Contacts of the helix formed by residues 110 - 133 (chain C) in PDB entry 1JT0
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 ASN 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LYS 3.1 6.6 + - - +
109C THR* 1.3 67.6 - - - +
111C SER* 1.3 58.5 + - - +
112C ILE 3.5 0.7 - - - -
113C ASN* 3.4 26.9 - - + +
114C GLU* 3.0 43.2 + - + +
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C THR* 2.5 33.9 + - - -
110C ASN* 1.3 76.1 - - - +
112C ILE* 1.3 68.4 + - - +
114C GLU* 4.1 2.8 + - - +
115C LYS* 3.2 40.7 + - - +
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLU* 3.7 22.9 - - - +
51C LEU* 4.5 10.8 - - + -
102C PHE* 3.2 33.7 - - + -
103C TYR* 5.8 1.1 - - - -
106C TYR* 3.1 35.4 - - + +
107C TYR* 5.6 0.4 - - - -
108C LYS* 3.9 2.7 - - - +
109C THR* 3.0 17.0 - - - +
111C SER* 1.3 100.5 - - - +
113C ASN* 1.3 63.1 + - - +
114C GLU 3.4 0.2 - - - -
115C LYS* 3.8 9.5 - - + +
116C MET* 2.9 43.9 + - + +
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Residues in contact with ASN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 5.9 1.0 - - - +
103C TYR* 2.8 34.4 + - - -
106C TYR 4.6 1.2 + - - -
107C TYR* 4.1 18.7 - - - +
109C THR 3.8 2.0 + - - -
110C ASN* 3.4 30.0 - - + +
111C SER 3.3 0.2 - - - -
112C ILE* 1.3 81.2 - - - +
114C GLU* 1.3 67.5 + - - +
116C MET* 3.7 1.6 - - - +
117C ASN* 3.1 30.3 + - - +
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Residues in contact with GLU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASN* 3.0 41.8 + - - +
111C SER 4.2 4.5 - - - +
112C ILE 3.4 0.2 - - - -
113C ASN* 1.3 80.0 - - - +
115C LYS* 1.3 65.8 + - + +
117C ASN* 3.1 9.4 + - - +
118C LYS* 3.0 23.6 + - - +
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Residues in contact with LYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLU* 4.9 7.5 + - - -
48C ASN* 5.3 5.1 - - - +
51C LEU* 3.7 36.6 - - + +
111C SER* 3.2 31.8 + - - +
112C ILE* 3.6 10.9 + - - +
114C GLU* 1.3 79.7 - - + +
116C MET* 1.3 59.3 + - - +
118C LYS* 3.0 35.5 - - - +
119C LEU* 3.4 9.4 + - - +
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Residues in contact with MET 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 4.5 5.8 - - - -
54C LEU* 4.1 24.2 - - + -
99C ILE* 3.5 23.3 - - + +
102C PHE* 3.3 34.1 - - + -
103C TYR* 3.5 51.8 - - + +
112C ILE* 2.9 31.7 + - + +
113C ASN 3.7 0.2 - - - +
114C GLU 3.2 0.2 - - - -
115C LYS* 1.3 72.4 - - - +
117C ASN* 1.3 68.4 + - - +
119C LEU* 2.7 20.4 + - - +
120C GLU* 2.8 17.9 + - - +
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Residues in contact with ASN 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 4.9 11.4 - - - +
103C TYR* 3.5 15.6 + - - -
113C ASN* 3.1 32.8 + - - +
114C GLU* 3.1 11.6 + - - +
116C MET* 1.3 76.7 - - - +
118C LYS* 1.3 56.1 + - - +
120C GLU* 2.9 26.5 + - - +
121C ASN* 2.5 49.3 + - - +
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Residues in contact with LYS 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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55C ASN* 3.5 32.1 + - - +
114C GLU 3.0 12.4 + - - +
115C LYS* 3.0 24.0 - - - +
117C ASN* 1.3 77.1 - - - +
119C LEU* 1.3 72.4 + - - +
121C ASN* 3.2 7.1 + - - +
122C LYS* 3.1 27.9 + - + +
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Residues in contact with LEU 119 (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 LEU* 5.2 3.8 - - + -
54C LEU* 3.5 41.5 - - + -
55C ASN* 3.7 31.4 - - - +
58C GLU* 3.7 33.4 - - + +
92C TYR* 4.3 14.4 - - + +
115C LYS 3.9 11.2 - - - +
116C MET* 2.7 17.2 + - - +
118C LYS* 1.3 82.2 - - + +
120C GLU* 1.3 60.0 + - - +
122C LYS* 3.3 17.8 + - + +
123C TYR* 3.3 21.8 - - - -
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Residues in contact with GLU 120 (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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162A PHE 5.2 6.6 - - - +
165A GLU* 4.9 13.3 - - - +
92C TYR* 4.4 10.3 - - - +
99C ILE* 5.9 2.8 - - - +
103C TYR* 4.6 12.6 + - - -
116C MET* 2.8 11.9 + - - +
117C ASN* 3.0 47.7 + - - +
119C LEU* 1.3 75.1 - - - +
121C ASN* 1.3 69.9 + - - +
123C TYR* 3.3 15.9 + - - +
124C ILE* 3.2 23.0 + - + +
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Residues in contact with ASN 121 (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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117C ASN* 2.5 39.0 + - - +
118C LYS* 3.7 7.6 - - - +
120C GLU* 1.3 80.0 - - - +
122C LYS* 1.3 65.3 + - - +
123C TYR 3.1 0.7 - - - -
124C ILE* 3.7 15.2 - - - +
125C ASP* 3.1 31.7 + - - +
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Residues in contact with LYS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLU* 2.9 40.4 + - + +
59C SER* 5.5 0.8 - - - +
62C GLN* 2.8 31.1 + - - +
118C LYS* 3.1 20.1 + - + +
119C LEU* 3.4 16.8 - - + +
120C GLU 3.2 0.6 - - - -
121C ASN* 1.3 76.6 - - - +
123C TYR* 1.3 62.1 + - - +
125C ASP* 3.2 21.3 - - - +
126C ALA* 3.3 7.3 + - - +
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Residues in contact with TYR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLU* 3.6 24.2 - - + +
61C TRP* 3.3 38.2 - + - +
82C TYR* 3.3 20.5 + - - +
91C TYR 4.6 0.2 + - - -
92C TYR* 3.0 50.5 - + - +
93C TYR* 3.5 36.1 - + - +
119C LEU 3.3 15.0 - - - -
120C GLU* 3.6 9.0 - - - +
121C ASN 3.1 0.4 - - - -
122C LYS* 1.3 75.6 - - - +
124C ILE* 1.3 66.1 + - + +
125C ASP 2.8 5.4 + - - -
126C ALA* 2.8 15.4 + - - +
127C TYR* 3.4 17.5 + - + -
153C ALA* 5.7 1.6 - - + -
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Residues in contact with ILE 124 (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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120C GLU* 3.2 22.4 - - + +
121C ASN* 3.5 21.5 + - - +
123C TYR* 1.3 76.8 - - + +
125C ASP* 1.3 60.0 + - - +
127C TYR* 3.3 5.6 + - - +
128C HIS* 3.1 22.3 + - + +
149C SER* 3.7 18.2 - - - +
150C LYS* 3.6 35.7 - - + +
153C ALA* 3.3 27.1 - - + -
154C ASN* 4.7 9.4 - - - +
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Residues in contact with ASP 125 (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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121C ASN* 3.1 22.6 + - - +
122C LYS* 3.2 16.6 - - - +
123C TYR 2.8 1.2 + - - -
124C ILE* 1.3 76.6 - - - +
126C ALA* 1.3 66.6 + - - +
127C TYR 3.0 1.3 - - - -
128C HIS* 3.0 14.3 + - - +
129C VAL* 2.9 26.9 + - + +
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Residues in contact with ALA 126 (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 TRP* 4.7 11.4 - - + +
82C TYR* 3.1 43.5 - - + +
122C LYS 3.3 5.9 + - - +
123C TYR 2.8 8.7 + - - +
125C ASP* 1.3 74.3 - - - +
127C TYR* 1.3 63.0 + - - +
129C VAL* 3.2 7.3 + - - +
130C ILE* 3.0 28.5 + - + +
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Residues in contact with TYR 127 (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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79C PHE* 4.1 28.0 - + - -
82C TYR* 3.3 35.5 - + + -
83C ASN* 2.9 25.8 + - - -
86C SER* 5.0 0.5 + - - -
93C TYR* 4.5 7.9 + - - -
123C TYR* 3.4 17.9 + - + -
124C ILE 3.3 6.4 + - - +
125C ASP 3.0 0.4 - - - -
126C ALA* 1.3 74.4 - - - +
128C HIS* 1.3 57.0 + - - +
129C VAL 2.9 0.7 + - - -
130C ILE* 3.0 8.1 + - + -
131C PHE* 2.7 40.5 + + + +
149C SER* 3.5 33.0 - - - +
152C ALA* 4.2 10.1 - - + -
153C ALA* 3.2 30.9 + - + -
156C VAL* 3.7 14.2 - - - +
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Residues in contact with HIS 128 (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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124C ILE* 3.1 13.1 + - + +
125C ASP* 3.0 19.6 + - - +
127C TYR* 1.3 75.1 - - - +
129C VAL* 1.3 57.1 + - + +
132C LYS* 3.0 47.3 + - + +
145C VAL* 3.5 20.1 - - + +
146C ASN* 2.9 35.8 + - - -
149C SER* 3.0 20.8 + - - +
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Residues in contact with VAL 129 (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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69C GLN* 6.0 1.3 - - - +
78C LYS* 5.6 0.7 - - - +
125C ASP* 2.9 16.5 + - + +
126C ALA* 3.3 10.3 - - - +
127C TYR 2.9 0.2 + - - -
128C HIS* 1.3 73.6 - - + +
130C ILE* 1.3 68.9 + - + +
131C PHE 2.7 14.9 + - - -
132C LYS* 3.8 2.1 - - - +
133C GLU* 2.9 47.8 + - - +
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Residues in contact with ILE 130 (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 TRP* 4.3 20.2 - - + +
69C GLN* 5.0 1.6 - - - +
75C ASN* 3.5 35.5 - - + +
78C LYS* 3.6 39.9 - - + +
79C PHE* 3.9 22.2 - - + +
82C TYR* 5.6 5.2 - - + -
126C ALA* 3.0 19.0 + - + +
127C TYR* 3.6 11.4 - - + +
129C VAL* 1.3 84.3 - - + +
131C PHE* 1.3 60.4 + - + +
133C GLU* 4.2 4.3 - - - +
134C GLY 3.8 2.1 + - - -
140C TRP* 3.2 16.7 - - + -
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Residues in contact with PHE 131 (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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79C PHE* 3.2 39.7 - + - -
127C TYR* 2.7 20.4 + + + +
129C VAL 2.7 2.8 + - - -
130C ILE* 1.3 71.0 - - + +
132C LYS* 1.3 62.7 + - - +
133C GLU 3.0 4.3 - - - -
134C GLY 3.0 12.1 + - - -
135C ASN* 3.2 5.2 + - - +
140C TRP* 3.1 33.5 + + - +
142C ILE* 5.0 5.4 - - + -
145C VAL* 3.3 21.5 - - + -
148C VAL* 3.1 45.8 - - + -
149C SER* 3.2 26.2 - - - -
152C ALA* 3.8 9.2 - - + -
182C PHE* 3.9 5.6 - + - -
186C LEU* 4.7 11.2 - - + -
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Residues in contact with LYS 132 (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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128C HIS* 3.0 43.1 + - + +
129C VAL* 4.2 1.3 - - - +
131C PHE* 1.3 72.7 - - - +
133C GLU* 1.3 60.2 + - - +
135C ASN* 3.4 11.4 + - + -
136C LEU* 3.5 39.8 - - + +
145C VAL* 3.7 17.0 - - + +
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Residues in contact with GLU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ASN* 3.0 34.8 + - - +
78C LYS* 4.6 9.6 + - - +
129C VAL* 2.9 38.7 + - - +
130C ILE 4.0 1.1 - - - +
132C LYS* 1.3 79.7 - - - +
134C GLY* 1.3 57.6 + - - +
136C LEU* 3.6 5.2 + - - +
137C ASN* 3.3 26.8 + - - +
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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
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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