Contacts of the helix formed by residues 91 - 112 (chain C) in PDB entry 1UDY
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 91 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.9 11.0 - - + +
39C ALA* 3.9 17.7 - - + -
42C TYR* 6.4 0.7 - - - -
87C LEU 3.3 4.9 + - - +
88C ALA 3.4 5.1 + - - -
90C GLY* 1.3 80.5 - - - +
92C THR* 1.3 59.7 + - - +
93C GLY* 3.0 30.1 + - - -
94C VAL* 3.4 14.9 + - + +
95C GLN* 3.2 19.4 + - - +
217C GLN* 5.9 0.7 - - - -
219C CYS* 4.7 5.8 - - - -
364C LYS* 3.2 31.0 - - - +
368C ASP* 5.8 0.2 - - - -
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Residues in contact with THR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA* 3.5 28.2 + - + +
91C CYS* 1.3 69.8 - - - +
93C GLY* 1.3 59.0 + - - +
94C VAL 3.5 0.2 - - - -
95C GLN* 3.7 10.3 - - - -
96C THR* 2.6 35.7 + - - -
217C GLN* 3.2 19.8 + - - +
266C LEU* 3.8 26.0 - - + +
364C LYS* 4.8 1.6 - - - +
368C ASP* 3.5 17.7 + - - +
372C TYR* 3.1 27.8 - - - +
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Residues in contact with GLY 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C CYS* 3.0 14.9 - - - -
92C THR* 1.3 79.8 + - - +
94C VAL* 1.3 64.0 + - - +
96C THR* 4.0 0.3 - - - -
97C ALA* 3.5 13.7 + - - +
217C GLN* 4.0 25.4 - - - +
219C CYS* 3.6 15.6 - - - -
220C SER* 3.7 14.4 - - - -
364C LYS* 5.1 0.6 - - - +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 5.7 0.2 - - + -
35C ILE* 4.2 26.0 - - + -
39C ALA* 6.1 2.0 - - - -
42C TYR* 5.7 2.9 - - + -
49C PRO* 4.2 14.1 - - + -
52C LEU* 3.7 41.7 - - + -
53C LEU* 4.8 3.4 - - + -
91C CYS* 3.4 13.5 + - + +
93C GLY* 1.3 74.1 - - - +
95C GLN* 1.3 65.0 + - - +
97C ALA* 3.2 5.9 + - - +
98C ILE* 3.0 40.5 + - + +
219C CYS* 4.1 16.6 - - - -
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Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 6.0 0.4 - - - +
84C THR* 3.1 36.6 + - - +
87C LEU* 3.7 15.0 - - + -
88C ALA* 3.5 28.0 - - - +
91C CYS 3.2 14.8 + - - +
92C THR* 3.7 6.9 + - - +
94C VAL* 1.3 81.4 - - - +
96C THR* 1.3 63.3 + - - +
98C ILE* 3.3 10.1 + - - +
99C GLU* 2.7 42.2 + - - +
258C PRO 4.6 0.7 - - - +
262C GLY* 4.3 4.4 - - - -
372C TYR* 3.7 21.2 + - - -
2400C CS8 4.3 8.4 - - - +
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Residues in contact with THR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C THR 2.6 23.9 + - - -
93C GLY 4.0 4.0 - - - -
94C VAL 3.3 0.2 - - - -
95C GLN* 1.3 81.1 + - - +
97C ALA* 1.3 60.9 + - - +
99C GLU 3.7 0.2 - - - -
100C ALA* 2.8 29.0 + - - +
168C THR* 4.2 13.2 - - + +
217C GLN* 3.3 11.9 + - - +
220C SER* 4.4 7.4 - - - +
375C TYR* 3.0 32.5 + - + +
2399C FAD 5.9 0.7 - - + -
2400C CS8 3.9 28.2 - - + +
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Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TYR* 4.1 17.0 - - + +
49C PRO* 5.1 3.6 - - + -
53C LEU* 4.3 10.8 - - + -
93C GLY 3.5 10.3 + - - +
94C VAL* 3.2 11.1 + - - +
96C THR* 1.3 77.1 - - - +
98C ILE* 1.3 63.6 + - - +
100C ALA* 3.3 5.2 - - - +
101C ASN 3.8 0.3 + - - -
130C MET* 3.5 8.8 - - - +
168C THR* 4.7 2.7 - - - -
169C ASN* 3.1 39.8 - - - +
220C SER* 4.7 6.8 + - - +
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 4.9 3.4 - - + -
35C ILE* 5.5 0.2 - - + -
52C LEU 5.3 0.4 - - - +
53C LEU* 3.5 19.7 - - + -
56C ALA* 4.0 20.4 - - + -
61C LEU 4.2 13.2 - - - +
62C MET* 3.8 27.2 - - + +
63C ASN 5.7 0.3 + - - -
87C LEU* 3.8 29.4 - - + -
94C VAL* 3.0 32.5 + - + +
95C GLN* 3.5 7.0 - - - +
96C THR 3.2 0.2 - - - -
97C ALA* 1.3 76.1 - - - +
99C GLU* 1.3 70.0 + - + +
101C ASN* 3.1 23.4 + - - +
102C THR* 4.1 1.7 + - - -
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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
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80C SER* 4.4 11.8 - - - +
84C THR* 2.9 31.0 + - + +
95C GLN* 2.7 29.5 + - - +
96C THR 4.1 0.2 - - - +
98C ILE* 1.3 75.1 - - + +
100C ALA* 1.3 64.7 + - - +
101C ASN 3.1 0.4 - - - -
102C THR* 3.2 27.4 + - - +
103C LEU* 3.1 20.4 + - - +
255C THR* 5.5 2.1 - - - +
258C PRO* 3.6 24.4 - - + +
2400C CS8 3.3 29.9 - - + +
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Residues in contact with ALA 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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96C THR 2.8 19.3 + - - +
97C ALA 3.3 1.8 - - - +
98C ILE 3.1 0.4 - - - -
99C GLU* 1.3 77.5 - - - +
101C ASN* 1.3 62.4 + - - +
103C LEU* 3.2 9.7 + - + +
104C GLY* 3.1 19.2 + - - -
131C CYS 4.4 6.1 - - - +
132C ALA* 5.1 2.4 - - - -
133C TYR 5.3 0.3 + - - -
168C THR* 3.6 24.9 - - + +
169C ASN* 3.2 24.5 - - + +
2400C CS8 3.9 9.9 - - + -
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Residues in contact with ASN 101 (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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62C MET* 4.3 10.2 - - + -
63C ASN* 3.0 30.2 + - - +
97C ALA 3.8 0.2 + - - -
98C ILE 3.1 12.4 + - - +
100C ALA* 1.3 79.7 - - - +
102C THR* 1.3 61.4 + - - +
104C GLY 3.2 1.7 + - - -
105C GLN* 3.0 30.1 + - - +
124C MET* 3.6 7.3 - - - +
129C LEU 3.4 22.8 + - - -
130C MET* 3.3 28.5 - - - +
131C CYS* 3.3 27.2 + - - -
169C ASN* 3.6 2.4 - - - +
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Residues in contact with THR 102 (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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63C ASN* 4.9 4.0 + - - -
64C THR* 4.9 10.9 + - - -
65C HIS* 4.8 14.8 - - + +
77C ILE* 5.8 4.5 - - + -
80C SER* 4.9 11.8 + - - +
98C ILE 4.1 1.1 + - - -
99C GLU* 3.2 31.7 + - - +
101C ASN* 1.3 76.3 - - - +
103C LEU* 1.3 66.1 + - - +
105C GLN* 3.1 14.2 + - - +
106C VAL* 2.9 39.7 + - + +
255C THR* 4.3 9.9 - - + -
258C PRO* 5.8 3.1 - - + -
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Residues in contact with LEU 103 (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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99C GLU 3.1 9.5 + - - +
100C ALA* 3.2 12.3 + - + +
102C THR* 1.3 79.7 - - - +
104C GLY* 1.3 57.0 + - - +
107C PRO* 3.2 19.6 - - - +
133C TYR* 3.5 39.4 - - + -
251C THR* 3.7 14.1 - - + +
252C PHE* 4.9 1.3 - - + -
255C THR* 3.6 33.7 - - + +
376C GLU* 3.6 11.7 - - - +
2399C FAD 4.3 4.3 - - - +
2400C CS8 3.3 44.9 - - + -
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Residues in contact with GLY 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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100C ALA 3.1 13.5 + - - -
101C ASN 3.7 2.9 - - - -
103C LEU* 1.3 74.7 - - - +
105C GLN* 1.3 60.5 + - - +
107C PRO* 3.1 16.3 - - - +
108C LEU* 4.7 1.0 + - - +
131C CYS* 4.1 8.1 - - - -
132C ALA 4.3 15.3 - - - -
133C TYR* 4.3 10.7 - - - +
175C TRP* 3.5 21.6 - - - -
177C PHE* 4.0 4.0 - - - +
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Residues in contact with GLN 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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63C ASN* 2.4 43.5 + - - +
65C HIS* 5.2 3.4 - - - +
66C ILE* 3.2 34.2 - - + +
101C ASN* 3.0 25.5 + - - +
102C THR* 3.1 10.7 + - - +
104C GLY* 1.3 76.1 - - - +
106C VAL* 1.3 56.2 + - + +
107C PRO 3.2 0.2 - - - -
108C LEU* 2.7 35.7 + - - +
109C ILE* 3.3 10.7 + - + +
121C LEU* 4.2 15.9 - - + -
124C MET* 4.0 10.2 - - + +
131C CYS* 3.9 10.1 - - - -
175C TRP* 4.1 10.8 - - + -
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Residues in contact with VAL 106 (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 HIS* 4.3 17.7 - - + +
77C ILE* 5.7 0.9 - - + -
102C THR* 2.9 35.9 + - + +
105C GLN* 1.3 75.9 - - + +
107C PRO* 1.3 67.2 - - + +
109C ILE* 3.1 19.6 + - + +
110C ILE* 3.1 27.2 + - + +
251C THR* 3.8 32.1 - - + -
254C LYS* 4.0 18.4 - - + +
255C THR* 4.0 9.6 - - + -
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Residues in contact with PRO 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 LEU 3.2 11.4 - - - +
104C GLY 3.1 19.3 - - - +
105C GLN 3.2 0.2 - - - -
106C VAL* 1.3 90.9 - - + +
108C LEU* 1.3 56.0 + - + +
110C ILE* 4.5 1.3 - - + -
111C GLY* 2.8 29.5 + - - -
133C TYR* 3.8 21.1 - - + -
177C PHE* 3.5 34.3 - - + -
238C LEU* 3.4 8.8 - - + +
247C ILE* 3.9 14.4 - - + +
251C THR* 3.5 16.4 - - + +
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Residues in contact with LEU 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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104C GLY 4.9 0.9 - - - +
105C GLN 2.7 16.6 + - - +
107C PRO* 1.3 73.6 - - + +
109C ILE* 1.3 59.2 + - - +
112C GLY* 3.0 24.7 + - - +
116C GLN* 4.2 19.1 - - + +
117C GLN* 3.4 16.2 - - + +
120C TYR* 3.7 20.0 - - + -
121C LEU* 3.3 29.4 - - + -
175C TRP* 3.5 27.6 - - + -
177C PHE* 6.2 2.0 - - + -
198C ILE* 4.2 16.8 - - + -
238C LEU* 3.2 28.7 - - + -
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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
----------------------------------------------------------
65C HIS* 3.4 55.2 - - + +
66C ILE* 4.1 3.6 - - - +
67C PRO* 3.7 21.5 - - + -
105C GLN* 3.3 10.9 + - + +
106C VAL* 3.1 17.8 + - - +
108C LEU* 1.3 78.6 - - - +
110C ILE* 1.3 67.1 + - + +
112C GLY 5.0 0.9 + - - +
117C GLN* 3.9 13.5 + - - +
121C LEU* 3.6 22.0 - - + -
254C LYS* 4.8 0.7 - - - +
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Residues in contact with ILE 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 VAL* 3.1 23.5 + - + +
107C PRO* 4.2 3.8 - - + +
109C ILE* 1.3 84.5 - - + +
111C GLY* 1.3 61.5 + - - +
112C GLY 3.8 1.1 - - - -
247C ILE* 4.3 12.3 - - + +
250C GLY* 3.8 34.8 - - - +
251C THR* 3.9 5.2 - - - +
254C LYS* 3.4 31.0 - - + +
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Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PRO 2.8 16.3 + - - -
110C ILE* 1.3 80.0 - - - +
112C GLY* 1.3 59.7 + - - +
113C ASN* 4.7 0.3 - - - +
238C LEU* 3.2 6.1 - - - +
239C THR* 2.7 43.5 + - - -
247C ILE* 4.5 14.4 - - - -
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Residues in contact with GLY 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PRO 3.6 1.4 + - - -
108C LEU* 3.0 16.2 + - - +
109C ILE 5.1 1.7 - - - +
110C ILE 5.3 0.7 - - - -
111C GLY* 1.3 81.2 - - - +
113C ASN* 1.3 66.4 + - - -
116C GLN* 3.3 12.8 - - - -
117C GLN* 3.1 16.4 + - - -
238C LEU* 3.8 8.7 - - - -
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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