Contacts of the helix formed by residues 97 - 123 (chain C) in PDB entry 5XVO
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 THR 97 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ALA 3.9 9.9 - - - +
96C TRP* 1.3 72.9 - - - +
98C GLU* 1.3 65.6 + - - +
99C GLU* 3.7 6.2 + - - +
100C ARG* 3.0 27.9 + - - +
101C LYS* 3.0 22.5 + - - +
278C GLN* 3.5 18.6 + - - +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TRP 3.9 1.2 + - - -
97C THR* 1.3 73.7 - - - +
99C GLU* 1.3 63.5 + - - +
101C LYS* 3.6 16.8 + - - +
102C GLY* 3.1 18.4 + - - -
142C PHE* 3.4 33.0 - - + -
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Residues in contact with GLU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C THR* 3.1 6.4 - - - +
98C GLU* 1.3 80.2 - - - +
100C ARG* 1.3 58.1 + - - +
102C GLY* 3.1 3.1 + - - -
103C GLN* 2.9 52.3 + - + +
141C LEU* 4.0 14.7 - - + +
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TRP* 6.0 0.2 - - + -
97C THR* 3.0 26.1 + - - +
99C GLU* 1.3 77.2 - - - +
101C LYS* 1.3 62.5 + - + +
103C GLN* 3.3 26.1 + - - +
104C VAL* 3.0 24.1 + - - +
275C VAL* 3.0 36.9 + - - +
276C LEU* 3.7 27.1 - - + +
278C GLN* 3.3 34.1 - - - +
280C GLU 3.4 12.5 + - - -
281C GLU* 2.6 35.8 + - - -
282C GLY 5.1 0.4 - - - +
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Residues in contact with LYS 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TRP* 4.0 33.9 + - + +
97C THR 3.0 14.9 + - - +
98C GLU* 3.8 27.6 - - - +
100C ARG* 1.3 76.9 - - - +
102C GLY* 1.3 52.3 + - - +
104C VAL* 3.1 10.2 - - - +
105C TRP* 2.8 38.7 + - - +
142C PHE* 4.0 2.7 - - + -
201C GLY 4.8 6.9 + - - +
202C LEU* 4.0 46.5 + - + +
276C LEU* 4.0 2.7 - - + -
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Residues in contact with GLY 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLU 3.1 8.4 + - - -
99C GLU 3.1 7.2 + - - -
101C LYS* 1.3 73.5 - - - +
103C GLN* 1.3 63.4 + - - +
105C TRP* 4.0 0.6 - - - +
106C THR* 2.6 32.7 + - - -
141C LEU* 4.0 12.3 - - - -
142C PHE* 3.0 29.5 - - - -
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Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLU* 2.9 44.0 + - - +
100C ARG* 3.6 36.5 + - - +
102C GLY* 1.3 75.3 - - - +
104C VAL* 1.3 58.9 + - - +
106C THR* 3.9 2.1 - - - -
107C ALA* 2.9 31.3 + - - +
141C LEU* 3.9 17.0 - - + +
281C GLU* 5.1 2.8 - - - +
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG* 3.0 11.2 + - - +
101C LYS 3.1 12.8 - - - +
103C GLN* 1.3 78.3 - - - +
105C TRP* 1.3 66.9 + - - +
107C ALA* 3.3 1.9 + - - +
108C ILE* 3.0 31.7 + - + +
202C LEU* 3.5 12.3 - - + -
272C VAL* 4.0 24.7 - - + +
275C VAL* 4.5 12.3 - - + -
276C LEU* 3.2 34.3 - - + -
283C VAL* 3.3 31.4 - - + -
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Residues in contact with TRP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LYS 2.8 24.4 + - - +
102C GLY* 4.0 3.1 - - - +
104C VAL* 1.3 73.7 - - - +
106C THR* 1.3 74.9 + - + +
108C ILE* 3.1 9.4 + - + +
109C ILE* 2.9 59.6 + - + +
142C PHE* 3.6 31.4 - + + -
143C ASP* 3.7 20.4 - - + -
148C GLU* 3.9 13.2 - - - -
202C LEU* 4.0 20.2 - - + -
203C LYS* 3.6 38.8 - - + +
216C ASP* 3.6 38.1 + - + +
219C GLU* 5.7 1.8 + - + +
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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
----------------------------------------------------------
102C GLY 2.6 22.1 + - - -
103C GLN* 3.9 2.7 - - - -
105C TRP* 1.3 84.7 - - + +
107C ALA* 1.3 65.7 + - - +
109C ILE* 3.4 1.9 + - - +
110C ALA* 3.0 23.9 + - - +
139C LEU* 3.9 29.1 - - + +
140C ARG* 3.9 17.3 - - - +
141C LEU* 3.6 7.3 - - + -
142C PHE 3.1 22.1 + - - +
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLN 2.9 19.2 + - - +
104C VAL 3.5 6.5 - - - +
106C THR* 1.3 76.2 - - - +
108C ILE* 1.3 62.9 + - - +
110C ALA* 3.3 8.2 - - - +
111C GLN* 3.2 27.0 + - - +
283C VAL* 4.2 24.2 - - + -
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL* 3.0 24.7 + - + +
105C TRP* 3.4 13.2 - - + +
106C THR 3.1 0.2 - - - -
107C ALA* 1.3 75.5 - - - +
109C ILE* 1.3 67.6 + - + +
111C GLN* 2.9 21.7 + - - +
112C LYS* 3.1 9.0 + - - +
202C LEU* 4.8 4.9 - - + -
216C ASP* 3.6 21.1 - - + +
217C LEU* 4.2 26.7 - - + +
219C GLU* 4.1 5.6 - - + -
220C PRO* 3.7 23.0 - - + +
268C TYR* 3.9 15.0 - - + +
272C VAL* 4.3 16.6 - - + -
283C VAL* 4.5 10.8 - - + -
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Residues in contact with ILE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C TRP* 2.9 53.1 + - + +
106C THR* 3.9 3.4 - - - +
108C ILE* 1.3 78.1 - - + +
110C ALA* 1.3 63.4 + - - +
112C LYS* 3.0 11.6 + - + +
113C ILE* 2.9 40.2 + - + +
139C LEU* 4.1 12.8 - - + -
148C GLU* 3.1 47.3 - - + +
219C GLU* 4.1 23.6 - - + +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C THR 3.0 13.2 + - - +
107C ALA* 3.3 13.5 - - - +
109C ILE* 1.3 77.7 - - - +
111C GLN* 1.3 57.6 + - + +
113C ILE* 3.2 5.0 + - - +
114C THR* 2.8 33.1 + - - -
136C ARG* 3.7 23.7 - - + +
139C LEU* 4.1 17.0 - - + -
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ALA* 3.3 13.4 + - - +
108C ILE* 2.9 9.0 + - - +
110C ALA* 1.3 77.9 - - + +
112C LYS* 1.3 64.0 + - - +
114C THR* 3.4 7.8 + - - -
115C ASN* 3.0 31.0 + - - +
220C PRO* 4.0 10.2 - - + +
268C TYR* 3.3 18.2 + - - -
283C VAL* 3.3 17.6 - - - +
284C PRO 2.8 23.2 + - - -
285C GLU* 3.6 22.9 - - + +
286C PHE 3.1 28.5 + - - +
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Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ILE 3.1 6.1 + - - +
109C ILE* 3.0 16.2 + - + +
111C GLN* 1.3 77.1 - - - +
113C ILE* 1.3 53.8 + - - +
115C ASN* 3.0 5.5 + - - +
116C GLN* 2.8 69.8 + - + +
148C GLU* 3.4 33.5 + - - +
152C ALA* 4.8 8.9 - - - +
219C GLU* 3.4 53.8 + - + +
220C PRO* 3.9 10.2 - - - +
222C ARG* 4.4 11.1 - - + +
223C PRO* 4.3 4.6 - - + +
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Residues in contact with ILE 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ILE* 2.9 33.3 + - + +
110C ALA 3.7 6.5 - - - +
112C LYS* 1.3 77.4 - - + +
114C THR* 1.3 64.7 + - - +
116C GLN* 3.1 14.3 + - - +
117C SER* 2.9 22.2 + - - -
132C LEU* 3.6 36.5 - - + +
133C LEU* 5.3 0.4 - - - -
135C MET 5.2 0.2 - - - -
136C ARG* 4.0 17.3 - - + +
139C LEU* 4.3 16.2 - - + -
147C ARG* 4.5 2.7 - - + +
148C GLU* 4.1 21.1 - - - +
151C ALA* 4.3 20.2 - - + -
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ALA 2.8 21.7 + - - -
111C GLN* 3.5 11.4 - - - -
113C ILE* 1.3 77.7 - - - +
115C ASN* 1.3 60.2 + - - +
117C SER* 2.4 26.6 + - - +
118C LEU* 2.8 29.1 + - + +
133C LEU* 4.4 12.6 - - + -
136C ARG* 3.3 26.5 + - - +
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Residues in contact with ASN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLN 3.0 17.5 + - - +
112C LYS 3.0 5.8 + - - +
114C THR* 1.3 77.0 - - - +
116C GLN* 1.3 67.3 + - - +
118C LEU* 3.9 9.4 - - - +
119C HIS* 3.0 20.8 + - - +
220C PRO* 3.0 24.0 + - - +
223C PRO* 3.7 11.6 - - + +
286C PHE* 3.1 26.1 + - - +
287C GLY* 3.2 23.8 - - - -
288C ILE* 3.4 30.9 + - + +
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C LYS* 2.8 49.0 + - + +
113C ILE* 3.4 15.7 - - - +
115C ASN* 1.3 77.8 - - - +
117C SER* 1.3 61.8 + - - +
119C HIS 3.3 1.6 + - - -
120C LEU* 3.0 19.8 + - - +
132C LEU* 3.7 5.4 - - + -
148C GLU 4.7 0.6 + - - -
151C ALA* 4.2 11.5 + - - +
152C ALA* 4.0 25.2 - - - +
155C TYR* 3.3 56.4 - - + -
156C PHE* 4.9 3.5 - - - -
222C ARG* 6.1 1.4 - - - +
223C PRO* 4.0 8.8 - - + +
226C ASP* 4.6 2.6 - - - +
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Residues in contact with SER 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ILE 2.9 11.7 + - - -
114C THR* 2.4 27.0 + - - +
116C GLN* 1.3 76.7 - - - +
118C LEU* 1.3 57.4 + - - +
120C LEU* 2.8 26.7 + - - +
121C ALA* 2.8 12.9 + - - +
129C ALA* 3.4 31.7 - - - +
132C LEU* 3.8 15.4 - - - +
133C LEU* 3.4 21.4 - - - +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C THR* 2.8 30.5 + - + +
115C ASN* 3.8 25.8 - - - +
117C SER* 1.3 74.9 + - - +
119C HIS* 1.3 58.0 + - - +
121C ALA* 3.4 11.7 - - + +
122C GLN* 2.9 28.8 + - - +
287C GLY* 5.1 1.8 - - - -
288C ILE* 4.1 30.7 - - + +
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Residues in contact with HIS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASN 3.0 14.5 + - - +
116C GLN 3.4 8.7 - - - +
117C SER 3.1 0.2 - - - -
118C LEU* 1.3 75.4 - - - +
120C LEU* 1.3 65.0 + - - +
122C GLN* 3.2 22.0 - - - +
123C ARG* 3.2 41.5 + - - +
155C TYR* 2.8 28.6 + - - +
159C LEU* 3.7 21.9 - - + +
223C PRO* 4.7 5.8 + - + -
226C ASP* 3.8 7.4 - - - +
227C GLN* 3.5 39.8 - - + +
230C TYR* 4.3 4.4 - - + +
288C ILE* 4.8 4.9 - - + +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLN 3.0 12.1 + - - +
117C SER 2.8 11.0 + - - +
119C HIS* 1.3 69.3 - - - +
121C ALA* 1.3 66.8 + - - +
123C ARG* 2.9 14.2 + - - +
125C TYR* 3.1 27.7 + - + +
128C LYS* 4.1 18.6 - - + +
129C ALA* 4.1 8.5 - - + +
132C LEU* 3.7 39.5 - - + -
155C TYR* 3.8 16.2 - - + +
158C THR* 3.8 29.6 - - + +
159C LEU* 3.8 27.1 - - + -
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C SER 2.8 11.2 + - - +
118C LEU* 3.4 18.2 - - + +
120C LEU* 1.3 76.9 - - - +
122C GLN* 1.3 57.2 + - - +
124C ASP* 2.8 26.2 + - - +
125C TYR 4.5 5.8 - - - +
126C GLY* 4.7 5.5 + - - +
129C ALA* 3.9 14.9 - - + +
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Residues in contact with GLN 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU 2.9 14.8 + - - +
119C HIS* 3.2 14.5 - - + +
121C ALA* 1.3 76.1 - - - +
123C ARG* 1.3 96.6 + - - +
124C ASP* 3.4 8.0 + - - +
227C GLN* 3.0 28.8 + - - +
231C GLU* 4.5 2.4 - - - +
288C ILE* 4.5 7.7 + - - +
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Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C HIS* 3.2 34.8 + - - +
120C LEU 2.9 7.9 + - - +
122C GLN* 1.3 102.2 + - - +
124C ASP* 1.3 70.3 + - - +
125C TYR* 3.3 27.7 + - + -
159C LEU* 4.2 11.9 - - + -
227C GLN* 3.5 11.9 + - - +
230C TYR* 3.2 36.4 - - + +
231C GLU* 3.1 39.8 + - - +
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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