Contacts of the helix formed by residues 111 - 132 (chain A) in PDB entry 4DTZ
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 ALA 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A PRO 3.5 20.4 - - - +
106A SER* 3.4 28.3 - - - +
107A PHE 4.3 0.2 - - - -
108A SER* 2.9 16.2 + - - +
110A GLN* 1.3 77.4 - - - +
112A MET* 1.3 62.6 + - - +
113A LYS 3.1 0.2 - - - -
114A GLY* 3.0 15.7 + - - -
115A TYR* 3.5 15.0 - - + +
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Residues in contact with MET 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A SER 4.3 0.2 - - - +
107A PHE* 3.6 22.2 - - + +
108A SER 3.2 20.0 + - - +
109A GLN* 3.1 24.3 + - - +
111A ALA* 1.3 76.6 - - - +
113A LYS* 1.3 61.6 + - - +
114A GLY 3.1 0.2 + - - -
115A TYR* 3.1 38.0 + - + +
116A HIS* 3.1 24.1 + - - +
119A MET* 4.2 7.2 - - - -
305A TYR* 3.8 13.9 - - + -
404A GLN 4.0 11.9 - - - +
405A PHE* 3.5 39.5 - - + +
408A HIS* 4.1 16.2 + - + -
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLN* 2.6 46.0 + - - +
111A ALA 3.1 1.0 - - - -
112A MET* 1.3 76.7 - - - +
114A GLY* 1.3 60.9 + - - +
116A HIS* 3.7 12.7 + - - +
117A ALA 4.8 1.6 + - - -
305A TYR* 3.7 48.8 - - + +
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Residues in contact with GLY 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 GLN 4.6 0.2 + - - -
111A ALA 3.0 10.3 + - - -
113A LYS* 1.3 81.2 - - - +
115A TYR* 1.3 63.1 + - - +
117A ALA* 4.8 4.3 + - - +
118A MET 5.4 0.7 + - - -
231A ASP* 3.8 27.7 - - - +
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Residues in contact with TYR 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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106A SER* 2.8 29.8 + - - -
107A PHE* 5.6 0.4 - + - -
111A ALA* 3.5 20.3 - - + +
112A MET* 3.1 31.9 + - + +
114A GLY* 1.3 75.5 - - - +
116A HIS* 1.3 65.6 + - - +
117A ALA 3.3 2.2 - - - -
118A MET* 3.1 8.2 + - - +
119A MET* 3.0 32.2 + - + +
156A CYS* 3.8 37.7 - - + -
231A ASP 3.3 26.0 - - - -
232A ASP 4.4 0.9 - - - -
233A LEU* 3.2 26.3 - - + +
236A HIS* 3.4 19.0 + + - -
405A PHE* 4.1 11.7 - + - -
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Residues in contact with HIS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A MET 3.1 14.8 + - - +
113A LYS 3.7 10.8 - - - +
114A GLY 3.4 1.8 - - - -
115A TYR* 1.3 75.4 - - - +
117A ALA* 1.3 59.8 + - - +
119A MET* 3.1 9.8 + - - +
120A VAL* 2.8 48.6 + - + +
303A PRO 2.8 25.2 + - - -
304A SER* 3.5 8.1 - - - -
305A TYR* 3.3 35.9 + - + -
308A VAL* 3.7 11.9 - - + -
408A HIS* 2.8 29.5 + - - +
412A LEU* 4.2 6.2 - - + +
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Residues in contact with ALA 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 LYS 4.8 2.0 + - - -
114A GLY 4.8 4.1 + - - +
115A TYR 3.3 0.8 - - - -
116A HIS* 1.3 81.3 - - + +
118A MET* 1.3 78.8 + - + +
120A VAL* 3.2 8.9 + - - +
121A ASP* 3.0 23.4 + - - +
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Residues in contact with MET 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 GLY 5.4 0.6 + - - -
115A TYR* 3.1 9.9 + - - +
117A ALA* 1.3 95.5 - - + +
119A MET* 1.4 65.4 + - - +
121A ASP* 3.3 23.6 - - + +
122A ILE* 3.3 14.9 + - - +
152A THR* 4.9 1.0 - - - +
155A LEU* 3.6 43.3 - - + +
156A CYS* 4.2 14.4 - - - -
159A ASN* 5.2 5.2 - - - +
161A ARG* 4.1 12.8 - - - -
231A ASP* 6.2 4.5 - - + -
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Residues in contact with MET 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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112A MET* 4.2 10.1 - - - -
115A TYR* 3.0 22.5 + - + +
116A HIS* 3.5 7.4 - - - +
118A MET* 1.4 76.8 - - - +
120A VAL* 1.3 56.9 + - - +
122A ILE* 3.3 4.0 + - - +
123A ALA* 3.0 27.4 + - - +
148A LEU* 5.6 0.2 - - - +
152A THR* 3.6 24.0 + - + -
156A CYS* 4.0 3.4 - - - -
405A PHE* 3.5 55.0 - - + +
408A HIS* 3.7 24.5 - - + -
409A GLU* 3.8 24.8 - - - +
412A LEU* 3.8 13.6 - - + +
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Residues in contact with VAL 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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116A HIS* 2.8 52.5 + - + +
117A ALA* 3.2 9.2 + - - +
119A MET* 1.3 68.3 - - - +
121A ASP* 1.4 60.8 + - - +
123A ALA* 4.2 6.7 - - - -
124A VAL* 2.8 46.7 + - + +
302A VAL* 4.0 23.3 - - + -
303A PRO* 4.0 10.8 - - + +
412A LEU* 4.1 11.7 - - + -
416A MET* 5.2 1.1 - - + -
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Residues in contact with ASP 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 ALA 3.0 13.6 + - - +
118A MET* 3.3 23.5 - - + +
119A MET 3.2 0.2 - - - -
120A VAL* 1.4 78.8 - - - +
122A ILE* 1.4 63.4 + - - +
124A VAL* 3.5 5.8 + - - +
125A GLN* 3.1 30.0 + - - +
155A LEU* 4.1 3.6 - - + -
161A ARG* 2.9 43.8 + - - -
132B ARG* 4.4 9.8 + - - -
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Residues in contact with ILE 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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118A MET 3.3 10.5 + - - +
119A MET 3.3 3.6 + - - +
121A ASP* 1.4 87.7 - - - +
123A ALA* 1.3 66.1 + - - +
125A GLN* 3.1 19.5 + - - +
126A LEU 3.0 18.2 + - - -
148A LEU* 3.6 28.1 - - + +
151A ASP* 3.9 26.0 - - + +
152A THR* 3.3 38.1 - - - +
155A LEU* 3.9 13.7 - - + -
161A ARG* 4.3 4.9 - - + +
165A PHE* 4.0 9.9 - - + -
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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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119A MET 3.0 18.2 + - - +
120A VAL* 3.2 5.4 + - - +
122A ILE* 1.3 78.6 - - - +
124A VAL* 1.3 57.2 + - - +
126A LEU* 3.2 4.7 + - + +
127A VAL* 3.0 33.0 + - + +
148A LEU* 3.9 10.4 - - - +
412A LEU* 4.4 3.8 - - + -
413A VAL* 4.0 23.1 - - + -
416A MET* 3.7 26.0 - - + -
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Residues in contact with VAL 124 (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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120A VAL* 2.8 31.0 + - + +
121A ASP* 3.8 6.1 - - - +
123A ALA* 1.3 69.0 - - - +
125A GLN* 1.3 59.4 + - + +
127A VAL* 3.2 6.3 + - - +
128A GLN* 2.8 46.9 + - - +
302A VAL* 3.8 29.2 - - + -
416A MET* 4.0 11.0 - - + -
455A LEU* 3.8 19.1 - - + -
132B ARG* 5.8 2.9 - - - +
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Residues in contact with GLN 125 (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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121A ASP* 3.1 33.1 + - - +
122A ILE* 3.1 26.5 + - - +
124A VAL* 1.3 75.5 - - - +
126A LEU* 1.4 57.1 + - - +
128A GLN* 4.0 7.8 - - - +
129A LYS* 3.0 29.6 + - - +
151A ASP* 5.2 2.9 + - - +
161A ARG* 3.6 4.9 - - - +
163A ASN* 5.1 3.8 + - - +
165A PHE* 3.8 26.8 + - + +
166A TYR* 3.8 19.3 - - - -
132B ARG* 3.4 41.3 + - - +
166B TYR* 4.7 4.4 + - + -
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Residues in contact with LEU 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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122A ILE 3.0 12.3 + - - +
123A ALA* 3.2 8.5 + - - +
125A GLN* 1.4 75.5 - - - +
127A VAL* 1.3 66.2 + - + +
129A LYS* 3.2 6.5 + - + +
130A TRP* 3.1 60.8 + - + +
144A ASP* 4.0 5.6 - - + +
145A MET* 3.5 27.4 - - + -
148A LEU* 3.9 10.3 - - + -
165A PHE* 3.7 31.9 - - + -
413A VAL* 3.8 24.2 - - + -
417A MET* 4.5 7.0 - - + -
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Residues in contact with VAL 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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123A ALA 3.0 16.3 + - - +
124A VAL* 3.2 3.6 + - - +
126A LEU* 1.3 80.7 - - + +
128A GLN* 1.3 57.7 - - - +
130A TRP* 3.2 3.0 + - + -
131A GLU* 2.8 38.6 + - + +
416A MET* 4.2 33.0 - - + -
417A MET* 5.0 3.8 - - + +
420A HIS* 4.0 25.6 - - + -
421A PHE* 3.6 23.4 - - + -
455A LEU* 3.7 24.0 - - + -
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Residues in contact with GLN 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 VAL* 2.8 34.8 + - - +
125A GLN* 4.0 9.9 - - - +
127A VAL* 1.3 77.4 - - - +
129A LYS* 1.4 61.4 + - - +
131A GLU* 3.2 9.5 + - + +
132A ARG* 3.0 65.4 + - - +
455A LEU* 3.7 18.9 - - + +
128B GLN* 4.5 19.3 + - - +
132B ARG* 5.0 5.0 + - - -
166B TYR* 3.9 4.0 - - - +
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Residues in contact with LYS 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 GLN 3.0 13.2 + - - +
126A LEU* 3.2 10.0 + - - +
128A GLN* 1.4 77.1 - - - +
130A TRP* 1.3 68.8 + - + +
132A ARG* 3.1 13.5 + - - +
133A LEU* 3.4 26.1 + - + +
144A ASP* 2.8 38.8 + - - +
147A ARG* 3.8 17.2 - - - +
165A PHE* 3.8 21.2 + - + +
163B ASN* 5.4 0.7 + - - -
166B TYR* 3.4 46.2 + - + +
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Residues in contact with TRP 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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126A LEU* 3.1 25.8 + - + +
127A VAL* 3.9 2.0 - - + +
129A LYS* 1.3 83.1 - - + +
131A GLU* 1.3 65.1 + - - +
132A ARG 3.2 0.3 + - - -
133A LEU* 3.3 26.0 + - + +
139A ILE* 3.3 50.3 - - + +
141A VAL* 5.5 1.3 - - + -
144A ASP* 2.8 25.4 + - + -
145A MET* 3.5 34.5 - - + -
277A LEU* 4.9 5.6 - - + -
417A MET* 3.8 28.9 - - + -
421A PHE* 3.7 39.4 - + + -
423A PHE* 3.8 22.2 - + - -
448A ALA* 5.1 2.7 - - + +
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Residues in contact with GLU 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 VAL* 2.8 32.1 + - + +
128A GLN* 3.2 13.2 + - + +
130A TRP* 1.3 77.4 - - - +
132A ARG* 1.3 63.4 + - + +
133A LEU 3.7 4.9 + - - +
420A HIS* 4.1 19.1 + - - +
421A PHE* 3.8 15.5 - - + -
450A SER* 2.7 36.2 + - - -
452A LYS* 4.9 12.4 + - - +
453A ILE 4.2 9.2 + - - +
455A LEU* 5.4 3.4 - - + +
161B ARG* 5.2 2.1 + - - -
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Residues in contact with ARG 132 (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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128A GLN* 3.0 50.6 + - - +
129A LYS* 3.6 7.0 - - - +
130A TRP 3.1 0.8 - - - -
131A GLU* 1.3 81.9 - - + +
133A LEU* 1.4 63.6 + - - +
121B ASP* 4.4 11.5 + - - -
124B VAL* 5.9 2.8 - - - +
125B GLN* 3.6 45.2 - - - +
128B GLN* 5.0 5.9 + - - -
161B ARG* 3.4 39.3 - - - +
163B ASN* 2.9 33.8 + - - +
166B TYR* 2.9 28.7 + - + +
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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
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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