4 32.1 - - + -
94S LEU* 6.0 0.2 - - + -
97S LEU* 5.2 1.8 - - + -
98S LEU* 3.9 14.4 - - + -
62T ILE 2.9 11.6 + - - +
63T MET* 3.3 28.7 - - + +
65T SER* 1.3 75.9 - - - +
67T VAL* 1.3 71.3 + - + +
69T ASP* 3.0 3.3 + - - +
70T ILE* 2.9 55.5 + - + +
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Residues in contact with VAL 67 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S PHE* 3.9 31.9 - - + -
56S LEU* 3.9 14.9 - - + +
60S THR* 4.0 11.0 - - + +
38T TYR* 3.6 40.6 - - + +
42T VAL* 4.2 11.9 - - + -
63T MET 2.9 21.0 + - - +
64T ASN 3.3 4.2 + - - +
66T PHE* 1.3 82.9 - - + +
68T ASN* 1.3 57.9 + - - +
70T ILE* 3.4 2.6 + - - -
71T PHE* 2.9 28.0 + - + +
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Residues in contact with ASN 68 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N GLY* 2.8 39.8 + - - +
34S LEU* 5.4 2.6 - - - +
37T SER* 6.3 0.6 - - - +
38T TYR* 3.5 27.5 + - - -
64T ASN* 3.2 15.9 + - - +
65T SER 3.9 0.4 - - - +
67T VAL* 1.3 77.9 - - - +
69T ASP* 1.3 57.7 + - - +
71T PHE* 3.7 10.5 - - - +
72T GLU* 3.0 29.3 + - - +
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Residues in contact with ASP 69 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N LYS* 5.2 4.7 - - - -
97N THR* 3.8 21.2 + - - +
99N TYR* 2.7 35.3 + - + +
98S LEU* 4.9 0.2 - - - +
65T SER 3.0 17.6 + - - +
66T PHE 3.0 1.3 + - - +
68T ASN* 1.3 75.3 - - - +
70T ILE* 1.3 66.2 + - - +
72T GLU* 3.4 10.1 + - - +
73T ARG* 3.2 53.7 + - - +
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Residues in contact with ILE 70 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S LEU* 3.6 17.0 - - + -
59S LEU* 3.9 23.6 - - + -
97S LEU* 4.3 13.9 - - + -
98S LEU* 4.4 5.6 - - + -
66T PHE* 2.9 53.4 + - + +
67T VAL* 4.6 0.4 - - - -
69T ASP* 1.3 75.2 - - + +
71T PHE* 1.3 68.2 + - - +
73T ARG* 3.1 25.5 + - + +
74T ILE* 3.0 45.5 + - + +
103T LEU* 5.7 2.0 - - + -
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Residues in contact with PHE 71 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31S VAL* 4.3 4.0 - - + -
34S LEU* 3.4 56.1 - - + -
35S LEU* 3.9 7.2 - - + -
40S TYR* 3.5 29.4 - + - -
52S MET* 3.3 39.5 - - + +
56S LEU* 3.7 19.7 - - + +
38T TYR* 4.7 2.2 - - - +
67T VAL* 2.9 20.5 + - + +
68T ASN* 3.7 14.6 - - - +
69T ASP 3.3 0.2 - - - -
70T ILE* 1.3 78.6 - - - +
72T GLU* 1.3 67.8 + - + +
75T ALA* 2.9 33.4 + - + +
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Residues in contact with GLU 72 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N LYS* 2.8 33.6 + - - -
80P ARG* 4.7 14.5 - - - +
83P HIS* 5.3 8.3 + - - -
84P TYR* 5.0 2.9 + - - -
40S TYR* 3.7 19.9 + - + +
68T ASN 3.0 15.7 + - - +
69T ASP* 3.8 9.3 - - - +
70T ILE 3.2 0.2 - - - -
71T PHE* 1.3 87.7 - - + +
73T ARG* 1.3 55.6 + - + +
75T ALA* 3.7 0.9 - - - +
76T GLY* 2.7 32.3 + - - -
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Residues in contact with ARG 73 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97N THR* 4.8 9.3 + - - +
97S LEU* 3.4 39.4 + - - +
98S LEU* 4.8 3.8 - - - +
100S LYS* 6.2 2.0 - - - +
101S VAL* 5.0 4.0 - - - +
69T ASP* 3.2 41.9 + - - +
70T ILE* 3.1 21.6 + - + +
72T GLU* 1.3 80.8 - - + +
74T ILE* 1.3 58.0 + - - +
76T GLY* 3.2 1.7 + - - -
77T GLU* 2.9 33.1 + - - +
102T LEU* 3.5 28.6 - - + +
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Residues in contact with ILE 74 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S MET* 3.4 23.3 - - + -
55S VAL* 3.6 33.4 - - + -
56S LEU* 4.6 7.0 - - + -
70T ILE* 3.0 35.4 + - + +
73T ARG* 1.3 76.6 - - - +
75T ALA* 1.3 58.2 + - - +
77T GLU 3.3 0.7 + - - -
78T ALA* 2.8 27.7 + - - +
95T ILE* 3.9 23.1 - - + +
98T ALA* 3.5 15.7 - - + +
99T VAL* 4.6 7.4 - - + -
102T LEU* 3.5 21.3 - - + -
103T LEU* 5.3 3.8 - - + -
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Residues in contact with ALA 75 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S LEU* 3.9 17.0 - - + -
40S TYR* 3.4 41.7 - - + +
52S MET* 3.7 4.2 - - + +
71T PHE* 2.9 22.9 + - + +
72T GLU 3.8 0.2 - - - +
74T ILE* 1.3 77.5 - - - +
76T GLY* 1.3 57.4 + - - +
78T ALA* 3.7 6.8 - - - +
79T SER* 2.8 30.3 + - - -
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Residues in contact with GLY 76 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S TYR* 3.9 11.0 - - - -
72T GLU* 2.7 23.3 + - - -
73T ARG* 3.5 2.0 - - - -
75T ALA* 1.3 73.3 - - - +
77T GLU* 1.3 61.9 + - - +
79T SER* 3.3 6.0 + - - -
80T ARG* 3.1 30.2 + - - +
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Residues in contact with GLU 77 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R TYR* 4.1 4.5 + - - -
93R ARG* 3.3 29.5 + - - +
73T ARG 2.9 17.1 + - - +
76T GLY* 1.3 70.9 - - - +
78T ALA* 1.3 61.3 + - - +
80T ARG* 2.7 37.9 + - - +
81T LEU* 2.8 37.5 + - + +
98T ALA* 3.3 24.2 - - + +
101T LEU* 4.0 14.2 - - + +
102T LEU* 3.8 23.8 - - + +
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Residues in contact with ALA 78 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74T ILE 2.8 17.5 + - - +
75T ALA* 3.7 5.4 - - - +
76T GLY 3.3 0.2 - - - -
77T GLU* 1.3 75.7 - - - +
79T SER* 1.3 62.2 + - - +
81T LEU* 3.3 2.4 + - - +
82T ALA* 3.0 24.4 + - - +
90T ILE* 3.9 19.5 - - + +
94T GLU* 3.9 24.2 - - + +
95T ILE* 3.9 26.5 - - + -
98T ALA* 4.0 0.4 - - - +
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Residues in contact with SER 79 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O GLY 5.2 2.8 + - - -
39O ASN* 4.4 6.6 + - - +
39S ASN 4.3 2.9 + - - -
40S TYR* 2.6 42.4 + - - +
75T ALA 2.8 14.5 + - - -
76T GLY* 3.3 11.2 - - - -
78T ALA* 1.3 78.3 - - - +
80T ARG* 1.3 57.2 + - - +
82T ALA* 3.3 3.9 + - - +
83T HIS* 3.0 26.7 + - - +
90T ILE* 4.1 4.4 - - - +
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Residues in contact with ARG 80 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P GLU* 4.9 15.2 + - - -
73R TYR* 5.0 10.5 + - + -
89R TYR* 4.7 22.7 - - + -
92R LYS* 5.0 13.3 - - - +
76T GLY* 3.1 9.9 + - - +
77T GLU* 2.7 58.0 + - - +
79T SER* 1.3 77.5 - - - +
81T LEU* 1.3 59.0 + - + +
83T HIS* 3.1 10.4 + - + +
84T TYR* 2.7 39.0 + - + +
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Residues in contact with LEU 81 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R TYR* 4.1 28.3 - - + -
76R HIS* 3.9 22.8 + - + +
77T GLU* 2.8 26.9 + - - +
78T ALA 3.7 3.8 - - - +
80T ARG* 1.3 73.5 - - + +
82T ALA* 1.3 63.8 + - - +
84T TYR* 4.4 6.5 - - + -
85T ASN* 3.0 31.9 + - - +
94T GLU* 3.2 34.8 - - + +
97T THR* 3.5 34.8 - - + -
98T ALA* 3.7 7.6 - - - +
101T LEU* 4.2 3.8 - - + -
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Residues in contact with ALA 82 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S ALA* 5.3 3.4 - - + -
78T ALA 3.0 13.5 + - - +
79T SER* 3.5 9.2 - - - +
81T LEU* 1.3 75.2 - - - +
83T HIS* 1.3 55.6 + - - +
85T ASN 3.5 1.0 + - - -
86T LYS 2.9 8.8 + - - -
87T ARG* 2.5 51.0 + - + +
88T SER 5.1 1.3 - - - -
89T THR 4.1 19.7 - - - +
90T ILE* 4.5 8.7 - - + -
94T GLU* 4.1 9.6 - - + +
----------------------------------------------------------
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Residues in contact with HIS 83 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O LYS* 6.1 1.6 - - + -
38O GLY* 4.7 23.3 + - - -
39O ASN* 6.3 1.1 - - - +
89R TYR* 6.1 0.9 - - - -
79T SER* 3.0 14.9 + - - +
80T ARG* 3.1 14.1 + - + +
82T ALA* 1.3 74.0 - - - +
84T TYR* 1.3 62.2 + - - +
86T LYS* 2.7 29.4 + - + +
87T ARG 4.3 3.3 + - - +
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Residues in contact with TYR 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R TYR* 4.6 24.2 - + + -
76R HIS* 5.7 0.2 - + - -
79R ARG* 2.9 19.3 + - - -
83R THR* 4.2 1.7 + - - -
85R MET* 4.2 11.6 - - + +
86R ASP* 2.6 29.5 + - - -
89R TYR* 3.4 47.3 - + + +
80T ARG* 2.7 24.4 + - + +
81T LEU* 3.8 8.3 - - + +
83T HIS* 1.3 77.8 - - - +
85T ASN* 1.3 77.0 + - - +
86T LYS* 3.4 3.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 85 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R HIS* 3.3 27.8 - - - +
77R ALA* 3.3 29.3 - - - +
81T LEU* 3.0 25.0 + - - +
82T ALA 3.5 0.9 - - - -
84T TYR* 1.3 93.3 - - - +
86T LYS* 1.3 71.2 + - - +
87T ARG* 3.5 31.4 + - - +
----------------------------------------------------------
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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).
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