Contacts of the helix formed by residues 119 - 140 (chain A) in PDB entry 5DH3
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 ILE 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 6.3 0.7 - - - +
117A THR 4.7 4.5 - - - +
118A LEU* 1.3 76.3 - - - +
120A GLU* 1.3 64.2 + - - +
121A ASP* 4.1 23.6 - - + +
122A GLU* 2.7 45.1 + - + +
123A ILE* 3.0 12.3 + - - +
247A TRP* 5.5 2.7 - - - -
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Residues in contact with GLU 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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119A ILE* 1.3 75.2 - - - +
121A ASP* 1.3 61.2 + - - +
123A ILE* 3.2 9.0 + - + +
124A ALA* 2.9 31.2 + - - +
246A LEU 4.5 1.6 - - - +
247A TRP* 3.6 23.2 - - + -
248A SER* 2.8 51.8 + - - -
251A PHE* 3.7 30.5 - - + +
277A PHE* 3.8 12.0 - - + -
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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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119A ILE* 3.1 18.1 + - + +
120A GLU* 1.3 84.9 - - - +
122A GLU* 1.3 60.4 + - + +
124A ALA* 3.5 5.3 + - - +
125A THR* 3.1 27.2 + - - -
282A LYS* 2.5 47.5 + - + +
286A ILE* 3.6 13.4 - - + +
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Residues in contact with GLU 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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114A ARG* 4.3 8.2 + - - -
117A THR 4.7 0.3 - - - +
118A LEU* 3.3 20.4 - - + +
119A ILE* 2.7 50.4 + - + +
121A ASP* 1.3 74.2 - - + +
123A ILE* 1.3 65.6 + - - +
125A THR* 3.4 2.6 + - - -
126A ILE* 3.1 30.0 + - - +
286A ILE* 4.3 11.1 - - + +
287A LEU* 4.0 25.3 - - + +
290A LEU* 4.1 29.0 - - + +
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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
----------------------------------------------------------
118A LEU* 3.6 38.6 - - + +
119A ILE 3.0 12.9 + - - +
120A GLU* 3.6 10.3 - - - +
122A GLU* 1.3 77.0 - - - +
124A ALA* 1.3 57.8 + - - +
126A ILE* 3.5 2.4 + - - +
127A LEU* 2.9 52.5 + - + +
211A SER 5.0 0.9 - - - +
214A MET* 3.8 21.3 - - + -
215A ALA* 3.8 29.8 - - + +
247A TRP* 5.0 1.6 - - + -
251A PHE* 4.0 23.3 - - + -
277A PHE* 4.0 1.8 - - + -
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Residues in contact with ALA 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 GLU 2.9 13.2 + - - +
121A ASP* 3.9 5.8 - - - +
123A ILE* 1.3 78.2 - - - +
125A THR* 1.3 62.3 + - - +
127A LEU* 3.9 1.9 - - - +
128A LYS* 3.0 25.3 + - - +
277A PHE* 3.5 41.1 - - + +
278A ILE* 4.1 2.1 - - - +
281A ALA* 3.6 21.9 - - + +
282A LYS 5.4 0.2 - - - +
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Residues in contact with THR 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 17.5 + - - -
122A GLU 4.0 3.1 - - - -
123A ILE 3.3 0.2 - - - -
124A ALA* 1.3 79.5 - - - +
126A ILE* 1.3 61.0 + - - +
128A LYS* 3.5 4.9 + - + +
129A SER* 3.4 18.4 + - - -
281A ALA* 4.1 4.7 - - - -
282A LYS 2.5 39.5 + - - +
283A PRO* 3.5 18.2 - - + +
284A VAL* 3.9 14.7 - - + +
286A ILE* 3.5 12.2 - - + +
287A LEU* 4.7 8.5 - - + -
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Residues in contact with ILE 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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107A VAL* 4.1 26.7 - - + -
118A LEU* 3.5 32.3 - - + -
122A GLU 3.1 15.4 + - - +
123A ILE* 3.9 2.9 - - - +
125A THR* 1.3 76.1 - - - +
127A LEU* 1.3 63.0 + - - +
129A SER* 3.2 8.4 + - - -
130A THR* 2.9 32.9 + - - +
152A ILE* 4.4 8.5 - - + -
154A LEU* 4.5 11.9 - - + -
160A ALA* 4.3 6.4 - - + +
214A MET* 4.4 11.9 - - + -
287A LEU* 3.7 30.1 - - + -
290A LEU* 5.3 2.9 - - + -
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Residues in contact with LEU 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 40.4 + - + +
124A ALA 3.9 3.1 - - - +
126A ILE* 1.3 76.8 - - + +
128A LYS* 1.3 57.9 + - - +
130A THR* 3.2 7.1 + - + +
131A LEU* 2.8 35.4 + - + +
152A ILE* 5.6 1.1 - - + -
207A LEU* 3.8 30.9 - - + +
210A THR* 4.9 2.7 - - + -
211A SER* 3.2 25.4 - - - +
214A MET* 3.1 23.1 - - + -
254A PHE* 3.6 20.9 - - + -
277A PHE* 4.0 7.2 - - + -
278A ILE* 4.2 9.0 - - + -
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Residues in contact with LYS 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 ALA 3.0 17.5 + - - +
125A THR* 3.7 6.1 - - + +
126A ILE 3.2 0.4 - - - -
127A LEU* 1.3 77.7 - - - +
129A SER* 1.3 64.1 + - - +
131A LEU* 3.3 4.7 + - - +
132A LYS* 3.2 37.7 + - - +
273A LEU* 3.8 5.2 - - + +
278A ILE* 3.6 43.9 + - + +
279A LYS* 4.9 6.3 + - - +
281A ALA* 4.4 15.3 + - + +
402A CL 3.8 26.9 - - - +
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Residues in contact with SER 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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81A TYR* 3.6 25.2 - - - +
125A THR 3.4 8.6 + - - -
126A ILE* 3.2 9.5 + - - -
128A LYS* 1.3 80.3 - - - +
130A THR* 1.3 63.1 + - - +
132A LYS* 3.3 8.2 + - - +
133A GLY 3.1 17.0 + - - -
159A HIS* 4.6 10.9 - - - -
160A ALA* 3.8 31.4 + - - -
284A VAL* 5.3 5.7 - - - +
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Residues in contact with THR 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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81A TYR* 5.9 0.2 - - - -
126A ILE* 2.9 24.3 + - - +
127A LEU* 3.4 11.0 - - - -
129A SER* 1.3 76.2 - - - +
131A LEU* 1.3 58.3 + - - +
133A GLY* 3.1 3.1 + - - -
134A LEU* 2.8 32.4 + - + +
147A ILE* 5.0 2.0 - - + -
152A ILE* 4.1 23.5 - - + +
160A ALA* 4.4 5.3 - - - +
161A LYS 6.4 0.2 - - - -
162A LEU* 3.7 27.6 - - + +
207A LEU* 3.9 24.2 - - + -
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Residues in contact with LEU 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 LEU 2.8 18.8 + - - +
128A LYS 3.6 0.7 - - - +
130A THR* 1.3 74.3 - - - +
132A LYS* 1.3 60.3 + - - +
134A LEU* 3.6 4.9 - - + +
135A GLU* 2.7 31.5 + - - +
204A ILE* 4.4 3.8 - - + -
207A LEU* 3.5 25.8 - - + -
254A PHE* 4.1 9.0 - - + -
269A ALA* 3.9 21.3 - - + +
272A LEU* 3.8 33.4 - - + -
273A LEU* 3.6 22.8 - - + +
278A ILE* 3.6 33.0 - - + -
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Residues in contact with LYS 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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81A TYR* 3.6 43.3 + - + +
128A LYS* 3.2 30.6 + - - +
129A SER* 3.5 10.5 - - - +
130A THR 3.2 0.2 - - - -
131A LEU* 1.3 75.3 - - - +
133A GLY* 1.3 61.8 + - - +
135A GLU* 3.4 16.3 + - - +
136A TYR* 3.1 21.7 + - - +
273A LEU* 4.0 17.5 - - + -
402A CL 3.1 31.8 - - - +
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Residues in contact with GLY 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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81A TYR* 3.3 27.0 - - - +
82A VAL* 4.6 2.5 - - - +
129A SER 3.1 11.3 + - - -
130A THR* 3.1 4.2 + - - -
132A LYS* 1.3 74.9 - - - +
134A LEU* 1.3 62.9 + - - +
136A TYR* 3.2 7.1 + - - +
137A LEU* 3.0 25.1 + - - +
162A LEU* 3.7 13.9 - - - +
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Residues in contact with LEU 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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130A THR* 2.8 22.1 + - + +
131A LEU* 3.2 7.4 + - + +
133A GLY* 1.3 69.9 - - - +
135A GLU* 1.3 60.8 + - - +
137A LEU* 3.2 5.4 + - + +
138A HIS* 2.8 46.3 + - + +
147A ILE* 3.6 28.7 - - + -
162A LEU* 3.8 11.0 - - + +
203A ASP* 3.9 25.8 - - + +
204A ILE* 4.2 14.4 - - + -
207A LEU* 4.1 38.1 - - + -
269A ALA* 4.3 8.1 - - + -
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Residues in contact with GLU 135 (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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131A LEU 2.7 16.9 + - - +
132A LYS* 3.4 14.6 - - - +
134A LEU* 1.3 78.6 - - - +
136A TYR* 1.3 56.4 + - - +
138A HIS* 3.8 3.7 - - - +
139A PHE* 2.9 30.6 + - + +
269A ALA* 4.0 11.8 - - + +
270A THR* 3.8 34.2 - - - +
273A LEU* 3.6 24.9 - - + +
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Residues in contact with TYR 136 (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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76A GLN 4.2 2.6 + - - -
77A CYS* 3.9 16.0 - - + -
78A ASP* 3.0 38.4 + - - +
79A SER* 3.7 36.1 - - - +
81A TYR* 5.4 0.4 - - + -
82A VAL* 4.2 9.2 - - + -
132A LYS 3.1 13.2 + - - +
133A GLY* 3.5 9.2 - - - +
134A LEU 3.2 0.2 - - - -
135A GLU* 1.3 75.0 + - - +
137A LEU* 1.3 69.1 + - - +
139A PHE* 3.3 9.6 + + - +
140A MET* 3.0 66.2 + - + +
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Residues in contact with LEU 137 (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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77A CYS* 3.5 31.2 - - - -
82A VAL* 4.5 7.0 - - + -
133A GLY 3.0 13.8 + - - +
134A LEU* 3.6 9.4 - - + +
136A TYR* 1.3 77.3 - - + +
138A HIS* 1.3 60.4 + - + +
140A MET* 2.9 20.9 + - + +
141A ARG 3.0 9.2 + - - -
142A LYS* 3.0 33.1 + - + +
144A HIS* 4.1 24.2 - - + +
162A LEU* 3.6 25.8 - - + -
165A PHE* 3.8 26.2 - - + -
203A ASP* 5.2 0.2 - - - +
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Residues in contact with HIS 138 (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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134A LEU* 2.8 34.7 + - + +
135A GLU* 3.9 4.9 - - - +
137A LEU* 1.3 77.7 - - + +
139A PHE* 1.3 60.6 + - - +
140A MET 3.0 1.1 - - - -
141A ARG* 2.9 21.1 + - - +
142A LYS 3.5 17.3 - - - -
200A CYS* 3.3 43.5 + - + +
201A VAL* 5.0 0.2 - - - -
203A ASP* 3.1 30.8 + - + +
204A ILE* 4.4 14.1 - - + +
269A ALA* 4.3 11.8 + - + +
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Residues in contact with PHE 139 (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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135A GLU* 2.9 19.0 + - + +
136A TYR* 3.5 10.5 - + - +
138A HIS* 1.3 76.3 - - - +
140A MET* 1.3 88.8 + - + +
141A ARG* 3.1 14.4 + - - +
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Residues in contact with MET 140 (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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76A GLN* 5.3 7.0 - - - +
77A CYS* 5.4 2.9 - - - -
136A TYR* 3.0 54.1 - - + +
137A LEU* 2.9 11.3 + - - +
139A PHE* 1.3 109.2 - - + +
141A ARG* 1.3 72.8 + - - +
142A LYS* 3.4 32.7 + - + +
170A GLN* 4.1 2.8 + - - -
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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