Contacts of the helix formed by residues 67 - 93 (chain G) in PDB entry 5TWV
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 LYS 67 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ASP 3.5 3.4 + - - +
66G LEU* 1.3 74.4 - - - +
68G TRP* 1.3 59.8 + - - +
69G PRO* 3.5 14.8 - - + -
70G HIS* 3.6 22.2 + - + +
71G THR* 2.4 30.4 + - - -
55H SER 5.3 1.0 + - - -
56H SER* 3.8 30.0 - - - +
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Residues in contact with TRP 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E GLN* 5.9 4.9 - - - -
60E PHE* 4.1 33.5 - + - -
162E ILE* 6.2 7.0 - - + -
66G LEU 5.9 0.4 - - - -
67G LYS* 1.3 72.1 - - - +
69G PRO* 1.3 74.7 - - + +
71G THR* 3.7 21.5 - - + -
72G LEU* 3.2 31.7 + - + +
167G ILE* 4.7 17.3 - - + -
170G LYS* 4.0 29.8 - - + -
173G GLN* 5.1 10.4 - - - +
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Residues in contact with PRO 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G LYS* 3.6 17.7 - - + -
68G TRP* 1.3 96.9 - - + +
70G HIS* 1.3 69.0 + - + +
72G LEU* 3.7 6.0 + - + +
73G LEU* 3.5 17.7 + - - +
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Residues in contact with HIS 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G LEU* 4.9 19.0 - - + +
67G LYS* 3.6 25.9 + - + +
68G TRP 3.3 0.2 - - - -
69G PRO* 1.3 84.2 - - + +
71G THR* 1.3 60.8 + - - +
73G LEU* 3.0 14.5 + - + +
74G ILE* 2.9 35.4 + - + +
51H TRP* 4.0 29.0 - + + -
52H GLY* 4.1 27.1 + - - -
55H SER* 4.9 10.8 - - - -
56H SER* 6.0 3.2 - - - -
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Residues in contact with THR 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LEU 4.6 8.5 + - - +
66G LEU* 3.0 17.3 + - - +
67G LYS 2.4 25.9 + - - -
68G TRP* 3.7 27.7 - - + -
69G PRO 3.3 0.4 - - - -
70G HIS* 1.3 80.4 - - - +
72G LEU* 1.3 59.3 + - - +
74G ILE* 3.5 11.8 + - + +
75G PHE* 3.1 54.7 + - + -
166G CYS* 6.1 2.0 - - - +
167G ILE* 5.6 2.0 - - + -
170G LYS* 6.1 3.4 - - + -
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E MET* 4.3 28.0 - - + -
68G TRP* 3.2 20.8 + - + +
69G PRO* 3.9 6.1 - - + +
70G HIS 3.2 0.2 - - - -
71G THR* 1.3 78.7 - - - +
73G LEU* 1.3 52.4 + - - +
75G PHE* 3.5 5.4 + - - +
76G THR* 2.7 52.8 + - + +
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Residues in contact with LEU 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G PRO 3.5 11.2 + - - +
70G HIS* 3.2 18.8 - - + +
72G LEU* 1.3 79.2 - - - +
74G ILE* 1.3 64.0 + - + +
76G THR* 3.1 18.2 + - - +
77G MET* 3.1 41.4 + - + +
48H PHE* 5.6 10.1 - - + -
51H TRP* 4.6 22.0 - - + -
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Residues in contact with ILE 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LEU* 5.0 23.1 - - + +
66G LEU* 4.3 24.0 - - + -
70G HIS* 2.9 21.1 + - + +
71G THR* 3.8 14.6 - - + +
72G LEU 3.3 0.2 - - - -
73G LEU* 1.3 79.8 - - + +
75G PHE* 1.3 73.6 + - + +
77G MET* 4.6 1.6 - - - +
78G SER* 2.8 33.4 + - - +
45H PRO* 5.5 14.1 - - + +
48H PHE* 5.1 17.0 - - + -
49H ILE* 5.1 10.3 - - + +
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Residues in contact with PHE 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E ILE* 4.6 3.7 - - - +
158E MET* 4.3 14.6 - - + -
63G LEU* 5.5 7.4 - - + -
71G THR* 3.1 39.7 + - + +
72G LEU* 3.5 3.8 + - - +
73G LEU 3.4 0.2 - - - -
74G ILE* 1.3 89.5 - - + +
76G THR* 1.3 63.7 + - - +
78G SER* 3.5 7.1 + - - -
79G PHE* 3.2 29.9 - + - +
162G ILE* 6.3 1.6 - - + -
163G MET* 3.8 39.7 - - + -
166G CYS* 3.8 35.7 - - + -
167G ILE* 3.8 22.2 - - + -
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Residues in contact with THR 76 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E ILE* 4.1 27.7 - - + +
158E MET* 5.6 2.9 - - + -
72G LEU* 2.7 41.5 + - + +
73G LEU* 3.1 15.2 + - - +
75G PHE* 1.3 79.6 - - + +
77G MET* 1.3 68.9 + - - +
79G PHE* 3.6 4.5 + - - +
80G LEU* 3.2 32.4 + - - +
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Residues in contact with MET 77 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G LEU* 3.1 36.2 + - + +
74G ILE* 4.6 1.3 - - - +
76G THR* 1.3 79.6 + - - +
78G SER* 1.3 54.5 - - - +
79G PHE 3.1 2.0 - - - -
80G LEU* 3.5 18.8 - - - +
81G CYS* 2.6 39.4 + - - +
44H PHE* 5.2 24.7 - - + -
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Residues in contact with SER 78 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ILE* 2.8 25.6 + - - +
75G PHE* 3.5 13.5 + - - -
77G MET* 1.3 78.6 - - - +
79G PHE* 1.3 68.1 + - - +
81G CYS* 3.9 7.3 - - - +
82G SER* 2.9 27.9 + - - -
159G ILE* 5.0 1.5 - - - +
41H PHE 5.8 0.2 - - - -
44H PHE* 6.0 0.2 - - - +
45H PRO* 4.6 22.2 - - - -
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Residues in contact with PHE 79 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E ILE* 4.3 11.9 - - + -
157E LEU* 4.5 16.2 - - + -
75G PHE* 3.2 24.0 + + + +
76G THR* 3.6 5.6 + - - +
77G MET 3.1 0.4 - - - -
78G SER* 1.3 87.6 + - - +
80G LEU* 1.3 60.0 + - - +
82G SER* 3.1 5.6 + - - -
83G TRP* 2.8 68.7 + + + +
129G VAL* 6.1 2.2 - - + -
156G GLY 5.7 1.1 - - - -
159G ILE* 3.9 31.4 - - + -
160G ASN* 4.0 30.1 - - + -
163G MET* 3.8 25.4 - - + -
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Residues in contact with LEU 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E ILE* 4.7 14.8 - - + -
76G THR* 3.2 23.3 + - - +
77G MET* 3.6 19.1 - - - +
79G PHE* 1.3 76.3 - - - +
81G CYS* 1.3 65.2 + - - +
83G TRP* 3.2 30.0 + - + +
84G LEU* 3.1 24.8 + - - +
121G PHE* 4.8 13.4 - - + -
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Residues in contact with CYS 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G MET 2.6 23.8 + - - +
78G SER* 3.9 8.5 - - - +
80G LEU* 1.3 72.6 - - - +
82G SER* 1.3 62.0 + - - +
84G LEU 3.9 0.5 + - - -
85G LEU* 3.8 4.5 + - - +
41H PHE* 3.3 67.8 - - + +
44H PHE* 4.4 13.0 - - + -
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Residues in contact with SER 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G SER 2.9 17.3 + - - -
79G PHE 3.1 9.1 + - - -
80G LEU 3.1 0.4 - - - -
81G CYS* 1.3 74.9 - - - +
83G TRP* 1.3 65.6 + - - +
84G LEU 3.1 2.2 - - - -
85G LEU* 3.0 20.0 + - - +
86G PHE* 2.9 39.5 + - - -
155G VAL* 6.2 0.2 - - - +
159G ILE* 4.1 20.6 - - - +
41H PHE* 5.7 0.2 - - - -
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Residues in contact with TRP 83 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E ILE* 3.6 37.5 - - + -
153E ASN* 5.5 4.9 - - + -
154E ILE* 4.8 15.9 - - + -
79G PHE* 2.8 61.0 + + + +
80G LEU* 3.6 27.4 - - + +
82G SER* 1.3 82.8 - - - +
84G LEU* 1.3 58.5 + - - +
86G PHE* 4.0 4.7 - + - -
87G ALA* 3.4 22.0 + - - +
121G PHE* 3.8 11.4 - + + -
124G SER* 3.5 8.9 + - - -
125G ILE* 3.1 40.4 - - + -
128G GLN* 4.3 26.9 - - + +
129G VAL* 4.5 18.1 - - + +
159G ILE* 5.7 1.8 - - - +
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Residues in contact with LEU 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G LEU 3.1 13.9 + - - +
81G CYS 4.2 0.7 - - - +
82G SER 3.1 1.0 - - - -
83G TRP* 1.3 76.5 - - - +
85G LEU* 1.3 60.6 + - - +
87G ALA* 3.5 6.1 + - - +
88G MET* 3.2 29.3 + - - +
121G PHE* 4.3 10.7 - - + -
41H PHE* 3.7 28.3 - - + -
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Residues in contact with LEU 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G CYS 3.8 4.6 + - - +
82G SER* 3.0 13.3 + - - +
84G LEU* 1.3 80.0 - - - +
86G PHE* 1.3 72.7 + - + +
87G ALA 3.1 2.3 + - - -
88G MET* 3.6 5.7 + - + +
89G VAL* 3.6 22.3 + - - +
34H VAL* 5.0 6.7 - - + +
37H VAL* 5.3 1.1 - - + -
38H PHE* 4.4 35.2 - - + +
41H PHE* 3.9 31.4 - - + -
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Residues in contact with PHE 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G SER* 2.9 45.0 + - - +
83G TRP* 4.1 1.8 - + - +
84G LEU 3.4 0.2 - - - -
85G LEU* 1.3 89.1 - - + +
87G ALA* 1.3 58.1 + - - +
89G VAL* 3.8 13.1 - - + +
90G TRP* 3.5 24.2 - - + +
124G SER* 2.8 23.8 + - - +
128G GLN* 3.1 40.2 - - + +
151G VAL* 4.6 4.5 - - + -
152G GLN* 3.8 29.4 - - + -
155G VAL* 4.5 21.3 - - + -
156G GLY* 4.9 3.8 - - - -
159G ILE* 5.8 0.4 - - + -
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Residues in contact with ALA 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G TRP 3.4 16.3 + - - +
84G LEU* 3.8 5.2 - - - +
85G LEU 3.1 0.6 - - - -
86G PHE* 1.3 81.4 - - - +
88G MET* 1.3 65.4 + - - +
89G VAL 3.4 0.4 - - - -
90G TRP* 3.4 4.9 + - - +
91G TRP* 3.1 22.7 + - - +
117G PHE* 5.7 5.1 - - + -
120G ALA* 3.9 5.0 - - - +
121G PHE* 3.3 42.4 - - + +
124G SER* 3.9 5.2 - - - -
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Residues in contact with MET 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G LEU 3.2 16.7 + - - +
85G LEU* 3.6 7.8 + - + +
87G ALA* 1.3 74.5 - - - +
89G VAL* 1.3 57.7 + - - +
90G TRP 3.1 4.5 - - - -
91G TRP* 3.2 35.0 + - + +
92G LEU* 3.1 28.2 + - + +
117G PHE* 4.5 18.8 - - + -
30H ALA* 5.3 4.9 - - - +
33H VAL* 3.7 29.8 - - + -
34H VAL* 4.5 24.7 - - + +
37H VAL* 5.3 11.4 - - + -
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Residues in contact with VAL 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LEU 3.6 17.3 + - - +
86G PHE* 3.8 16.4 - - + +
88G MET* 1.3 78.2 - - - +
90G TRP* 1.3 71.7 + - + +
92G LEU* 3.7 19.8 - - + +
93G ILE* 3.0 28.4 + - + +
148G ILE* 4.4 24.2 - - + -
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Residues in contact with TRP 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G PHE* 3.5 22.0 - - + +
87G ALA* 3.4 6.7 + - - +
88G MET 3.1 0.8 - - - -
89G VAL* 1.3 81.9 - - + +
91G TRP* 1.3 59.3 + - - +
92G LEU 3.0 4.9 - - - -
93G ILE* 3.1 38.3 - - + +
94G ALA* 3.8 8.1 + - - +
111G VAL* 3.8 22.2 - - + +
114G ILE* 5.5 5.1 - - + +
120G ALA* 4.1 17.2 - - + +
123G PHE* 2.8 55.5 - + + -
138G VAL* 5.8 1.8 - - + -
145G ALA* 3.4 23.1 - - + -
148G ILE* 3.6 31.6 - - + -
149G LEU* 3.5 28.5 - - + -
152G GLN* 5.1 7.0 - - + -
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Residues in contact with TRP 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G ALA 3.1 17.5 + - - +
88G MET* 3.6 24.2 - - + +
90G TRP* 1.3 76.6 - - - +
92G LEU* 1.3 61.2 + - + +
94G ALA* 4.0 5.4 + - + +
95G PHE* 3.3 52.1 + + - +
100G LEU* 5.1 10.6 - - + +
114G ILE* 5.9 1.3 - - + -
116G SER 4.5 4.9 - - - -
117G PHE* 3.1 67.3 - + + +
120G ALA* 4.0 9.9 - - + -
6H CYS* 6.2 2.5 - - + -
30H ALA* 4.3 24.0 - - + -
105H HIS* 5.0 16.6 - - + -
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Residues in contact with LEU 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G MET* 3.1 16.2 + - + +
89G VAL* 3.7 21.8 - - + +
91G TRP* 1.3 81.6 - - + +
93G ILE* 1.3 60.4 + - + +
94G ALA 3.1 2.2 - - - -
95G PHE* 3.3 10.5 + - + -
96G ALA* 2.8 37.0 + - + +
27H PHE* 5.8 6.1 - - + +
30H ALA* 4.8 24.2 - - + +
31H LEU* 5.4 14.1 - - + +
34H VAL* 5.7 9.4 - - + -
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Residues in contact with ILE 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G VAL* 3.0 21.3 - - + +
90G TRP* 3.1 52.5 - - + +
92G LEU* 1.3 77.9 - - + +
94G ALA* 1.3 58.6 + - + +
96G ALA* 3.9 6.9 - - - +
97G HIS* 3.4 24.4 + - - +
110G CYS* 5.5 5.8 - - + +
111G VAL* 4.6 9.0 - - + -
142G CYS* 5.3 6.0 - - - -
144G LEU* 5.3 12.6 - - + -
145G ALA* 3.6 37.0 - - + +
148G ILE* 5.6 5.2 - - + -
----------------------------------------------------------
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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