Contacts of the helix formed by residues 112 - 134 (chain A) in PDB entry 2H6D
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 GLU 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 4.1 6.1 + - - +
111A VAL* 1.3 75.5 - - - +
113A GLU* 1.3 71.1 + - - +
114A MET* 3.1 46.4 + - - +
115A GLU* 3.1 18.3 + - + +
116A ALA* 3.0 18.7 + - - +
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 5.9 1.0 - - - +
111A VAL 3.5 1.0 + - - -
112A GLU* 1.3 80.2 - - - +
114A MET* 1.3 57.6 + - - +
116A ALA* 3.2 3.1 + - - +
117A ARG* 3.0 34.7 + - - +
208A LEU* 4.3 18.4 - - + -
236A TYR 5.7 0.9 - - - +
237A LEU* 6.1 4.5 - - + -
238A ASN* 3.1 22.5 + - - -
241A VAL* 5.2 1.9 - - - +
267A TRP* 2.9 35.8 + - + +
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Residues in contact with MET 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 3.1 27.4 + - - +
113A GLU* 1.3 77.1 - - - +
115A GLU* 1.3 63.8 + - + +
117A ARG* 3.4 20.9 + - - +
118A ARG* 2.9 28.5 + - - +
271A ASP* 4.9 12.8 - - - +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 3.2 25.1 - - + -
112A GLU* 3.1 21.4 + - + +
114A MET* 1.3 79.7 - - + +
116A ALA* 1.3 62.5 + - - +
118A ARG* 2.6 48.9 + - - +
119A LEU* 2.9 31.4 + - + +
151A MET* 4.8 9.5 - - - +
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Residues in contact with ALA 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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111A VAL* 3.3 12.7 - - + +
112A GLU 3.0 11.3 + - - +
113A GLU 3.2 9.4 + - - +
115A GLU* 1.3 74.1 - - - +
117A ARG* 1.3 58.6 + - - +
119A LEU* 3.3 1.6 + - - +
120A PHE* 2.9 32.1 + - - +
204A LEU* 4.9 0.7 - - + -
207A LEU* 3.9 28.3 - - + +
208A LEU* 3.6 27.6 - - + -
267A TRP* 4.5 3.4 - - + -
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Residues in contact with ARG 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 GLU* 3.0 18.5 + - - +
114A MET* 3.6 28.2 - - - +
115A GLU 3.2 0.2 - - - -
116A ALA* 1.3 78.7 - - - +
118A ARG* 1.3 63.0 + - - +
120A PHE* 3.8 1.2 - - - +
121A GLN* 2.9 45.8 + - + +
267A TRP* 2.8 80.0 + - + +
268A PHE 4.6 0.9 - - - +
270A GLN* 3.1 53.7 + - - +
271A ASP* 4.7 10.2 + - - -
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Residues in contact with ARG 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 MET 2.9 18.4 + - - +
115A GLU* 2.6 44.9 + - - +
117A ARG* 1.3 77.7 - - - +
119A LEU* 1.3 73.9 + - - +
121A GLN* 3.5 14.7 + - - +
122A GLN* 3.3 38.7 + - + +
150A HIS 4.7 1.6 + - - -
151A MET* 2.9 39.6 + - - +
152A ASN* 3.1 22.2 - - - +
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Residues in contact with LEU 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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101A LEU* 4.4 12.3 - - + -
104A TYR* 6.2 0.2 - - + -
111A VAL* 4.7 9.9 - - + -
115A GLU* 2.9 23.4 + - + +
116A ALA 3.9 2.7 - - - +
118A ARG* 1.3 85.9 - - - +
120A PHE* 1.3 58.7 + - - +
122A GLN* 3.2 18.3 + - - +
123A ILE* 3.0 38.4 + - + +
147A LEU* 4.1 9.0 - - + -
151A MET* 3.5 40.2 - - + +
153A ALA* 3.9 13.0 - - + +
207A LEU* 3.9 29.4 - - + -
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Residues in contact with PHE 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 ALA 2.9 18.5 + - - +
117A ARG* 3.2 4.5 + - - +
119A LEU* 1.3 74.4 - - - +
121A GLN* 1.3 60.3 + - - +
123A ILE* 3.3 10.0 + - + -
124A LEU* 2.8 43.4 + - + +
200A CYS* 3.4 33.7 - - + -
203A ILE* 5.0 5.2 - - + -
204A LEU* 3.9 42.2 - - + -
207A LEU* 4.4 5.8 - - + -
244A LEU* 4.8 2.0 - - + -
248A MET* 3.6 26.2 - - + -
262A ILE* 4.0 9.6 - - + -
267A TRP* 4.5 4.9 - + - -
268A PHE* 3.5 33.7 - + - -
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Residues in contact with GLN 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 ARG* 2.9 31.8 + - + +
118A ARG* 3.7 13.2 - - - +
120A PHE* 1.3 75.9 - - - +
122A GLN* 1.3 57.1 + - - +
124A LEU* 3.6 0.5 + - - -
125A SER* 3.0 30.0 + - - -
268A PHE* 2.8 50.6 + - + +
270A GLN 3.0 21.4 + - - -
271A ASP* 3.9 3.6 - - - +
272A LEU* 3.6 19.4 - - + +
273A PRO* 3.6 16.3 - - - +
276A LEU* 3.9 16.4 - - + +
277A PHE* 4.1 4.2 - - - -
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Residues in contact with GLN 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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75A HIS* 3.4 39.7 + - + +
118A ARG* 3.3 29.5 + - + +
119A LEU* 3.2 11.6 + - - +
120A PHE 3.2 0.4 - - - -
121A GLN* 1.3 77.6 - - - +
123A ILE* 1.3 57.4 - - - +
125A SER* 3.4 3.6 + - - -
126A ALA* 3.0 28.2 + - - +
152A ASN* 2.9 28.6 - - - +
153A ALA* 2.9 32.2 + - + +
275A TYR* 4.4 7.5 + - - +
276A LEU* 4.1 13.0 - - + -
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Residues in contact with ILE 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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75A HIS* 5.8 0.2 - - - -
101A LEU* 3.9 11.0 - - + -
119A LEU* 3.0 26.9 + - + +
120A PHE* 3.7 10.1 - - + +
122A GLN* 1.3 73.9 - - - +
124A LEU* 1.3 66.0 + - - +
126A ALA* 3.1 8.0 + - - +
127A VAL* 2.9 34.0 + - + +
140A LEU* 4.9 0.7 - - + -
145A VAL* 3.7 21.8 - - + -
153A ALA* 3.6 19.1 - - + -
155A ILE* 4.5 12.3 - - + -
200A CYS* 4.6 6.5 - - - -
203A ILE* 3.7 40.6 - - + -
207A LEU* 4.5 2.0 - - + -
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Residues in contact with LEU 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 PHE* 2.8 30.9 + - + +
121A GLN 4.1 2.9 - - - +
123A ILE* 1.3 74.7 - - - +
125A SER* 1.3 56.8 + - - +
127A VAL* 3.3 4.8 + - + +
128A ASP* 2.9 28.8 + - - +
197A ILE* 4.7 2.7 - - + -
200A CYS* 4.0 24.0 - - + -
259A ILE* 4.1 32.3 - - + +
262A ILE* 3.4 52.0 - - + -
268A PHE* 3.6 20.4 - - + -
277A PHE* 4.0 5.2 - - + -
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Residues in contact with SER 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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73A HIS* 2.7 27.4 + - - -
121A GLN 3.0 11.7 + - - -
122A GLN 3.6 2.5 - - - -
123A ILE 3.2 0.2 - - - -
124A LEU* 1.3 76.5 - - - +
126A ALA* 1.3 58.1 + - - +
128A ASP* 3.3 3.1 + - - +
129A TYR* 2.9 24.4 + - - +
276A LEU* 2.6 55.5 + - - +
277A PHE* 3.6 13.4 - - - -
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Residues in contact with ALA 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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73A HIS* 3.5 15.2 - - + -
75A HIS* 3.9 6.7 - - + +
76A ILE* 3.6 23.3 - - + +
122A GLN 3.0 13.2 + - - +
123A ILE* 3.1 9.4 + - - +
125A SER* 1.3 78.3 + - - +
127A VAL* 1.3 55.1 + - - +
129A TYR* 3.3 3.5 + - - +
130A CYS* 3.0 32.7 + - - -
155A ILE* 3.9 19.1 - - + -
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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 ILE* 2.9 22.3 + - + +
124A LEU* 3.7 6.3 - - - +
126A ALA* 1.3 73.6 - - + +
128A ASP* 1.3 67.0 + - - +
130A CYS* 3.1 10.6 + - + +
131A HIS* 3.0 52.3 + - + +
140A LEU* 3.7 36.3 - - + -
155A ILE* 5.5 2.7 - - + -
196A ASP* 4.2 13.0 - - + +
197A ILE* 5.6 1.3 - - + -
200A CYS* 4.0 13.7 - - - -
259A ILE* 4.1 7.0 - - + -
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Residues in contact with ASP 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 17.8 + - - +
125A SER 3.5 5.1 - - - +
127A VAL* 1.3 76.2 - - - +
129A TYR* 1.3 64.3 + - - +
131A HIS* 3.4 4.6 + - - +
132A ARG* 2.6 70.3 + - - +
259A ILE* 3.5 37.2 - - + +
276A LEU 5.5 0.3 - - - +
277A PHE* 4.0 18.9 - - + +
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Residues in contact with TYR 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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70A LEU 3.7 10.2 + - - -
71A PHE* 3.7 37.0 - + - -
72A ARG* 3.2 37.0 + - - +
73A HIS* 3.5 34.3 - + + -
76A ILE* 4.1 5.6 - - + -
125A SER 2.9 7.9 + - - +
126A ALA 3.5 7.2 - - - +
127A VAL 3.2 0.2 - - - -
128A ASP* 1.3 80.4 + - - +
130A CYS* 1.3 56.4 + - - +
132A ARG* 3.2 3.6 + - - +
133A HIS* 2.8 75.7 + + + +
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Residues in contact with CYS 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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71A PHE* 4.0 13.5 - - - -
76A ILE* 3.7 20.0 - - - -
126A ALA 3.0 19.9 + - - -
127A VAL* 3.4 11.7 - - + +
129A TYR* 1.3 73.8 - - - +
131A HIS* 1.3 65.9 + - + +
134A MET* 2.7 62.0 + - + +
155A ILE* 5.6 9.4 - - - -
196A ASP* 6.0 0.2 - - - +
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Residues in contact with HIS 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* 3.0 38.9 + - + +
128A ASP* 3.9 6.3 - - - +
130A CYS* 1.3 80.5 - - + +
132A ARG* 1.3 62.5 + - + +
134A MET* 4.4 7.9 - - + +
137A HIS* 4.4 9.9 - - - -
193A PRO* 3.7 47.5 - - + +
196A ASP* 2.7 29.2 + - + -
197A ILE* 4.9 2.2 - - + -
259A ILE* 3.9 18.5 - - + +
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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 ASP* 2.6 50.1 + - - +
129A TYR* 4.8 1.6 - - - +
130A CYS 3.1 0.6 - - - -
131A HIS* 1.3 81.1 - - + +
133A HIS* 1.3 87.0 + - + +
134A MET 5.1 0.4 - - - -
263A ARG* 3.9 21.6 - - - +
277A PHE* 6.1 0.2 - - - +
278A PRO 5.2 9.5 + - - -
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Residues in contact with HIS 133 (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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67A ASN* 3.2 16.6 - - - +
70A LEU* 5.6 1.2 - - - +
71A PHE* 3.8 9.4 - - + -
129A TYR* 2.8 73.4 + + + +
132A ARG* 1.3 105.9 - - + +
134A MET* 1.3 62.6 + - - +
135A VAL* 3.4 7.0 + - - +
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Residues in contact with MET 134 (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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67A ASN* 3.4 13.7 - - - +
71A PHE* 3.9 14.2 - - + -
130A CYS* 2.7 52.7 + - + +
131A HIS* 4.4 8.4 - - + +
132A ARG 5.1 0.3 - - - -
133A HIS* 1.3 72.3 - - - +
135A VAL* 1.3 66.6 + - - +
136A VAL 3.1 24.2 - - - +
137A HIS* 3.8 15.5 + - - +
138A ARG* 3.3 53.8 - - - +
196A ASP* 5.8 0.4 - - - +
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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