Contacts of the helix formed by residues 80 - 109 (chain M) in PDB entry 7KHI
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 GLU 80 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C ASN* 5.9 1.6 - - - +
747D MET* 5.6 8.6 - - + +
748D ALA* 6.0 1.9 - - - +
778D GLY* 2.6 49.3 - - - +
779D ALA* 4.1 6.7 - - - +
781D LYS* 4.7 9.6 - - - +
782D GLY* 4.1 15.4 + - - -
76M ALA 2.9 16.2 + - - +
77M ALA* 3.5 6.7 + - - +
78M GLN 3.5 0.8 - - - -
79M GLU* 1.3 79.3 - - - +
81M GLU* 1.3 60.5 + - - +
82M PHE 3.5 0.2 - - - -
83M SER* 3.9 14.4 - - - -
84M LEU* 4.0 13.7 + - - +
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Residues in contact with GLU 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735D ALA* 5.0 18.1 - - + +
736D GLN* 6.4 0.2 - - - +
738D ARG* 5.5 2.9 + - - -
739D GLN* 4.6 17.9 - - - +
61M HIS* 4.2 7.5 - - - -
77M ALA 4.0 8.3 + - - +
78M GLN* 4.3 5.8 - - - +
80M GLU* 1.3 76.7 - - - +
82M PHE* 1.3 101.9 + - + +
83M SER 3.2 0.4 - - - -
84M LEU* 3.3 8.1 + - - +
85M GLU* 3.0 41.4 + - - +
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Residues in contact with PHE 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931D THR* 6.1 4.9 - - - +
61M HIS* 4.0 12.8 - + - -
62M MET* 3.4 43.5 - - + -
65M GLU* 3.7 27.1 - - + -
66M ALA* 5.0 1.1 - - + -
78M GLN* 2.8 51.1 - - + +
79M GLU* 4.5 10.3 - - + -
80M GLU 3.5 0.8 - - - +
81M GLU* 1.3 104.3 - - + +
83M SER* 1.3 59.9 + - - +
85M GLU* 4.2 10.5 - - - -
86M LEU* 2.8 47.3 + - + +
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Residues in contact with SER 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781D LYS* 5.9 3.3 - - - +
931D THR* 6.0 2.7 - - - -
79M GLU* 4.0 17.9 + - - +
80M GLU* 3.9 21.6 + - - -
81M GLU 3.2 0.6 - - - -
82M PHE* 1.3 79.4 - - - +
84M LEU* 1.3 57.7 + - - +
86M LEU* 3.4 5.4 + - - +
87M ARG* 2.9 27.9 + - - +
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Residues in contact with LEU 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746D LEU* 2.7 40.6 - - + +
747D MET* 3.6 17.3 - - + -
748D ALA* 4.2 15.0 - - + +
754D ILE* 4.2 13.7 - - + -
80M GLU 4.0 8.4 + - - +
81M GLU* 3.3 10.1 + - - +
82M PHE 3.3 0.6 - - - -
83M SER* 1.3 76.5 + - - +
85M GLU* 1.3 68.3 + - - +
87M ARG* 3.0 7.3 + - - +
88M ASN* 3.0 41.3 + - - +
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Residues in contact with GLU 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738D ARG* 5.9 1.0 + - - -
58M THR* 3.2 40.6 - - + +
61M HIS* 4.1 20.0 + - - -
62M MET* 5.1 0.9 - - - +
81M GLU* 3.0 33.0 + - - +
82M PHE* 3.6 17.5 - - - +
84M LEU* 1.3 79.2 - - - +
86M LEU* 1.3 60.6 + - + +
88M ASN* 3.1 9.4 + - - +
89M ARG* 2.9 38.7 + - - +
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Residues in contact with LEU 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931D THR* 5.5 7.2 - - + +
935D PHE* 3.3 53.0 - - + +
936D HIS 4.6 2.3 - - - +
937D ILE* 4.3 13.7 - - + -
58M THR* 5.6 4.0 - - + -
62M MET* 3.9 25.4 - - - -
82M PHE* 2.8 42.4 + - + +
83M SER* 3.8 5.8 - - - +
85M GLU* 1.3 79.6 - - + +
87M ARG* 1.3 57.9 + - - +
89M ARG* 3.3 8.6 + - + +
90M ASP* 2.9 30.0 + - - +
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Residues in contact with ARG 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752D GLY* 3.6 29.0 + - - +
753D SER* 5.3 3.6 - - - +
754D ILE* 4.2 18.2 - - + +
83M SER 2.9 15.9 + - - +
84M LEU* 3.3 12.3 - - + +
86M LEU* 1.3 76.0 - - - +
88M ASN* 1.3 62.8 + - - +
90M ASP* 3.2 32.9 + - - +
91M ARG* 3.0 38.7 + - + +
94M LYS* 5.9 3.6 - - - +
202M G4P 2.2 38.4 + - - -
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Residues in contact with ASN 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D ILE* 4.5 3.1 - - - +
687D ALA* 4.9 16.7 - - - +
746D LEU* 5.3 6.1 - - - +
754D ILE* 3.2 21.7 - - - +
84M LEU* 3.0 30.6 + - - +
85M GLU* 3.5 10.2 - - - +
87M ARG* 1.3 76.4 - - - +
89M ARG* 1.3 73.1 + - - +
91M ARG* 3.3 24.6 + - - +
92M GLU* 2.9 37.6 + - - +
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Residues in contact with ARG 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936D HIS 4.5 7.6 - - - +
937D ILE* 4.2 12.3 - - + +
54M GLU* 4.0 19.9 + - - +
55M VAL* 4.0 29.4 - - + +
58M THR* 3.1 47.5 + - + +
85M GLU* 2.9 28.7 + - - +
86M LEU* 3.7 15.0 - - + +
87M ARG 3.2 0.2 - - - -
88M ASN* 1.3 86.4 - - - +
90M ASP* 1.3 57.1 + - - +
92M GLU* 2.4 36.9 + - - +
93M ARG* 2.8 30.0 + - - +
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Residues in contact with ASP 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935D PHE* 6.4 0.2 - - + -
936D HIS* 3.9 18.8 + - - +
86M LEU 2.9 17.8 + - - +
87M ARG* 3.2 27.0 + - - +
89M ARG* 1.3 77.2 - - - +
91M ARG* 1.3 62.3 + - - +
93M ARG* 2.3 39.6 + - - +
94M LYS* 2.9 26.7 + - - +
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Residues in contact with ARG 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679D TYR* 5.0 1.8 - - - -
680D ASN* 4.2 17.2 + - - +
683D ILE* 3.1 43.9 - - - +
684D ASP* 2.2 33.5 + - - -
754D ILE* 5.4 5.6 - - + +
87M ARG* 3.0 30.6 + - + +
88M ASN* 3.6 21.3 + - - +
90M ASP* 1.3 78.4 - - - +
92M GLU* 1.3 65.0 + - - +
94M LYS* 3.1 11.6 + - - +
95M LEU* 3.0 19.9 + - - +
202M G4P 2.8 59.7 + - - +
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Residues in contact with GLU 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D ASP* 5.1 5.5 - - - +
51M LEU* 3.1 39.2 - - + +
54M GLU* 5.1 2.7 - - - +
55M VAL* 5.7 5.4 - - + -
88M ASN* 2.9 19.5 + - - +
89M ARG* 2.4 40.3 + - - +
91M ARG* 1.3 78.4 + - + +
93M ARG* 1.3 57.9 + - - +
95M LEU* 3.0 10.9 + - - +
96M ILE* 3.0 32.9 + - + +
202M G4P 3.9 20.9 + - - +
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Residues in contact with ARG 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936D HIS* 3.6 32.1 + - - +
937D ILE 3.1 31.2 - - - +
938D GLY* 3.4 19.5 - - - +
1133D ASP* 4.4 21.0 + - - +
89M ARG 2.8 14.6 + - - +
90M ASP* 2.3 40.0 + - - +
92M GLU* 1.3 75.8 - - - +
94M LYS* 1.3 81.1 + - - +
96M ILE* 3.3 21.4 + - - +
97M LYS* 3.8 14.1 + - - +
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Residues in contact with LYS 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M ARG* 5.9 2.9 - - - +
90M ASP* 2.9 23.0 + - - +
91M ARG* 3.1 11.6 + - - +
93M ARG* 1.3 95.5 - - - +
95M LEU* 1.3 59.8 + - - +
96M ILE 3.5 0.3 + - - -
97M LYS* 3.6 14.7 + - - +
98M LYS* 3.8 7.8 + - - +
202M G4P 3.1 55.1 - - + +
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Residues in contact with LEU 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D ASP* 5.0 0.7 - - - +
47M TRP* 4.0 20.6 - - + +
51M LEU* 4.1 17.7 - - + -
91M ARG 3.0 12.3 + - - +
92M GLU* 3.0 10.3 + - - +
94M LYS* 1.3 75.9 - - - +
96M ILE* 1.3 60.1 + - - +
97M LYS 3.2 0.9 - - - -
98M LYS* 3.2 15.8 + - + -
99M ILE* 3.0 41.9 + - + +
131M THR* 5.1 4.0 - - + -
202M G4P 3.6 61.2 - - + +
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Residues in contact with ILE 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938D GLY 4.9 13.0 - - - +
1131D THR* 5.5 7.6 - - + +
48M ARG* 4.4 27.2 - - + +
51M LEU* 3.5 40.6 - - + -
52M ARG* 4.6 24.7 - - + +
92M GLU 3.0 20.9 + - - +
93M ARG* 3.3 12.5 + - - +
95M LEU* 1.3 77.1 - - - +
97M LYS* 1.3 57.8 + - - +
99M ILE* 3.4 5.9 + - + +
100M GLU* 2.9 28.2 + - + +
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Residues in contact with LYS 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131D THR* 5.6 7.9 - - - -
1133D ASP* 4.7 15.7 + - - -
93M ARG* 3.8 14.0 + - - +
94M LYS* 3.6 11.6 + - - +
95M LEU 3.2 0.4 - - - -
96M ILE* 1.3 76.0 - - - +
98M LYS* 1.3 60.4 + - - +
100M GLU* 3.3 8.6 + - + +
101M LYS* 2.9 28.9 + - + +
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Residues in contact with LYS 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94M LYS 3.8 3.7 + - - +
95M LEU* 3.2 21.4 + - + +
97M LYS* 1.3 77.0 - - - +
99M ILE* 1.3 65.0 + - - +
101M LYS* 3.3 10.3 + - + +
102M THR* 2.9 26.7 + - - +
129M ARG* 3.3 13.3 - - - +
131M THR* 3.0 38.1 - - + +
133M ASP* 5.9 5.2 - - - -
202M G4P 2.3 74.7 + - - +
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Residues in contact with ILE 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M LEU* 3.8 39.7 - - + +
47M TRP* 3.3 43.1 - - + -
48M ARG* 4.3 17.7 - - + +
51M LEU* 5.2 5.4 - - + -
95M LEU* 3.0 32.0 + - + +
96M ILE* 3.8 8.3 - - + +
98M LYS* 1.3 76.2 - - - +
100M GLU* 1.3 63.3 + - - +
102M THR* 3.2 5.3 + - - -
103M LEU* 2.9 27.5 + - + +
131M THR* 4.5 9.0 - - - -
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Residues in contact with GLU 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023D HIS* 3.8 24.3 + - - -
1127D GLU* 4.7 9.7 - - - +
1130D GLY 5.9 2.0 + - - +
1131D THR* 6.1 0.9 - - - +
48M ARG* 5.5 12.7 - - - +
96M ILE* 2.9 20.0 + - + +
97M LYS* 3.6 10.7 - - + +
98M LYS 3.3 0.2 - - - -
99M ILE* 1.3 76.2 - - - +
101M LYS* 1.3 68.7 + - - +
103M LEU* 3.1 13.7 + - + +
104M LYS* 3.0 23.8 + - - +
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Residues in contact with LYS 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127D GLU* 5.9 2.2 - - - +
97M LYS* 2.9 15.9 + - + +
98M LYS* 3.7 9.0 - - + +
99M ILE 3.3 0.2 - - - -
100M GLU* 1.3 85.1 + - - +
102M THR* 1.3 59.5 + - - +
104M LYS* 3.0 7.9 + - + +
105M LYS* 2.9 42.9 + - + +
115M GLU* 5.8 2.9 - - - +
133M ASP* 4.4 21.1 + - - -
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Residues in contact with THR 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M LEU* 3.7 28.5 - - + -
98M LYS* 2.9 14.8 + - - +
99M ILE* 3.2 8.5 + - - -
101M LYS* 1.3 77.0 - - - +
103M LEU* 1.3 57.3 + - - +
105M LYS* 3.2 15.7 + - - +
106M VAL* 3.0 27.2 + - - +
111M PHE* 3.6 29.8 - - + -
130M PRO 3.7 7.9 - - - +
131M THR* 3.1 22.0 + - - -
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Residues in contact with LEU 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M ARG* 4.5 15.0 - - + +
44M LEU* 4.1 26.7 - - + -
45M GLU* 4.4 22.0 - - + +
48M ARG* 3.8 34.8 - - - +
99M ILE* 2.9 19.0 + - + +
100M GLU* 3.1 13.4 + - + +
102M THR* 1.3 76.9 - - - +
104M LYS* 1.3 56.7 + - - +
106M VAL* 3.0 20.2 - - + +
107M GLU* 2.9 29.8 + - - +
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Residues in contact with LYS 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023D HIS* 3.1 46.1 + - + +
1125D PRO* 5.4 6.1 - - - +
1127D GLU* 4.0 29.2 - - + +
100M GLU* 3.0 20.2 + - - +
101M LYS* 3.0 14.1 + - + +
103M LEU* 1.3 75.2 - - - +
105M LYS* 1.3 60.0 + - + +
107M GLU* 4.5 11.1 - - + +
108M ASP* 2.9 47.5 + - + +
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Residues in contact with LYS 105 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101M LYS* 2.9 29.8 + - + +
102M THR* 3.8 19.5 - - - +
104M LYS* 1.3 76.4 - - + +
106M VAL* 1.3 63.8 + - - +
108M ASP* 3.3 4.6 + - - +
109M GLU 3.0 4.7 + - - -
110M ASP* 3.0 50.1 + - + +
111M PHE* 4.1 20.2 - - + +
112M GLY 5.1 1.6 - - - +
113M TYR 4.9 8.9 + - - -
115M GLU* 4.0 20.0 + - - +
131M THR 5.6 1.3 + - - -
132M ALA 4.2 14.8 + - - -
133M ASP* 3.6 24.4 + - - +
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Residues in contact with VAL 106 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M LEU* 3.3 45.8 - - + +
40M PHE* 4.9 4.9 - - + -
41M ARG* 4.8 19.2 + - + +
44M LEU* 4.8 4.9 - - + -
102M THR 3.0 10.5 + - - +
103M LEU* 3.0 40.2 - - + +
105M LYS* 1.3 76.8 - - - +
107M GLU* 1.3 75.2 + - + +
109M GLU* 3.0 22.7 + - - +
111M PHE* 3.9 20.8 - - + +
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Residues in contact with GLU 107 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M ARG* 2.4 36.9 + - - +
103M LEU* 2.9 19.6 + - + +
104M LYS* 3.9 13.9 - - + +
106M VAL* 1.3 77.5 - - - +
108M ASP* 1.3 52.7 + - - +
109M GLU* 2.5 28.4 - - - +
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Residues in contact with ASP 108 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M LYS* 2.9 33.8 + - + +
105M LYS* 3.9 5.6 - - - +
107M GLU* 1.3 73.2 - - - +
109M GLU* 1.3 75.6 + - - +
110M ASP* 3.6 9.7 + - + +
----------------------------------------------------------
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Residues in contact with GLU 109 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M LEU* 4.0 27.7 - - + +
41M ARG* 5.1 1.7 + - - -
105M LYS 3.0 0.4 + - - -
106M VAL 3.0 23.8 + - - +
107M GLU* 2.5 35.1 - - - +
108M ASP* 1.3 83.0 - - - +
110M ASP* 1.3 58.4 + - - +
111M PHE 3.7 2.7 - - - +
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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