Contacts of the helix formed by residues 100 - 125 (chain C) in PDB entry 1CD9
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 LEU 100 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.8 18.6 - - + -
35C LYS* 3.8 25.1 - - + -
36C LEU* 3.1 39.7 - - + +
39C THR* 4.2 7.0 - - + -
40C TYR* 3.9 23.6 - - + +
95C GLY 3.8 8.5 - - - +
96C ILE* 4.2 11.9 - - + -
97C SER* 2.9 9.5 + - - +
99C GLU* 1.3 91.1 - - + +
101C GLY* 1.3 64.8 + - - +
102C PRO* 3.2 4.3 - - - -
103C THR* 3.0 8.2 + - - +
104C LEU* 2.9 21.5 + - + +
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Residues in contact with GLY 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C GLY* 3.4 20.9 + - - -
97C SER 2.8 16.1 + - - -
98C PRO* 3.8 2.7 + - - -
100C LEU* 1.3 71.6 - - - +
102C PRO* 1.3 63.3 - - - +
104C LEU* 3.8 1.1 - - - +
105C ASP* 2.8 33.3 + - - +
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Residues in contact with PRO 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PRO 3.7 15.0 - - - +
99C GLU 4.0 6.1 - - - +
100C LEU 3.4 4.5 - - - -
101C GLY* 1.3 86.3 - - - +
103C THR* 1.3 65.6 + - - +
105C ASP* 3.1 8.1 + - + +
106C THR* 3.1 25.7 + - - -
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Residues in contact with THR 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ASP* 4.6 2.6 - - - +
31C ALA* 3.9 15.9 - - + +
32C LEU* 3.7 39.7 - - + +
35C LYS* 4.2 24.7 - - + +
99C GLU 4.9 1.9 + - - -
100C LEU 3.0 8.5 + - - -
102C PRO* 1.3 80.0 - - - +
104C LEU* 1.3 61.4 + - - +
106C THR* 3.5 7.7 + - - -
107C LEU* 3.4 18.7 + - - +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.8 32.7 - - + +
90C LEU* 3.9 40.4 - - + +
93C LEU* 4.1 8.7 - - + -
95C GLY* 3.6 37.5 - - - +
96C ILE* 3.8 13.5 - - + -
100C LEU 2.9 15.9 + - - +
101C GLY 3.9 2.9 - - - +
103C THR* 1.3 75.1 - - - +
105C ASP* 1.3 61.5 + - - +
107C LEU* 3.0 7.6 + - + +
108C GLN* 2.8 29.5 + - + +
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C GLY 2.8 19.0 + - - +
102C PRO* 3.5 7.0 - - + +
104C LEU* 1.3 75.9 - - - +
106C THR* 1.3 63.7 + - - +
108C GLN* 3.6 10.6 - - - +
109C LEU* 2.9 47.1 + - - +
73D LYS* 5.0 6.6 - - - +
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Residues in contact with THR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ASP* 3.7 17.0 - - + +
102C PRO 3.1 13.0 + - - -
103C THR* 3.7 11.2 - - - -
104C LEU 3.1 0.2 - - - -
105C ASP* 1.3 77.2 - - - +
107C LEU* 1.3 63.2 + - - +
109C LEU* 3.3 7.4 + - - +
110C ASP* 3.1 38.7 + - - +
20D ASN* 4.8 15.0 + - - +
72D ARG* 5.2 5.3 - - - +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 3.6 32.5 - - + +
28C ASP* 3.7 26.9 - - + +
29C GLY* 4.1 14.4 - - - +
32C LEU* 3.8 27.6 - - + -
90C LEU* 3.9 23.8 - - + -
103C THR 3.4 9.4 + - - +
104C LEU* 3.0 10.4 + - + +
106C THR* 1.3 80.2 - - - +
108C GLN* 1.3 62.2 + - - +
110C ASP* 3.5 0.7 + - - +
111C VAL* 3.1 22.7 + - + +
155C ALA* 5.4 2.9 - - + -
158C LEU* 4.0 12.3 - - + -
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLN* 3.1 46.5 + - - +
90C LEU* 4.2 30.7 - - + +
91C GLN* 3.6 24.3 + - + +
104C LEU* 2.8 17.8 + - + +
105C ASP* 3.6 14.3 - - - +
106C THR 3.2 0.2 - - - -
107C LEU* 1.3 74.1 - - - +
109C LEU* 1.3 71.7 + - - +
111C VAL* 3.2 2.3 + - - +
112C ALA* 2.8 30.9 + - - +
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Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASP* 2.9 41.9 + - - +
106C THR* 3.8 2.2 - - - +
108C GLN* 1.3 85.0 - - - +
110C ASP* 1.3 63.9 + - - +
112C ALA* 3.1 5.2 + - + +
113C ASP* 2.9 32.7 + - - +
72D ARG* 3.5 35.4 - - + +
73D LYS* 4.1 33.0 - - + +
75D LEU 5.8 1.3 - - - +
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLN* 4.6 2.4 + - - +
24C LYS* 3.4 30.4 + - + +
25C ILE* 3.5 17.9 - - + +
28C ASP* 2.5 29.8 - - - +
106C THR* 3.1 25.3 + - - +
107C LEU 3.9 3.1 - - - +
109C LEU* 1.3 76.7 - - - +
111C VAL* 1.3 61.2 + - - +
113C ASP* 4.1 4.4 - - - +
114C PHE* 3.2 22.7 + - - +
20D ASN* 5.7 0.3 - - - +
72D ARG* 2.8 22.1 + - - +
77D LEU* 3.9 4.9 - - - +
78D TYR* 5.7 0.9 - - - -
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 4.0 19.1 - - + -
83C LEU* 3.4 37.5 - - + +
86C TYR* 4.6 3.8 - - + -
87C GLN* 4.1 14.8 - - + +
90C LEU* 4.0 13.7 - - + -
107C LEU* 3.1 34.9 + - + +
108C GLN 3.6 4.5 - - - +
109C LEU 3.1 0.2 - - - -
110C ASP* 1.3 74.8 - - - +
112C ALA* 1.3 68.1 + - - +
114C PHE* 3.3 2.3 + - - +
115C ALA* 3.0 21.1 + - - +
158C LEU* 4.0 9.6 - - + -
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Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLN* 3.6 31.1 + - + +
108C GLN* 2.8 21.5 + - - +
109C LEU* 3.1 12.1 + - + +
111C VAL* 1.3 78.4 - - - +
113C ASP* 1.3 62.5 + - - +
115C ALA* 3.2 5.5 + - - +
116C THR* 2.9 32.6 + - - +
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Residues in contact with ASP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLN* 3.9 5.8 - - - +
109C LEU* 2.9 20.3 + - - +
110C ASP* 4.1 5.8 - - - +
112C ALA* 1.3 78.3 - - - +
114C PHE* 1.3 62.2 + - - +
116C THR* 3.4 3.1 + - - -
117C THR* 2.8 34.8 + - - -
72D ARG* 3.1 17.7 + - - -
75D LEU 5.1 0.2 - - - +
76D LEU* 3.2 29.1 - - + +
77D LEU* 2.9 37.3 + - + +
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Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C CYS* 3.7 38.4 - - + -
21C GLN* 3.2 33.8 - - + +
22C VAL* 3.7 24.7 - - + -
25C ILE* 3.7 20.9 - - + -
79C LEU* 4.7 5.6 - - + -
83C LEU* 3.3 25.1 - - + -
110C ASP 3.2 15.9 + - - +
111C VAL 3.7 4.3 - - - +
112C ALA 3.3 0.2 - - - -
113C ASP* 1.3 79.1 - - - +
115C ALA* 1.3 61.8 + - - +
117C THR* 3.6 0.8 + - + -
118C ILE* 3.2 45.1 + - + +
162C LEU* 4.9 1.6 - - + -
169C LEU* 4.7 5.2 - - + -
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Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C HIS* 3.2 29.2 - - + +
83C LEU* 4.0 24.8 - - + +
84C PHE* 4.5 4.3 - - - +
87C GLN* 4.0 16.2 - - - +
111C VAL 3.0 13.4 + - - +
112C ALA 3.4 8.3 - - - +
113C ASP 3.1 0.2 - - - -
114C PHE* 1.3 78.4 - - - +
116C THR* 1.3 61.9 + - - +
118C ILE* 3.3 3.4 + - - +
119C TRP* 3.0 17.7 + - - +
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Residues in contact with THR 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C HIS* 5.7 0.2 - - - -
87C GLN* 5.6 0.3 + - - -
112C ALA* 2.9 16.7 + - - +
113C ASP* 3.4 11.9 + - - -
115C ALA* 1.3 73.6 - - - +
117C THR* 1.3 66.8 + - - +
119C TRP* 3.0 8.1 + - + +
120C GLN* 2.9 52.7 + - + +
76D LEU* 4.6 19.5 - - + +
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 4.3 17.7 - - + -
17C LYS* 5.8 5.4 - - + -
18C CYS* 5.1 1.1 - - - -
21C GLN* 3.1 23.1 + - - +
113C ASP 2.8 22.0 + - - -
114C PHE* 3.7 7.4 - - + +
116C THR* 1.3 73.5 - - - +
118C ILE* 1.3 64.0 + - + +
120C GLN* 3.5 9.3 + - - +
121C GLN* 3.1 23.4 + - - +
76D LEU* 5.2 1.7 - - - +
77D LEU 4.2 3.3 + - - -
78D TYR* 3.6 31.9 + - + +
79D GLN* 5.4 2.5 - - - +
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 4.4 8.1 - - + -
18C CYS* 4.6 10.3 - - - -
76C LEU* 4.2 22.7 - - + +
79C LEU* 4.0 25.6 - - + -
80C HIS* 4.1 20.0 - - + +
83C LEU* 4.0 14.8 - - + -
114C PHE* 3.2 44.0 + - + +
115C ALA 3.6 6.1 - - - +
116C THR 3.2 0.2 - - - -
117C THR* 1.3 73.2 - - - +
119C TRP* 1.3 66.6 - - - +
121C GLN* 3.3 2.3 + - - +
122C MET* 3.0 32.3 + - + +
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Residues in contact with TRP 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C HIS* 3.9 25.8 - + + +
115C ALA 3.0 13.0 + - - +
116C THR* 3.0 11.4 + - + +
118C ILE* 1.3 76.6 - - - +
120C GLN* 1.3 63.9 + - + +
122C MET* 3.0 26.6 + - + +
123C GLU* 2.9 61.4 + - + +
128C ALA* 4.3 5.8 - - + -
129C PRO* 3.6 41.3 - - + -
132C GLN* 3.2 35.5 + - + -
133C PRO* 4.2 23.1 - - + -
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Residues in contact with GLN 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C THR* 2.9 36.5 + - + +
117C THR* 3.9 7.5 - - - +
119C TRP* 1.3 82.2 - - + +
121C GLN* 1.3 61.9 + - - +
123C GLU* 3.4 14.0 + - - +
124C GLU* 3.1 24.2 + - - +
46D ARG* 4.0 28.5 + - - +
76D LEU* 5.4 3.0 - - - +
79D GLN* 3.0 35.2 - - - +
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Residues in contact with GLN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 4.8 0.9 - - + -
11C PRO* 3.5 26.2 - - - +
14C PHE* 3.4 56.8 - - + +
76C LEU* 5.3 0.9 - - + -
117C THR 3.1 11.8 + - - +
118C ILE 3.6 2.7 - - - +
119C TRP 3.2 0.2 - - - -
120C GLN* 1.3 73.4 - - - +
122C MET* 1.3 67.9 + - + +
124C GLU* 3.1 30.5 + - - +
125C LEU* 3.1 40.4 + - + +
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Residues in contact with MET 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ALA 4.2 6.7 - - - +
76C LEU* 3.5 41.1 - - + -
77C SER* 3.7 14.1 - - - -
80C HIS* 4.4 13.7 - - + -
118C ILE* 3.0 14.6 + - + +
119C TRP* 3.0 41.6 + - + +
121C GLN* 1.3 78.1 - - - +
123C GLU* 1.3 60.6 + - - +
125C LEU* 3.3 3.0 + - - +
126C GLY 2.9 3.3 + - - -
127C MET* 2.8 38.4 + - + +
128C ALA* 3.8 13.5 - - - +
129C PRO* 3.5 21.5 - - + -
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Residues in contact with GLU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASN* 4.8 3.3 + - - -
119C TRP* 2.9 52.0 + - - +
120C GLN* 3.7 12.0 - - - +
121C GLN 3.2 0.4 - - - -
122C MET* 1.3 75.5 - - - +
124C GLU* 1.3 58.6 + - - +
126C GLY* 2.8 20.9 + - - -
128C ALA* 4.1 15.6 - - + +
132C GLN* 5.0 3.8 + - - +
46D ARG* 4.6 13.2 + - - +
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Residues in contact with GLU 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASN* 5.2 3.3 + - - +
161B TRP 5.0 4.2 - - - +
163B LEU* 5.5 4.0 - - - +
165B PHE* 6.1 0.5 - - - -
11C PRO* 5.7 1.2 - - - +
120C GLN 3.1 13.3 + - - +
121C GLN* 3.1 34.3 + - - +
123C GLU* 1.3 76.4 - - - +
125C LEU* 1.3 67.4 + - + +
126C GLY 3.7 0.2 + - - -
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASN* 4.7 2.6 + - - -
161B TRP 4.5 10.4 - - - +
162B THR* 5.2 6.6 + - - +
163B LEU* 5.2 12.8 + - + +
165B PHE* 4.1 27.1 - - + -
9C SER 3.4 11.7 - - - +
10C LEU* 3.3 25.1 - - + -
11C PRO* 4.6 0.9 - - + -
121C GLN* 3.1 32.4 + - + +
122C MET* 4.0 0.4 - - - +
124C GLU* 1.3 87.0 - - + +
126C GLY* 1.3 63.7 - - - +
127C MET* 3.2 37.9 + - + +
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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