Contacts of the helix formed by residues 91 - 119 (chain F) in PDB entry 6V3O
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 ALA 91 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F GLY 4.0 0.8 + - - -
90F LEU* 1.3 73.5 - - - +
92F PRO* 1.4 65.8 - - + -
93F ALA* 3.2 3.6 - - + +
94F ASP* 2.6 47.4 + - - +
95F ALA* 3.0 9.0 + - - -
922F GLN* 4.5 18.6 + - - +
924F PRO* 5.0 10.5 - - + -
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Residues in contact with PRO 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LEU 3.9 3.3 - - - +
91F ALA* 1.4 83.6 - - + -
93F ALA* 1.3 63.3 + - - +
95F ALA* 3.2 8.6 + - + +
96F ILE* 3.1 29.2 + - - +
911F ARG* 6.1 6.1 - - - +
938F LEU* 3.9 22.0 - - + -
949F PRO 3.9 20.4 - - - +
950F GLY* 4.4 7.4 - - - -
954F THR* 4.9 0.4 + - - +
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Residues in contact with ALA 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ALA* 3.0 3.2 + - + +
92F PRO* 1.3 79.5 - - - +
94F ASP* 1.3 67.0 + - - +
96F ILE* 3.6 6.0 + - - +
97F LEU* 3.3 22.9 + - - +
926F SER* 5.9 2.2 - - - +
934F LYS* 5.9 9.4 - - + -
938F LEU* 3.9 16.6 - - + +
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Residues in contact with ASP 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F LEU* 5.3 0.9 - - - -
90F LEU* 4.0 12.7 - - + +
91F ALA* 2.6 28.5 + - - +
93F ALA* 1.3 75.2 - - - +
95F ALA* 1.3 57.4 - - - +
97F LEU* 3.3 4.8 + - - +
98F VAL* 2.9 36.4 + - - +
922F GLN* 5.0 0.9 - - - +
923F PRO 4.6 0.5 - - - +
924F PRO* 3.4 15.4 - - - +
925F LEU* 3.2 42.1 + - + +
926F SER* 3.5 29.1 + - - -
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F LEU 5.1 0.9 - - - +
90F LEU* 4.3 15.3 - - + +
91F ALA 3.0 9.8 + - - +
92F PRO* 3.2 12.3 + - + +
94F ASP* 1.3 75.7 - - - +
96F ILE* 1.3 56.9 + - - +
98F VAL* 3.3 0.7 + - - -
99F ALA* 2.9 32.4 + - - +
904F PHE* 3.6 30.0 - - + -
954F THR* 3.9 14.4 - - + +
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Residues in contact with ILE 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F PRO 3.1 17.6 + - - +
93F ALA* 3.9 5.8 - - - +
95F ALA* 1.3 74.9 - - - +
97F LEU* 1.3 58.7 + - - +
99F ALA* 4.6 0.2 - - - -
100F SER* 2.9 35.1 + - - +
231F ARG* 3.6 44.4 - - - +
937F GLY 4.4 0.2 - - - +
938F LEU* 3.6 36.3 - - + +
950F GLY* 4.3 7.6 - - - +
953F ASP* 3.9 9.9 - - + -
954F THR* 3.9 14.1 - - - +
957F LEU* 3.8 17.9 - - + +
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Residues in contact with LEU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F LEU* 4.9 0.2 - - + -
53F HIS* 3.7 41.3 - - + +
57F LEU* 3.5 37.9 - - + -
93F ALA 3.3 14.9 + - - +
94F ASP* 3.3 5.1 + - - +
95F ALA 3.3 0.2 - - - -
96F ILE* 1.3 76.4 - - - +
98F VAL* 1.3 61.3 + - - +
100F SER* 3.7 5.8 - - - -
101F SER* 2.8 39.5 + - - +
225F PHE* 4.5 13.0 - - + -
926F SER* 4.0 9.2 - - - +
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Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F LEU* 4.2 13.5 - - + -
60F PHE* 4.0 35.9 - - + -
61F VAL* 4.1 23.8 - - + -
64F CYS* 4.7 6.5 - - + -
87F LEU* 4.5 3.6 - - + -
90F LEU* 4.3 5.8 - - + -
94F ASP* 2.9 24.3 + - + +
95F ALA* 3.9 3.1 - - - +
97F LEU* 1.3 75.7 - - - +
99F ALA* 1.3 62.8 + - - +
101F SER* 3.4 1.4 + - - -
102F ILE* 3.1 32.4 + - + +
900F THR* 5.8 0.9 - - + -
904F PHE* 4.2 16.6 - - + -
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ALA 2.9 18.4 + - - +
96F ILE* 3.8 3.6 - - - +
98F VAL* 1.3 77.5 - - - +
100F SER* 1.3 62.3 + - - +
102F ILE* 3.4 3.4 + - - +
103F LEU* 3.0 23.7 + - - +
901F LEU* 4.3 18.3 - - + +
904F PHE* 4.2 15.6 - - + -
954F THR* 4.9 9.4 - - + +
957F LEU* 4.0 25.2 - - + +
958F THR* 5.1 0.9 - - + -
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Residues in contact with SER 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ILE* 2.9 28.8 + - - +
97F LEU* 3.7 8.5 - - - -
99F ALA* 1.3 76.1 - - - +
101F SER* 1.3 57.2 + - - +
103F LEU* 3.1 9.0 + - - +
104F HIS* 2.9 38.4 + - - -
225F PHE* 5.1 5.6 - - - -
228F ASP* 4.9 4.8 + - - -
230F ILE* 4.2 16.2 - - - +
231F ARG* 4.4 7.4 - - - +
957F LEU* 3.5 19.1 - - - +
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Residues in contact with SER 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PHE* 3.7 26.6 - - - -
49F LEU* 3.7 28.4 - - - +
57F LEU* 5.5 0.2 - - - +
61F VAL* 4.4 6.5 - - - +
97F LEU* 2.8 23.4 + - - +
98F VAL* 3.9 3.5 - - - -
99F ALA 3.3 0.2 - - - -
100F SER* 1.3 76.2 - - - +
102F ILE* 1.3 63.6 + - - +
104F HIS* 3.1 3.5 + - - +
105F MET* 2.9 34.8 + - - +
225F PHE* 4.0 5.6 - - - -
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Residues in contact with ILE 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F VAL* 4.4 15.7 - - + +
64F CYS* 4.7 3.8 - - + -
65F TYR* 4.8 7.9 - - + +
98F VAL* 3.1 25.9 + - + +
99F ALA* 3.8 3.8 - - - +
101F SER* 1.3 75.4 - - - +
103F LEU* 1.3 61.7 + - - +
105F MET* 3.3 23.6 + - + +
106F LEU* 3.0 21.0 + - - +
897F TYR* 3.4 39.1 - - + +
900F THR* 3.9 27.6 - - + +
901F LEU* 4.0 17.5 - - + -
904F PHE* 6.4 0.4 - - + -
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Residues in contact with LEU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F ALA 3.0 13.8 + - - +
100F SER 3.1 9.2 + - - +
102F ILE* 1.3 77.9 - - - +
104F HIS* 1.3 61.3 + - - +
106F LEU* 3.2 8.6 + - + +
107F ASN* 3.0 44.1 + - - +
230F ILE* 3.6 34.8 - - + -
901F LEU* 4.9 7.1 - - + +
957F LEU* 3.9 27.8 - - + +
960F LYS* 4.6 8.5 - - + -
961F GLY* 3.5 29.8 - - - +
964F ALA* 4.7 7.2 - - + -
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Residues in contact with HIS 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PHE* 3.9 17.3 - + + -
100F SER* 2.9 30.5 + - - -
101F SER 3.1 6.3 + - - +
103F LEU* 1.3 75.3 - - - +
105F MET* 1.3 57.8 + - - +
107F ASN* 3.0 16.8 + - - +
108F LEU* 2.8 34.7 + - + +
224F ALA* 3.5 28.1 - - + +
225F PHE* 3.5 37.3 + + - -
228F ASP* 4.3 7.0 + - - -
229F GLU 5.9 0.7 - - - -
230F ILE* 3.3 30.5 - - + +
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Residues in contact with MET 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F VAL* 3.9 28.8 - - + +
45F PHE* 3.6 18.8 - - + -
46F LEU* 4.2 15.7 - - - -
61F VAL* 3.4 30.5 - - + +
62F GLN* 6.5 0.2 - - - -
65F TYR* 5.5 6.7 - - + -
101F SER* 2.9 26.9 + - - +
102F ILE* 3.4 30.3 - - + +
103F LEU 3.3 0.2 - - - -
104F HIS* 1.3 76.4 - - - +
106F LEU* 1.3 57.8 - - - +
108F LEU* 3.4 10.5 + - - +
109F ALA* 3.0 26.7 + - - +
897F TYR* 3.7 24.5 + - + -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ILE 3.0 13.5 + - - +
103F LEU* 3.5 10.1 - - + +
105F MET* 1.3 74.1 - - - +
107F ASN* 1.3 65.8 + - - +
109F ALA* 3.2 2.8 + - + +
110F ASN* 3.1 41.1 + - - +
894F ARG* 3.9 34.3 - - + +
897F TYR* 3.9 27.0 - - + -
898F ILE* 4.2 10.8 - - + +
901F LEU* 5.1 3.6 - - + -
961F GLY* 3.4 32.1 - - - +
964F ALA* 4.6 3.1 - - + -
965F GLY* 3.9 15.5 - - - +
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Residues in contact with ASN 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F LEU* 3.0 37.6 + - - +
104F HIS* 3.3 23.7 + - - +
106F LEU* 1.3 78.2 - - - +
108F LEU* 1.3 61.8 + - + +
110F ASN* 3.2 11.9 + - - +
111F LEU* 3.0 30.5 + - + +
190F ASN* 6.1 0.7 - - - +
230F ILE* 4.8 8.5 - - - +
964F ALA* 4.7 10.9 - - - +
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ASP* 6.2 0.2 - - - -
41F LEU* 3.3 44.9 - - + +
42F VAL* 4.6 5.6 - - + +
45F PHE* 3.8 34.5 - - + -
104F HIS* 2.8 18.5 + - + +
105F MET* 3.7 12.1 - - - +
106F LEU 3.2 0.2 - - - -
107F ASN* 1.3 78.0 - - + +
109F ALA* 1.3 55.9 + - - +
111F LEU* 3.2 18.5 + - + +
112F ALA* 2.9 24.1 + - - +
193F ILE* 4.4 16.6 - - + -
221F ILE* 4.4 19.7 - - + -
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Residues in contact with ALA 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU* 4.9 0.7 - - - +
38F ASP* 3.6 27.6 - - - +
42F VAL* 5.5 2.2 - - + +
105F MET 3.0 14.9 + - - +
106F LEU* 3.2 11.2 + - + +
108F LEU* 1.3 77.1 - - - +
110F ASN* 1.3 60.5 + - - +
112F ALA* 3.4 3.3 + - - +
113F GLU* 3.0 26.6 + - - +
893F LEU* 4.7 5.2 - - + +
894F ARG* 5.6 2.7 - - + -
897F TYR* 3.9 22.2 - - + +
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Residues in contact with ASN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F LEU* 3.1 27.5 + - - +
107F ASN* 3.6 13.9 + - - +
108F LEU 3.2 0.2 - - - -
109F ALA* 1.3 77.1 - - - +
111F LEU* 1.3 62.0 + - + +
113F GLU* 3.4 10.1 + - - +
114F GLU* 3.0 38.0 + - - +
678F GLU* 6.2 2.2 - - + -
679F PHE* 6.0 1.2 - - + -
894F ARG* 3.7 30.9 + - - +
964F ALA* 4.0 20.2 + - - +
965F GLY* 5.1 0.4 - - - -
967F GLN* 4.8 10.7 - - - +
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Residues in contact with LEU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F LEU* 4.8 4.7 - - + -
107F ASN* 3.0 23.2 + - + +
108F LEU* 3.2 15.9 + - + +
110F ASN* 1.3 75.3 - - + +
112F ALA* 1.3 65.3 + - - +
114F GLU* 3.2 13.0 + - - +
115F VAL* 3.1 27.5 + - - +
190F ASN* 3.7 34.8 - - + +
193F ILE* 4.1 34.1 - - + -
194F ARG* 3.5 36.1 - - + +
197F LEU* 5.5 0.7 - - - -
678F GLU* 4.6 2.7 - - - +
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Residues in contact with ALA 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU* 3.7 4.3 - - + +
37F TYR* 3.8 23.6 - - + -
38F ASP* 3.2 28.7 - - - +
41F LEU* 4.0 10.0 - - + +
108F LEU 2.9 12.4 + - - +
109F ALA 3.6 1.8 - - - +
111F LEU* 1.3 76.8 - - - +
113F GLU* 1.3 61.0 + - - +
115F VAL* 3.3 3.9 + - - +
116F GLN* 3.0 23.7 + - - +
197F LEU* 4.4 11.2 - - - -
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Residues in contact with GLU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU* 3.6 24.2 - - + +
109F ALA 3.0 16.8 + - - +
110F ASN* 3.7 11.9 - - - +
111F LEU 3.3 0.2 - - - -
112F ALA* 1.3 75.2 - - - +
114F GLU* 1.3 61.9 + - - +
116F GLN* 3.3 2.5 + - + +
117F ILE* 3.0 43.6 + - + +
679F PHE* 3.8 18.7 - - + -
886F PHE 5.6 0.2 - - - +
887F LEU* 6.0 2.1 - - - +
890F GLY* 3.8 23.4 - - - +
891F LEU* 5.8 0.2 - - - +
894F ARG* 3.1 38.2 + - - +
1004F FLC 5.0 0.7 - - - +
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Residues in contact with GLU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ASN* 3.0 23.2 + - - +
111F LEU* 3.5 15.7 - - - +
113F GLU* 1.3 77.1 - - - +
115F VAL* 1.3 62.0 + - - +
117F ILE* 3.4 3.4 + - - +
118F ALA* 3.0 25.0 + - - +
194F ARG* 2.9 34.1 + - - -
678F GLU* 2.8 42.8 - - - +
679F PHE* 4.4 15.8 - - + -
682F GLY* 5.3 0.4 - - - -
683F GLU* 4.7 8.5 - - + -
686F LEU* 4.0 25.9 - - + +
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F TYR* 3.9 23.6 - - + +
111F LEU 3.1 14.7 + - - +
112F ALA 3.7 7.0 - - - +
114F GLU* 1.3 75.7 - - - +
116F GLN* 1.3 64.0 + - - +
118F ALA* 3.2 4.9 + - - -
119F HIS* 3.1 29.7 + - + +
194F ARG* 3.6 41.5 - - + +
197F LEU* 4.4 13.0 - - + -
198F THR* 3.6 24.9 - - + +
683F GLU* 5.7 1.6 - - + -
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Residues in contact with GLN 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ASP* 3.5 19.3 + - - +
32F ASP* 4.3 5.5 - - - +
33F LYS* 2.9 33.2 + - - +
34F LEU* 3.4 27.1 + - + -
37F TYR* 4.5 11.2 - - + -
112F ALA 3.0 17.1 + - - +
113F GLU* 3.7 4.5 - - + +
115F VAL* 1.3 78.5 - - - +
117F ILE* 1.3 62.7 + - + +
119F HIS* 3.5 3.0 + - - -
120F ARG* 3.2 56.4 + - - +
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Residues in contact with ILE 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F GLU* 3.0 34.7 + - + +
114F GLU* 3.8 6.1 - - - +
116F GLN* 1.3 76.7 - - + +
118F ALA* 1.3 63.5 + - - +
119F HIS 3.4 0.3 + - - -
120F ARG* 3.6 34.1 + - - +
137F ALA* 5.6 10.8 - - + -
679F PHE* 3.6 33.0 - - + -
686F LEU* 3.5 24.6 - - + +
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Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLU 3.0 17.5 + - - +
115F VAL* 3.2 5.6 + - - +
117F ILE* 1.3 79.2 - - - +
119F HIS* 1.3 69.1 + - + +
120F ARG 3.8 2.3 + - - +
683F GLU* 3.5 34.8 - - - +
685F HIS* 3.9 19.4 - - + +
686F LEU* 3.8 10.7 - - + +
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Residues in contact with HIS 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ASP* 4.1 3.8 - - - +
115F VAL* 3.1 40.3 + - + +
116F GLN* 3.8 5.6 + - - +
118F ALA* 1.3 86.5 + - + +
120F ARG* 1.3 61.7 + - - +
121F ARG 3.6 2.1 + - - -
198F THR* 3.9 21.7 - - + +
683F GLU* 4.4 6.9 + - - -
685F HIS* 4.0 26.6 + + - -
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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