Contacts of the helix formed by residues 109 - 131 (chain A) in PDB entry 2JAV
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 ASP 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLN* 5.5 1.4 + - - -
107A TYR 4.5 1.9 - - - +
108A LEU* 1.3 75.6 - - - +
110A GLU* 1.3 64.4 + - - +
111A GLU* 4.1 11.9 - - + +
112A PHE* 3.2 22.5 + - + +
113A VAL* 3.3 11.4 + - - +
239A ARG* 3.3 17.8 + - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU 3.5 2.4 + - - -
109A ASP* 1.3 71.4 - - - +
111A GLU* 1.3 57.6 - - + +
113A VAL* 3.1 5.0 + - - +
114A LEU* 2.8 39.7 + - + +
239A ARG* 4.0 6.9 - - - +
240A TYR* 3.3 24.8 - - + -
241A SER* 2.7 49.1 + - - -
244A LEU* 3.6 23.1 - - + +
270A LEU* 4.0 13.0 - - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 3.1 9.1 - - + +
110A GLU* 1.3 78.3 - - + +
112A PHE* 1.3 57.3 + - - +
114A LEU* 3.4 13.0 + - - +
115A ARG* 3.1 44.1 + - - +
274A HIS* 2.5 32.1 + - - -
275A HIS* 2.9 25.9 + - - -
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.6 29.8 - - + -
97A VAL* 4.2 15.7 - - + -
108A LEU* 4.1 21.5 - - + -
109A ASP* 3.2 19.9 + - + +
111A GLU* 1.3 74.9 - - - +
113A VAL* 1.3 69.8 + - - +
115A ARG* 3.2 16.8 + - + +
116A VAL* 3.1 40.8 + - + +
149A LEU* 3.9 29.8 - - + -
153A GLN* 6.0 2.9 - - - -
155A VAL* 5.2 2.0 - - + -
209A LEU* 4.3 10.1 - - + -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.4 14.6 - - + -
109A ASP 3.3 13.4 + - - +
110A GLU 3.1 7.4 + - - +
112A PHE* 1.3 76.3 - - - +
114A LEU* 1.3 58.1 + - - +
116A VAL* 3.4 2.3 + - - +
117A MET* 3.0 26.9 + - + +
206A LEU* 3.9 19.5 - - + +
209A LEU* 4.4 21.5 - - + +
210A CYS* 3.7 31.9 - - - -
240A TYR* 4.1 11.7 - - + +
244A LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 2.8 33.8 + - + +
111A GLU* 3.7 11.2 - - - +
112A PHE 3.2 0.4 - - - -
113A VAL* 1.3 73.7 - - - +
115A ARG* 1.3 59.0 + - - +
117A MET* 3.6 28.7 - - + +
118A THR* 2.8 36.6 + - - +
244A LEU* 3.9 18.8 - - + -
270A LEU* 3.9 31.0 - - + +
271A ILE* 5.6 0.4 - - + -
275A HIS* 3.6 39.0 - - + +
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Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 3.1 40.2 + - - +
112A PHE* 3.2 17.0 + - + +
114A LEU* 1.3 74.7 - - - +
116A VAL* 1.3 60.2 + - + +
119A GLN* 2.8 44.0 + - - +
153A GLN* 3.7 58.5 + - - +
155A VAL* 4.2 5.6 - - + -
274A HIS* 3.3 46.3 + - - +
275A HIS* 3.5 21.1 - - + +
276A HIS 5.4 0.4 + - - -
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.0 10.1 - - + -
112A PHE* 3.1 44.2 + - + +
113A VAL 3.7 6.7 - - - +
114A LEU 3.4 0.2 - - - -
115A ARG* 1.3 75.0 - - - +
117A MET* 1.3 59.0 + - - +
120A LEU* 2.8 59.4 + - + +
155A VAL* 3.9 21.5 - - + -
205A LEU* 4.0 5.8 - - + -
206A LEU* 3.9 7.4 - - + -
209A LEU* 3.8 20.4 - - + -
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Residues in contact with MET 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 3.0 18.2 + - + +
114A LEU* 3.6 30.5 - - + +
116A VAL* 1.3 76.8 - - - +
118A THR* 1.3 59.5 + - - +
120A LEU* 4.6 0.2 - - - +
121A THR* 2.5 36.0 + - - +
202A LEU* 4.9 2.4 - - - +
206A LEU* 3.6 28.2 - - + +
244A LEU* 4.5 5.6 - - + -
247A ILE* 3.9 31.0 - - + -
251A MET* 4.0 14.1 - - + -
265A ILE* 4.2 16.6 - - + +
268A ASN* 5.3 2.0 - - + +
270A LEU* 4.7 4.9 - - + -
271A ILE* 3.7 25.6 - - + -
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU 2.8 25.7 + - - -
117A MET* 1.3 74.3 - - - +
119A GLN* 1.3 58.6 + - - +
121A THR* 3.7 2.1 - - - -
122A LEU* 3.1 31.8 + - + +
266A LEU* 3.9 5.3 - - + +
271A ILE* 3.3 34.8 - - + +
275A HIS* 3.6 18.2 - - - +
276A HIS* 3.6 45.5 - - + +
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Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASN* 3.0 43.8 + - - +
115A ARG* 2.8 29.0 + - - +
118A THR* 1.3 73.8 - - + +
120A LEU* 1.3 57.3 + - - +
122A LEU* 3.5 2.5 + - + -
123A ALA* 3.0 20.6 + - - +
153A GLN 3.7 17.0 + - - -
154A ASN* 3.4 8.4 + - - +
155A VAL* 2.8 38.7 + - + -
275A HIS 2.9 23.9 + - - +
276A HIS* 3.3 14.3 + - - -
277A HIS* 3.6 16.2 - - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASN 5.2 0.4 - - - +
116A VAL* 2.8 40.1 + - + +
119A GLN* 1.3 70.8 - - - +
121A THR* 1.3 60.7 + - - +
123A ALA* 3.3 3.9 + - + +
124A LEU* 2.9 34.0 + - - +
142A LEU* 5.0 7.9 - - + -
147A VAL* 3.9 26.9 - - + -
155A VAL* 4.0 20.2 - - + -
157A LEU* 4.0 37.1 - - + +
202A LEU* 4.1 17.7 - - + -
205A LEU* 4.0 16.6 - - + -
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A MET* 2.5 25.2 + - - +
118A THR 3.7 3.8 - - - -
120A LEU* 1.3 77.3 - - - +
122A LEU* 1.3 57.2 + - - +
124A LEU* 3.3 7.4 + - - +
125A LYS* 2.8 26.7 + - - +
202A LEU* 3.4 20.7 - - + +
262A VAL* 3.8 40.2 - - + +
265A ILE* 3.6 23.7 - - + +
266A LEU* 3.9 10.5 - - + -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A HIS* 3.7 17.8 + - + +
66A ASN* 4.0 15.7 - - - +
118A THR* 3.1 24.2 + - + +
119A GLN* 3.8 5.8 - - + +
121A THR* 1.3 74.4 - - - +
123A ALA* 1.3 64.5 - - - +
125A LYS* 3.4 18.6 + - + +
126A GLU* 3.2 16.5 + - - +
266A LEU* 3.7 26.0 - - + -
276A HIS* 3.5 36.6 - - + +
277A HIS* 5.9 2.9 - - + +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A HIS* 4.4 6.1 - - - -
66A ASN* 3.4 25.4 - - - +
67A ILE* 3.9 9.7 - - + +
119A GLN 3.0 12.6 + - - +
120A LEU* 3.3 11.6 + - + +
122A LEU* 1.3 74.1 - - - +
124A LEU* 1.3 58.6 + - - +
126A GLU* 3.3 4.5 + - - +
127A CYS* 3.0 32.4 + - - -
157A LEU* 3.9 23.6 - - + -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LEU 2.9 17.2 + - - +
121A THR* 3.5 5.6 - - - +
122A LEU 3.3 0.2 - - - -
123A ALA* 1.3 73.4 - - - +
125A LYS* 1.3 66.9 + - - +
127A CYS* 4.2 6.7 - - + -
128A HIS* 2.9 40.4 + - + +
142A LEU* 4.1 31.4 - - + -
157A LEU* 4.7 11.4 - - + -
160A PHE* 4.8 5.2 - - + -
198A ASP* 4.0 46.2 - - + +
199A ILE* 4.5 9.9 - - + -
202A LEU* 4.2 19.1 - - + -
262A VAL* 4.4 3.6 - - + -
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A THR 2.8 14.6 + - - +
122A LEU* 3.4 20.7 + - + +
124A LEU* 1.3 72.6 - - - +
126A GLU* 1.3 60.3 + - - +
128A HIS* 3.5 5.2 + - - +
129A ARG* 3.2 37.8 + - + +
262A VAL* 3.5 33.5 - - + +
263A GLU* 4.1 17.1 + - + +
266A LEU* 4.5 13.6 - - + +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.5 28.4 - - + +
63A LYS 5.4 2.9 - - - +
64A HIS* 3.6 37.1 + - + +
67A ILE* 4.1 5.2 - - + -
122A LEU 3.2 8.7 + - - +
123A ALA 3.5 8.3 - - - +
124A LEU 3.1 0.4 - - - -
125A LYS* 1.3 76.9 - - - +
127A CYS* 1.3 65.4 + - - +
129A ARG* 3.0 43.8 + - - +
130A ARG* 3.1 12.3 + - - +
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Residues in contact with CYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 4.6 10.5 - - - -
67A ILE* 4.1 13.5 - - - -
123A ALA 3.0 19.7 + - - +
124A LEU* 3.3 10.3 + - + +
126A GLU* 1.3 74.7 - - - +
128A HIS* 1.3 66.8 - - + +
130A ARG* 3.3 22.2 + - - +
131A SER* 3.4 10.6 + - - -
157A LEU* 4.1 15.0 - - - -
160A PHE* 4.0 29.6 - - + -
198A ASP* 6.0 0.2 - - - +
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Residues in contact with HIS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 2.9 35.6 + - + +
125A LYS* 3.8 5.4 - - - +
127A CYS* 1.3 81.9 - - + +
129A ARG* 1.3 62.7 + - - +
131A SER* 3.5 23.2 + - - +
193A TYR* 4.0 4.7 - - - -
195A GLU* 3.6 62.0 + - + +
198A ASP* 2.7 34.5 + - + +
199A ILE* 5.1 1.8 - - + -
262A VAL* 4.2 16.5 - - + +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LYS* 3.2 31.9 + - + +
126A GLU* 3.0 34.8 + - - +
128A HIS* 1.3 75.8 - - - +
130A ARG* 1.3 67.1 + - - +
131A SER 3.4 5.0 + - - -
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Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLU* 3.6 31.2 - - - -
62A LEU* 4.4 21.8 - - + -
126A GLU* 3.1 11.3 + - - +
127A CYS* 3.4 13.0 - - - +
129A ARG* 1.3 78.0 - - - +
131A SER* 1.3 60.3 + - - +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A CYS 3.4 11.1 + - - -
128A HIS* 3.5 21.0 - - - -
129A ARG 3.3 5.5 - - - -
130A ARG* 1.3 81.7 - - - +
193A TYR* 6.5 0.4 - - - -
195A GLU* 5.3 5.8 - - - -
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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