Contacts of the helix formed by residues 94 - 115 (chain C) in PDB entry 1RX0
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 CYS 94 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C MET* 4.0 12.2 - - + +
42C MET* 4.0 25.1 - - + -
45C TRP* 4.2 17.0 - - + -
90C LEU 3.4 3.6 + - - -
91C ALA 3.6 2.2 - - - -
93C GLY* 1.3 79.1 - - - +
95C THR* 1.3 65.6 + - - +
96C SER* 3.8 11.0 - - - -
97C THR* 3.1 36.3 - - - +
98C THR* 2.8 28.6 + - - -
218C SER* 4.4 2.9 - - - -
364C GLN* 4.2 4.3 - - - -
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Residues in contact with THR 95 (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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42C MET* 5.0 3.0 - - - -
91C ALA* 3.0 22.4 + - - +
94C CYS* 1.3 70.0 - - - +
96C SER* 1.3 60.3 + - - +
98C THR* 3.4 1.4 + - - -
99C ALA* 2.9 29.3 + - - +
261C CYS* 3.8 16.5 - - + +
265C ALA* 3.4 23.4 - - + +
365C TYR* 3.7 8.7 - - - -
368C ASP* 4.0 22.4 + - + -
369C SER 4.8 1.1 - - - +
372C HIS* 3.5 32.8 - - + +
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Residues in contact with SER 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C CYS* 3.4 6.9 - - - -
95C THR* 1.3 80.1 - - - +
97C THR* 1.3 62.1 + - - +
99C ALA* 3.3 1.2 + - - +
100C TYR 3.2 7.3 + - - -
216C TRP* 3.1 44.7 - - - +
217C ASN 4.5 1.3 - - - -
218C SER* 2.7 24.1 + - - -
219C GLN* 2.7 26.3 - - - +
364C GLN* 4.5 2.9 - - - -
368C ASP* 3.3 19.3 + - - -
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MET* 4.2 12.1 - - + -
45C TRP* 3.5 11.7 - - + -
52C PRO* 3.7 22.1 - - + +
55C VAL* 6.1 0.9 - - + -
56C MET* 4.1 20.2 - - + -
94C CYS* 3.1 25.7 - - - -
96C SER* 1.3 74.8 - - - +
98C THR* 1.3 66.4 + - - +
100C TYR* 3.2 7.1 + - - +
101C ILE* 3.0 25.0 + - + +
218C SER* 2.9 23.4 + - - +
219C GLN* 5.2 0.2 - - - -
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Residues in contact with THR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MET* 3.4 4.9 - - - +
87C PHE* 3.4 38.5 - - + +
90C LEU* 3.1 34.7 + - + +
91C ALA* 3.9 4.9 - - - -
94C CYS 2.8 22.9 + - - -
95C THR 3.8 3.1 - - - -
97C THR* 1.3 74.4 - - - +
99C ALA* 1.3 66.4 + - - +
101C ILE* 3.1 11.5 + - - +
102C SER* 3.0 20.6 + - - -
261C CYS* 3.8 12.6 - - - -
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C THR 2.9 18.5 + - - +
96C SER 3.5 4.9 - - - +
97C THR 3.2 0.2 - - - -
98C THR* 1.3 76.0 - - - +
100C TYR* 1.3 63.7 + - - +
102C SER* 3.1 6.4 + - - -
103C ILE* 3.1 26.4 + - - +
216C TRP* 3.3 37.2 - - + +
219C GLN* 4.2 0.2 - - - -
258C ILE* 4.4 6.0 - - + +
261C CYS* 3.8 17.4 - - - -
372C HIS* 4.5 3.4 - - - +
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Residues in contact with TYR 100 (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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51C PHE* 3.5 28.7 - + + -
56C MET* 3.7 20.0 - - - -
96C SER 3.2 6.4 + - - +
97C THR* 3.5 8.5 - - - +
98C THR 3.2 0.4 - - - -
99C ALA* 1.3 75.1 - - - +
101C ILE* 1.3 69.5 + - - +
103C ILE* 2.9 10.4 + - + +
104C HIS* 2.9 32.3 + - + +
130C MET* 4.4 1.6 - - + -
133C PHE* 3.3 35.4 - + - +
134C ALA 2.8 30.8 + - - -
171C SER* 4.0 22.9 - - - -
172C GLY* 4.2 6.7 - - - -
176C SER* 3.5 2.3 + - - -
219C GLN* 3.5 34.7 + - + -
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Residues in contact with ILE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MET* 5.0 7.6 - - + -
56C MET* 4.3 23.6 - - + -
59C ALA* 4.7 15.7 - - + -
64C PHE* 3.5 16.6 - - + +
87C PHE* 3.9 13.0 - - + -
90C LEU* 4.6 14.6 - - + -
97C THR* 3.0 28.6 + - + +
98C THR* 3.1 15.4 + - - +
100C TYR* 1.3 79.1 - - - +
102C SER* 1.3 54.9 + - - +
104C HIS* 3.4 5.3 + - - +
105C ASN* 2.7 52.3 + - - +
130C MET* 4.5 11.9 - - + -
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 4.5 1.7 + - - -
87C PHE* 3.7 26.7 - - - -
98C THR 3.0 11.7 + - - -
99C ALA* 3.3 13.2 - - - -
100C TYR 3.0 0.2 - - - -
101C ILE* 1.3 74.7 - - - +
103C ILE* 1.3 60.5 - - - +
105C ASN* 3.3 3.5 + - - +
106C MET* 2.9 27.9 + - - +
254C GLY* 4.5 7.0 + - - -
257C ASN* 3.0 29.8 + - - +
258C ILE* 4.6 6.3 + - - +
261C CYS* 4.9 3.8 - - - -
376C GLU* 5.3 0.9 + - - -
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA 3.1 14.3 + - - +
100C TYR* 2.9 17.6 + - + +
102C SER* 1.3 75.9 - - - +
104C HIS* 1.3 65.3 + - - +
106C MET* 3.1 10.4 + - + +
107C CYS* 3.1 22.5 + - - -
134C ALA 4.9 4.9 - - - +
135C SER* 5.0 0.7 - - - -
136C TYR* 4.0 24.0 - - + +
171C SER* 3.9 25.8 - - - +
216C TRP* 3.9 11.2 - - + -
258C ILE* 5.0 1.3 - - + -
376C GLU* 3.9 10.1 - - - +
399C FAD 4.8 2.5 - - - +
400C 2MC 3.6 45.5 - - + -
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Residues in contact with HIS 104 (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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65C GLY 3.3 18.5 + - - -
100C TYR* 2.9 27.3 + - + +
101C ILE 3.5 7.6 - - - +
103C ILE* 1.3 78.8 - - - +
105C ASN* 1.3 63.5 + - - +
107C CYS* 3.3 7.0 + - - +
108C ALA* 3.1 19.2 + - + +
127C LEU* 2.7 43.6 + - + +
130C MET* 3.6 25.5 - - + +
132C LYS 3.4 25.4 - - - -
133C PHE* 3.7 3.7 - - - -
134C ALA* 3.1 30.4 + - - +
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Residues in contact with ASN 105 (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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64C PHE 3.1 22.4 + - - -
65C GLY* 3.5 10.1 + - - -
66C GLY* 3.2 7.3 - - - -
67C VAL* 2.8 33.4 + - - +
68C TYR* 3.9 18.2 + - + -
69C ILE* 4.0 3.6 - - - +
87C PHE* 3.9 9.8 - - + -
101C ILE* 2.7 32.1 + - - +
102C SER* 3.4 11.2 - - - +
103C ILE 3.2 0.2 - - - -
104C HIS* 1.3 78.3 - - - +
106C MET* 1.3 59.4 + - - +
108C ALA* 3.2 5.7 + - - +
109C TRP* 2.9 28.6 + - - +
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Residues in contact with MET 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 3.4 14.8 + - - +
102C SER 2.9 13.1 + - - +
103C ILE* 3.1 9.6 + - + +
105C ASN* 1.3 76.2 - - - +
107C CYS* 1.3 64.1 + - - +
109C TRP* 3.2 5.6 + - + +
110C MET* 3.0 29.2 + - - +
136C TYR* 3.4 39.9 - - + -
250C GLY* 3.2 41.5 - - - +
251C LEU* 4.0 14.8 - - + -
254C GLY* 4.1 14.1 - - - -
376C GLU* 4.4 4.5 - - - +
400C 2MC 4.0 19.7 - - + -
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Residues in contact with CYS 107 (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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103C ILE 3.1 18.5 + - - -
104C HIS 3.5 7.9 - - - +
106C MET* 1.3 76.1 - - - +
108C ALA* 1.3 62.5 + - - +
110C MET* 3.3 16.8 + - - +
111C ILE* 3.3 20.2 + - - +
127C LEU* 4.9 0.2 - - - -
134C ALA* 3.6 16.6 - - + -
135C SER* 3.4 40.4 - - - -
136C TYR* 3.5 17.0 - - - -
180C VAL* 3.7 18.2 - - + +
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Residues in contact with ALA 108 (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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65C GLY 5.0 5.4 - - - +
69C ILE* 3.5 19.3 - - + -
104C HIS 3.1 9.8 + - - +
105C ASN* 3.5 9.6 - - - +
107C CYS* 1.3 79.6 - - - +
109C TRP* 1.3 58.3 + - - +
111C ILE* 3.4 2.5 + - - +
112C ASP* 2.9 28.9 + - - +
124C CYS* 3.7 9.3 - - - -
127C LEU* 4.0 33.3 - - + +
128C CYS* 5.4 2.7 - - - -
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Residues in contact with TRP 109 (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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68C TYR* 3.4 49.9 + + + +
69C ILE* 3.2 11.8 - - + +
80C ARG* 3.4 27.6 - - - +
105C ASN 2.9 12.3 + - - +
106C MET* 3.2 6.7 + - + +
108C ALA* 1.3 75.5 - - - +
110C MET* 1.3 72.8 + - + +
112C ASP* 4.2 4.0 - - - -
113C SER* 2.8 58.6 + - - -
114C PHE* 3.9 17.3 - + - -
249C ARG* 3.3 47.3 - - - -
250C GLY* 3.7 30.1 - - - -
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Residues in contact with MET 110 (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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106C MET* 3.0 23.0 + - - +
107C CYS* 3.3 8.0 + - - +
109C TRP* 1.3 91.3 - - + +
111C ILE* 1.3 59.3 + - + +
114C PHE* 3.0 38.2 + - - +
136C TYR* 3.5 40.2 - - + -
180C VAL* 3.9 24.9 - - + -
182C MET* 4.2 6.3 - - + -
195C CYS* 4.3 4.7 - - - -
237C ILE* 3.8 3.4 - - - +
246C ILE* 3.4 45.3 - - + +
247C ALA* 4.0 7.0 - - - +
250C GLY* 4.5 3.6 - - - -
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Residues in contact with ILE 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 CYS 3.3 13.8 + - - +
108C ALA 3.7 5.8 - - - +
109C TRP 3.2 0.6 - - - -
110C MET* 1.3 77.8 - - + +
112C ASP* 1.3 57.6 + - - +
115C GLY* 2.8 27.2 + - - -
119C GLN* 3.9 22.4 - - + +
120C ARG* 3.7 2.9 - - - +
123C PHE* 3.8 24.2 - - + -
124C CYS* 3.9 14.4 - - - -
127C LEU* 4.3 14.1 - - + -
178C ILE* 4.4 9.2 - - + -
180C VAL* 4.5 8.3 - - + -
197C VAL* 3.9 26.2 - - + -
237C ILE* 4.2 22.9 - - + -
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Residues in contact with ASP 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR 4.6 1.7 - - - +
69C ILE* 3.4 21.1 - - + +
70C GLN* 3.0 32.5 + - - +
73C VAL* 4.4 0.9 - - - -
108C ALA 2.9 18.1 + - - +
109C TRP* 3.7 5.9 - - - +
111C ILE* 1.3 77.6 - - - +
113C SER* 1.3 64.4 + - - +
115C GLY 4.6 0.7 + - - +
120C ARG* 2.6 54.8 + - - +
124C CYS* 3.7 15.7 - - - -
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Residues in contact with SER 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TRP* 2.8 62.1 + - - -
112C ASP* 1.3 78.1 + - - +
114C PHE* 1.3 74.4 + - - +
115C GLY 5.0 1.0 - - - +
249C ARG* 5.0 2.7 - - - -
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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
----------------------------------------------------------
109C TRP* 3.9 24.5 - + - -
110C MET* 3.0 21.0 + - - +
113C SER* 1.3 84.1 - - - +
115C GLY* 1.3 65.7 + - - +
237C ILE* 3.6 13.5 - - + -
238C GLY* 3.8 16.8 + - - +
242C GLN* 4.4 15.9 - - - -
245C LEU 5.6 0.4 - - - -
246C ILE* 3.7 47.1 - - + -
249C ARG* 3.7 37.2 - - + -
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Residues in contact with GLY 115 (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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111C ILE 2.8 23.3 + - - -
112C ASP 4.7 0.5 - - - +
113C SER 3.8 1.4 - - - +
114C PHE* 1.3 77.2 - - - +
116C ASN* 1.3 66.3 + - - -
117C GLU* 5.2 0.9 - - - +
119C GLN* 3.2 15.9 - - - -
120C ARG* 3.8 14.4 - - - -
237C ILE* 3.8 11.0 - - - +
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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) + - + + + + + -
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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