Contacts of the helix formed by residues 86 - 116 (chain D) in PDB entry 5NJ8
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 86 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 4.6 10.7 + - - +
91B ARG* 3.1 26.3 - - - +
84D ALA 3.3 7.5 + - - -
85D ASP* 1.3 68.1 - - - +
87D GLU* 1.3 65.0 + - - +
88D ARG* 3.0 26.6 + - + +
89D LEU* 3.2 21.5 + - + +
90D ALA* 3.9 3.5 + - - +
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ALA* 3.4 34.3 + - - +
85D ASP 2.8 6.8 + - - +
86D LYS* 1.3 77.0 + - - +
88D ARG* 1.3 58.3 + - + +
90D ALA* 3.3 7.9 + - - +
91D ARG* 2.5 47.9 + - + +
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LYS* 4.2 21.6 - - - +
87D GLU* 1.3 85.8 - - + +
89D LEU* 1.3 69.0 + - - +
91D ARG* 3.9 15.9 - - - +
92D GLU* 2.5 41.7 + - + +
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LYS* 3.2 15.3 + - + +
88D ARG* 1.3 89.0 - - + +
90D ALA* 1.3 61.5 + - - +
92D GLU* 3.9 3.3 - - - +
93D ASN* 3.0 35.5 + - - +
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Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LYS 3.9 1.7 + - - +
87D GLU* 3.3 12.5 + - - +
89D LEU* 1.3 78.7 - - - +
91D ARG* 1.3 57.2 + - - +
93D ASN* 3.6 2.4 - - - -
94D HIS* 2.7 34.5 + - - +
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Residues in contact with ARG 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D GLU* 2.5 31.5 + - + +
88D ARG* 3.6 13.6 - - - +
90D ALA* 1.3 68.5 - - - +
92D GLU* 1.3 59.2 + - - +
93D ASN 2.7 15.6 + - - -
94D HIS* 3.0 15.2 + - - +
95D SER* 3.8 13.3 + - - +
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ARG* 2.5 25.0 + - + +
89D LEU* 3.9 2.9 - - - +
91D ARG* 1.3 77.1 - - - +
93D ASN* 1.3 88.8 + - - +
95D SER* 5.3 2.0 - - - -
96D GLU* 5.2 4.7 + - - +
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Residues in contact with ASN 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D LEU* 3.0 27.0 + - - +
90D ALA* 3.6 2.9 - - - +
91D ARG 2.7 5.3 + - - -
92D GLU* 1.3 100.0 + - - +
94D HIS* 1.3 62.0 + - - +
95D SER 3.5 2.0 - - - -
96D GLU* 3.4 18.2 + - - +
97D ILE* 3.1 26.5 + - + +
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Residues in contact with HIS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ALA* 2.7 22.8 + - + +
91D ARG* 3.0 6.2 + - - +
93D ASN* 1.3 69.6 - - - +
95D SER* 1.3 67.7 + - - +
96D GLU 2.9 3.4 + - - -
97D ILE* 3.3 13.3 + - + +
98D GLU* 3.2 39.2 + - + +
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Residues in contact with SER 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ARG* 3.8 8.7 + - - +
92D GLU 6.0 1.3 - - - -
93D ASN 3.5 0.2 - - - -
94D HIS* 1.3 79.1 - - - +
96D GLU* 1.3 56.5 + - - +
98D GLU* 4.7 2.4 - - - +
99D ARG* 3.3 30.6 + - - +
102D ARG* 4.9 3.6 + - - -
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Residues in contact with GLU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLU 5.2 3.5 + - - +
93D ASN* 3.4 23.5 + - - +
94D HIS 3.0 0.8 - - - -
95D SER* 1.3 76.6 - - - +
97D ILE* 1.3 56.4 + - - +
98D GLU 3.2 0.9 - - - -
99D ARG* 2.9 35.7 + - - +
100D ARG* 2.6 38.3 + - + +
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ASN* 3.1 18.2 + - + +
94D HIS* 3.4 20.6 - - + +
96D GLU* 1.3 78.5 - - - +
98D GLU* 1.3 64.6 + - - +
100D ARG* 3.0 14.0 + - + -
101D ARG* 2.9 41.6 + - + +
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Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D HIS* 3.2 32.0 + - + +
95D SER* 4.7 2.5 - - - +
97D ILE* 1.3 83.6 - - - +
99D ARG* 1.3 63.0 + - - +
101D ARG* 2.9 49.0 + - - +
102D ARG* 3.4 34.7 + - - +
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Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D SER* 3.3 18.2 + - - +
96D GLU* 2.9 44.5 + - - +
98D GLU* 1.3 78.8 - - - +
100D ARG* 1.3 62.0 + - - +
102D ARG* 3.2 40.9 + - - +
103D ASN* 3.3 32.6 + - - +
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLU* 2.6 20.3 + - + +
97D ILE* 3.0 22.0 + - + +
99D ARG* 1.3 72.5 - - - +
101D ARG* 1.3 61.1 + - - +
103D ASN* 3.6 15.0 + - - +
104D LYS* 3.4 23.0 + - - +
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Residues in contact with ARG 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASP* 6.0 1.8 - - - +
66C LYS* 5.1 5.1 - - - +
67C LEU* 3.5 37.1 - - + +
97D ILE* 2.9 31.2 + - + +
98D GLU* 2.9 45.2 + - - +
99D ARG 3.1 0.4 - - - -
100D ARG* 1.3 75.6 - - - +
102D ARG* 1.3 66.0 + - - +
104D LYS* 3.2 8.0 + - - +
105D MET* 3.0 37.3 + - + +
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Residues in contact with ARG 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D SER 4.9 3.2 + - - -
98D GLU* 3.4 29.7 + - - +
99D ARG* 3.2 47.8 + - - +
101D ARG* 1.3 76.8 - - - +
103D ASN* 1.3 67.0 + - - +
104D LYS 3.2 0.3 + - - -
105D MET* 3.2 7.9 + - - +
106D THR* 3.0 28.0 + - - +
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Residues in contact with ASN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ARG* 3.3 30.1 + - - +
100D ARG* 3.8 16.2 - - - +
101D ARG 3.3 0.6 - - - -
102D ARG* 1.3 78.0 - - - +
104D LYS* 1.3 57.7 + - + +
106D THR* 3.6 5.0 + - - -
107D ALA* 3.0 27.4 + - - +
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Residues in contact with LYS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 4.5 20.5 - - + +
100D ARG 3.4 10.9 + - - +
101D ARG* 3.2 9.8 + - - +
102D ARG 3.2 0.4 - - - -
103D ASN* 1.3 77.4 - - + +
105D MET* 1.3 67.5 + - - +
107D ALA* 2.7 20.1 + - + +
108D TYR* 2.8 52.8 + - + +
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Residues in contact with MET 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 5.9 6.5 - - - -
47C LEU* 4.9 8.3 - - + -
66C LYS* 3.8 30.3 - - + -
67C LEU* 3.9 25.2 - - + +
70C LEU* 3.5 25.3 - - + +
101D ARG* 3.0 22.1 + - - +
102D ARG* 3.7 10.3 - - - +
104D LYS* 1.3 76.1 - - - +
106D THR* 1.3 58.9 + - - +
108D TYR* 3.6 3.9 + - - +
109D ILE* 3.0 32.1 + - + +
128D LYS* 5.7 3.6 - - - -
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Residues in contact with THR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ARG* 3.0 17.4 + - - +
103D ASN* 4.0 5.6 - - - -
105D MET* 1.3 74.4 - - - +
107D ALA* 1.3 59.5 + - - +
109D ILE* 3.2 6.5 - - - +
110D THR* 2.7 45.8 + - - +
128D LYS* 3.5 31.0 + - - +
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN 3.0 15.0 + - - +
104D LYS* 2.7 19.7 + - + +
106D THR* 1.3 69.3 - - - +
108D TYR* 1.3 57.7 + - + +
110D THR* 3.3 5.5 + - - -
111D GLU* 2.7 36.1 + - - +
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Residues in contact with TYR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.3 42.7 - - + +
70C LEU* 3.7 24.7 - - + +
71C ARG* 3.4 34.7 - - + +
74C VAL* 4.6 3.7 - - + +
155C HIS* 4.1 20.7 - + - -
156C GLN* 5.8 1.6 - - - +
104D LYS* 2.8 54.5 + - + +
105D MET 3.9 2.0 - - - +
107D ALA* 1.3 74.8 - - + +
109D ILE* 1.3 59.1 + - - +
111D GLU* 2.8 35.0 + - - +
112D LEU* 3.0 16.5 + - - +
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 5.7 0.4 - - + -
70C LEU* 4.8 7.8 - - + +
105D MET* 3.0 20.5 + - + +
106D THR* 3.2 18.4 - - - +
108D TYR* 1.3 76.7 - - - +
110D THR* 1.3 69.1 + - - +
112D LEU* 3.5 10.9 - - + +
113D SER 3.1 17.5 + - - -
128D LYS* 3.5 46.0 - - + +
131D ILE* 3.4 32.8 - - + +
132D LEU* 3.6 37.9 - - + -
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Residues in contact with THR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D THR* 2.7 33.1 + - - +
107D ALA* 3.6 5.2 - - - -
109D ILE* 1.3 78.3 - - - +
111D GLU* 1.3 64.9 + - - +
113D SER* 2.8 25.5 + - - +
114D ASP* 3.2 9.5 + - - +
131D ILE* 5.0 4.9 - - + +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL* 3.8 17.2 - - + +
78C ARG* 2.9 44.9 + - - +
155C HIS* 4.3 12.9 + - - -
107D ALA 2.7 17.2 + - - +
108D TYR* 2.8 36.9 + - - +
110D THR* 1.3 73.2 - - - +
112D LEU* 1.3 54.9 + - - +
114D ASP* 3.1 26.8 + - - +
115D MET* 3.2 6.8 + - - +
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 4.8 4.7 - - + -
70C LEU* 4.4 15.5 - - + +
73C SER* 4.4 17.3 - - - +
74C VAL* 3.8 21.8 - - + +
77C LEU* 4.2 14.1 - - + -
108D TYR 3.0 14.0 + - - +
109D ILE* 3.5 15.0 - - + +
111D GLU* 1.3 74.1 - - - +
113D SER* 1.3 57.4 + - - +
115D MET* 2.8 8.2 + - - -
116D VAL* 2.6 39.0 + - + +
131D ILE* 3.4 26.9 - - + -
132D LEU* 5.2 1.3 - - + +
135D ALA* 3.6 28.7 - - + -
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ILE 3.1 15.4 + - - -
110D THR* 2.8 27.9 + - - +
112D LEU* 1.3 77.3 - - - +
114D ASP* 1.3 58.6 + - - +
115D MET 3.5 0.2 + - - -
116D VAL* 4.2 1.0 + - - -
119D CYS* 2.9 38.8 - - - +
120D SER 3.8 0.2 + - - -
126D PRO* 4.5 10.7 - - - +
131D ILE* 3.6 34.5 - - - +
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Residues in contact with ASP 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C GLN* 6.4 0.2 - - - -
250C LYS* 3.5 40.4 + - - +
110D THR* 3.2 6.5 + - + +
111D GLU* 3.1 16.4 + - + +
113D SER* 1.3 81.7 + - - +
115D MET* 1.3 60.6 + - - +
120D SER* 3.9 22.1 - - - +
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Residues in contact with MET 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL* 4.8 3.4 - - + +
77C LEU* 3.7 29.6 - - + +
78C ARG* 3.8 25.1 - - + +
81C SER* 3.1 33.7 - - - +
248C GLY 4.6 0.2 - - - -
249C GLN* 3.3 38.4 - - + -
250C LYS 5.1 0.2 - - - +
111D GLU 3.2 4.8 + - - +
112D LEU* 2.8 23.7 + - + +
114D ASP* 1.3 78.9 - - - +
116D VAL* 1.3 67.4 + - - +
117D PRO* 3.3 7.1 - - - +
120D SER* 4.5 2.3 - - - -
138D HIS* 5.6 0.2 - - - -
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 4.3 14.4 - - + -
112D LEU* 2.6 28.0 + - + +
113D SER* 4.2 0.9 + - - -
114D ASP 3.8 0.2 - - - -
115D MET* 1.3 69.4 - - - +
117D PRO* 1.3 64.6 - - + +
118D THR* 3.0 27.1 - - + +
119D CYS* 4.3 9.4 - - + +
120D SER* 2.6 36.4 + - - -
131D ILE* 5.4 0.9 - - + +
134D MET* 4.1 6.7 - - + +
135D ALA* 3.8 28.7 - - + +
138D HIS* 3.7 21.8 - - + +
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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