Contacts of the helix formed by residues 91 - 115 (chain D) in PDB entry 7CR3
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 TRP 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D GLY* 1.3 70.0 - - - -
92D ALA* 1.3 58.1 + - - +
93D PHE* 3.1 2.7 - - - -
94D ILE* 2.9 52.0 + - + +
95D TYR 3.9 1.2 + - - -
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Residues in contact with ALA 92 (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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84D VAL* 3.7 38.1 - - + +
88D PRO* 3.5 28.5 - - + -
89D ARG* 4.8 2.5 - - + +
90D GLY 3.0 3.8 + - - +
91D TRP* 1.3 77.2 - - - +
93D PHE* 1.3 60.3 + - - +
94D ILE 3.1 1.2 + - - -
95D TYR* 3.1 13.8 + - - +
96D HIS* 3.0 21.5 + - + -
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Residues in contact with PHE 93 (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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230B LYS* 4.9 23.8 - - - -
88D PRO* 3.5 35.0 - - + -
89D ARG 4.3 12.8 - - - -
90D GLY* 3.3 18.3 + - - +
91D TRP* 3.1 1.0 - - - -
92D ALA* 1.3 77.4 - - - +
94D ILE* 1.3 60.9 + - + +
96D HIS* 4.0 12.2 - + + +
97D ALA* 2.8 29.4 + - - +
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Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TRP* 2.9 48.1 + - + +
93D PHE* 1.3 78.3 - - + +
95D TYR* 1.3 58.4 + - - +
97D ALA* 3.2 8.2 + - + +
98D TYR* 2.9 55.4 + - + +
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Residues in contact with TYR 95 (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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84D VAL* 4.2 19.5 - - + -
85D LEU* 3.6 29.8 - - + +
91D TRP 3.9 1.2 + - - -
92D ALA* 3.1 8.5 + - - +
94D ILE* 1.3 80.0 - - - +
96D HIS* 1.3 105.1 + + - +
98D TYR* 3.1 18.1 + - + +
99D VAL* 3.1 27.9 + - + +
136D VAL* 5.7 7.2 - - + +
140D GLU* 3.7 23.4 + - - +
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Residues in contact with HIS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D VAL 3.2 20.7 + - - -
85D LEU* 3.8 17.2 + - + -
88D PRO* 4.6 13.2 - - + +
92D ALA* 3.0 32.7 + - + +
93D PHE* 4.0 13.0 - + + +
95D TYR* 1.3 98.7 - + - +
97D ALA* 1.3 57.4 + - - +
99D VAL* 3.1 11.6 - - - +
100D PHE* 2.9 29.5 + - - +
211D MET* 3.5 24.2 - - + +
213D ARG* 5.5 11.1 - - - -
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Residues in contact with ALA 97 (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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93D PHE 2.8 20.2 + - - +
94D ILE* 3.4 14.1 - - + +
95D TYR 3.1 0.4 - - - -
96D HIS* 1.3 77.5 - - - +
98D TYR* 1.3 63.1 + - + +
100D PHE* 3.2 6.6 + - - +
101D LEU* 2.8 41.6 + - + +
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Residues in contact with TYR 98 (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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94D ILE* 2.9 35.5 + - + +
95D TYR* 3.1 11.0 + - + +
97D ALA* 1.3 81.6 - - + +
99D VAL* 1.3 57.8 + - - +
101D LEU* 3.4 15.4 + - + +
102D LEU* 3.0 27.2 + - - +
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Residues in contact with VAL 99 (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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95D TYR* 3.1 24.8 + - + +
96D HIS* 3.1 30.1 - - - +
98D TYR* 1.3 74.3 - - - +
100D PHE* 1.3 63.4 + - - +
102D LEU* 3.6 9.6 - - + +
103D VAL* 3.0 24.4 + - + +
136D VAL* 4.3 17.5 - - + -
137D PHE* 3.6 30.5 - - + -
140D GLU* 5.0 4.9 - - - +
210D ARG* 6.3 0.4 - - - +
211D MET* 4.3 13.9 - - + -
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Residues in contact with PHE 100 (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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96D HIS 2.9 20.1 + - - +
97D ALA* 3.3 8.5 - - - +
99D VAL* 1.3 77.8 - - - +
101D LEU* 1.3 71.7 + - + +
103D VAL* 3.2 9.6 - - + +
104D PHE* 2.9 48.9 + + - +
208D MET* 3.5 31.4 - - + -
211D MET* 3.9 28.9 - - + -
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Residues in contact with LEU 101 (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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97D ALA* 2.8 40.0 + - + +
98D TYR* 3.9 15.3 - - + +
100D PHE* 1.3 82.3 - - + +
102D LEU* 1.3 57.0 + - - +
104D PHE* 3.8 6.2 - - - +
105D SER* 2.9 34.8 + - - +
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Residues in contact with LEU 102 (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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98D TYR 3.0 17.6 + - - +
99D VAL* 3.6 11.0 - - + +
100D PHE 3.2 0.2 - - - -
101D LEU* 1.3 77.9 - - - +
103D VAL* 1.3 62.8 + - - +
105D SER* 3.3 5.2 + - - -
106D CYS* 3.0 21.7 + - - +
129D LEU* 4.0 22.6 - - + +
132D VAL* 4.8 13.0 - - + -
133D THR* 3.7 38.6 - - - +
136D VAL* 4.4 22.2 - - + -
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Residues in contact with VAL 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 VAL* 3.0 18.0 + - + +
100D PHE* 3.2 17.9 - - + +
102D LEU* 1.3 76.6 - - - +
104D PHE* 1.3 60.4 + - - +
106D CYS* 3.3 10.4 + - + +
107D LEU* 3.0 26.5 + - + +
133D THR* 4.8 4.9 - - + +
137D PHE* 4.2 20.2 - - + -
204D GLN* 5.2 2.4 - - + +
207D ARG* 3.8 42.4 - - + +
208D MET* 4.4 18.2 - - - +
211D MET* 6.1 4.9 - - + -
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Residues in contact with PHE 104 (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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240B PHE* 3.8 37.5 - + - -
100D PHE* 2.9 36.0 + + + +
101D LEU* 3.8 7.4 - - - +
103D VAL* 1.3 75.3 - - + +
105D SER* 1.3 61.0 + - - +
107D LEU* 3.1 13.4 + - + +
108D VAL* 2.9 43.5 + - + +
208D MET* 3.8 25.6 - - + -
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Residues in contact with SER 105 (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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101D LEU* 2.9 19.8 + - - +
102D LEU* 3.8 5.6 - - - -
104D PHE* 1.3 73.5 - - - +
106D CYS* 1.3 60.1 + - - +
108D VAL* 3.8 7.7 - - - +
109D LEU* 2.9 38.9 + - - +
129D LEU* 4.8 12.3 - - - -
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Residues in contact with CYS 106 (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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102D LEU 3.0 14.4 + - - +
103D VAL* 3.4 16.8 - - + +
104D PHE 3.2 0.2 - - - -
105D SER* 1.3 76.8 - - - +
107D LEU* 1.3 58.6 + - - +
109D LEU* 3.4 5.0 + - - +
110D SER* 2.9 26.0 + - - -
126D LEU* 4.3 11.8 - - - +
129D LEU* 3.8 20.1 - - + +
130D GLU* 5.3 6.3 - - - -
133D THR* 4.9 14.8 - - + -
204D GLN* 2.9 39.4 + - - -
207D ARG* 5.1 6.3 - - - -
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Residues in contact with LEU 107 (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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240B PHE* 4.7 8.7 - - + -
244B ILE* 4.6 21.5 - - + -
264B TYR* 6.4 0.2 - - + -
268B LEU* 5.7 3.4 - - + -
103D VAL* 3.0 12.5 + - + +
104D PHE* 3.1 16.1 + - + +
106D CYS* 1.3 76.7 - - - +
108D VAL* 1.3 67.4 + - + +
110D SER* 2.4 21.9 + - - +
111D VAL* 3.0 29.5 + - + +
204D GLN* 3.3 23.1 - - + +
205D ILE* 5.1 5.8 - - + +
208D MET* 4.3 33.9 - - + -
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Residues in contact with VAL 108 (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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292A LEU* 5.2 12.1 - - + -
104D PHE* 2.9 41.8 + - + +
105D SER* 3.8 8.3 - - - +
106D CYS 3.4 0.2 - - - -
107D LEU* 1.3 80.4 - - + +
109D LEU* 1.3 61.6 + - + +
111D VAL* 3.1 11.3 + - + +
112D PHE* 2.9 46.9 + - + -
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Residues in contact with LEU 109 (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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105D SER* 2.9 22.6 + - - +
106D CYS* 3.9 4.3 - - - +
108D VAL* 1.3 80.8 - - + +
110D SER* 1.3 56.4 + - - +
112D PHE* 3.1 18.7 + - + +
113D SER* 2.9 25.9 + - - -
122D SER* 4.3 16.2 - - - +
125D ALA* 4.2 29.8 - - + +
126D LEU* 4.5 12.5 - - + +
129D LEU* 4.1 26.2 - - + -
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Residues in contact with SER 110 (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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106D CYS 2.9 9.2 + - - -
107D LEU* 2.4 23.9 + - - +
109D LEU* 1.3 74.8 - - - +
111D VAL* 1.3 59.5 + - - +
113D SER* 2.6 29.8 + - - -
114D THR* 3.7 3.1 + - - -
126D LEU* 4.1 7.5 - - - +
200D LEU* 3.9 14.8 - - - -
201D ARG* 5.3 6.8 - - - +
204D GLN* 2.4 39.3 + - - -
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Residues in contact with VAL 111 (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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264B TYR* 4.2 15.0 - - + -
265B ALA* 4.2 23.1 - - + +
268B LEU* 4.0 28.9 - - + -
107D LEU* 3.0 29.9 + - + +
108D VAL* 3.1 13.0 + - + +
110D SER* 1.3 78.4 - - - +
112D PHE* 1.3 65.1 + - + +
114D THR* 3.1 26.4 - - - +
115D ILE* 4.1 3.3 + - - +
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Residues in contact with PHE 112 (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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288A TRP* 3.9 40.2 - + + -
292A LEU* 5.0 16.2 - - + -
108D VAL* 2.9 35.5 + - + +
109D LEU* 3.1 18.8 + - + +
111D VAL* 1.3 79.7 - - + +
113D SER* 1.3 62.0 + - - +
114D THR 3.3 0.2 - - - -
115D ILE* 3.4 31.6 + - + +
118D TYR* 4.0 39.8 - + + +
122D SER* 3.9 13.5 - - - -
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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
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109D LEU 2.9 10.6 + - - -
110D SER* 2.6 23.6 + - - -
111D VAL 3.1 1.0 - - - -
112D PHE* 1.3 77.0 - - - +
114D THR* 1.3 64.2 + - - +
115D ILE 3.2 9.9 - - - +
119D GLU* 3.5 21.5 - - - +
122D SER* 3.2 21.5 - - - -
123D GLU* 5.3 1.6 - - - -
126D LEU* 4.3 13.4 - - - +
197D LEU* 5.5 7.0 - - - +
200D LEU* 6.0 0.7 - - - +
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Residues in contact with THR 114 (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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251B TYR* 5.2 5.2 + - - -
263B THR* 4.2 16.0 - - - +
264B TYR* 4.1 35.2 + - + +
265B ALA 4.5 2.9 - - - +
110D SER 4.8 2.0 - - - -
111D VAL* 3.1 20.1 + - - +
113D SER* 1.3 81.3 + - - +
115D ILE* 1.3 66.5 + - + +
116D LYS* 3.5 3.1 + - - +
119D GLU* 5.0 2.6 - - - +
201D ARG* 5.5 5.2 + - - -
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Residues in contact with ILE 115 (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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288A TRP* 6.4 0.2 - - + -
263B THR* 4.2 15.9 - - + +
265B ALA* 4.0 29.2 - - + -
111D VAL 4.6 3.1 - - - +
112D PHE* 3.4 24.3 + - + +
113D SER 3.2 13.3 - - - +
114D THR* 1.3 77.6 - - - +
116D LYS* 1.3 68.1 + - - +
117D GLU* 3.8 13.5 - - + +
118D TYR* 3.5 38.8 - - + +
119D GLU* 3.4 12.5 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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