Contacts of the helix formed by residues 112 - 133 (chain A) in PDB entry 1WVY
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 THR 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A SER* 4.0 5.5 + - - -
111A LEU* 1.3 76.6 - - - +
113A GLU* 1.3 69.0 + - + +
114A GLU* 2.9 33.4 - - + +
115A GLU* 2.9 43.8 + - + +
116A ALA* 3.1 9.0 + - - +
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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
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111A LEU 3.4 3.0 + - - -
112A THR* 1.3 75.2 - - + +
114A GLU* 1.3 62.3 - - + +
116A ALA* 3.8 6.5 + - - +
117A THR* 2.9 24.8 + - - -
211A LEU* 4.3 12.5 - - + +
243A ASN 3.5 8.1 - - - +
244A THR* 3.2 15.5 + - - +
245A SER* 2.6 51.3 + - - -
248A ALA* 3.5 8.5 - - - +
274A TRP* 3.2 24.7 + - + +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 2.9 15.7 - - + +
113A GLU* 1.3 81.8 - - + +
115A GLU* 1.3 65.8 + - + +
116A ALA 3.0 3.2 + - - -
117A THR* 3.2 16.1 + - - -
118A GLU* 3.3 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
----------------------------------------------------------
108A LYS* 5.5 4.3 - - - -
110A SER* 4.4 6.8 + - - +
111A LEU* 3.4 25.8 - - + +
112A THR* 2.9 37.8 + - + +
114A GLU* 1.3 77.3 - - + +
116A ALA* 1.3 57.1 + - - +
118A GLU* 3.8 14.6 - - - +
119A PHE* 3.3 24.5 - - + -
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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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105A LEU* 5.1 0.2 - - + -
111A LEU* 3.2 19.3 - - + +
112A THR 3.1 7.9 + - - +
113A GLU* 4.0 6.1 - - - +
114A GLU 3.0 0.6 - - - -
115A GLU* 1.3 76.0 - - - +
117A THR* 1.3 59.6 + - - +
118A GLU 3.0 2.2 - - - -
119A PHE* 2.8 26.8 + - - +
120A LEU* 2.9 12.3 + - - +
210A LEU* 4.0 33.0 - - + +
211A LEU* 4.3 10.3 - - + -
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Residues in contact with THR 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 2.9 15.7 + - - -
114A GLU* 3.2 12.5 + - - -
116A ALA* 1.3 78.4 - - - +
118A GLU* 1.3 57.6 + - - +
120A LEU* 3.7 8.1 - - - -
121A LYS* 2.8 46.1 + - - +
274A TRP* 3.3 32.3 + - + +
275A ILE* 3.8 27.4 - - + -
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Residues in contact with GLU 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 GLU 3.3 8.8 + - - +
115A GLU* 3.8 16.6 - - - +
116A ALA 3.0 0.6 - - - -
117A THR* 1.3 79.8 - - - +
119A PHE* 1.3 63.8 + - + +
121A LYS* 3.4 13.9 - - + +
122A GLN* 3.4 24.3 + - - +
154A LYS* 3.3 34.5 + - - +
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Residues in contact with PHE 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* 3.5 38.4 - - + -
104A PHE* 3.8 25.6 - + - -
105A LEU* 4.2 20.4 - - + -
108A LYS* 5.9 1.3 - - + -
111A LEU* 5.2 7.2 - - + -
115A GLU* 3.3 27.4 - - + -
116A ALA* 2.8 10.6 + - - +
118A GLU* 1.3 77.1 - - + +
120A LEU* 1.3 65.0 + - - +
121A LYS 3.0 1.3 - - - -
122A GLN* 3.0 23.4 + - - +
123A ILE* 3.2 16.8 + - - +
147A LEU* 4.5 1.6 - - + -
155A PRO* 4.0 31.4 - - + -
157A ILE* 4.0 10.0 - - + +
210A LEU* 5.5 2.2 - - + -
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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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116A ALA 2.9 13.2 + - - +
117A THR* 3.9 9.0 - - - +
119A PHE* 1.3 77.4 - - - +
121A LYS* 1.3 57.6 + - - +
123A ILE* 3.3 27.9 + - + -
124A LEU* 2.9 58.6 + - + +
203A ILE* 4.7 5.2 - - + -
206A ILE* 5.1 3.8 - - + -
207A THR* 3.3 37.7 - - + +
210A LEU* 3.9 16.8 - - + +
251A PHE* 4.0 13.2 - - + -
274A TRP* 4.4 4.7 - - + -
275A ILE* 4.4 7.9 - - + -
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Residues in contact with LYS 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 THR* 2.8 36.2 + - + +
118A GLU* 3.4 15.3 - - + +
120A LEU* 1.3 77.1 - - - +
122A GLN* 1.3 62.6 + - - +
124A LEU* 3.2 10.7 + - - +
125A ASN* 3.0 35.0 + - - +
270A LEU* 5.4 4.5 - - + -
275A ILE* 3.2 45.6 + - + +
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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 ASN* 3.1 20.6 + - - +
118A GLU* 3.4 14.6 + - - +
119A PHE* 3.0 17.4 + - - +
121A LYS* 1.3 78.7 - - + +
123A ILE* 1.3 66.2 + - - +
125A ASN* 3.0 21.8 + - - +
126A GLY 3.1 9.0 + - - -
154A LYS* 5.1 2.6 + - - +
155A PRO 2.8 27.3 + - - -
156A ARG* 3.2 14.4 - - - +
157A ILE* 3.0 42.4 + - + +
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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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101A LEU* 4.3 13.0 - - + -
102A PHE* 5.8 0.2 - - + -
119A PHE 3.2 10.6 + - - +
120A LEU* 3.6 30.1 - - + +
121A LYS 3.3 0.2 - - - -
122A GLN* 1.3 77.1 - - - +
124A LEU* 1.3 66.8 + - + +
125A ASN 2.9 1.2 + - - -
126A GLY* 3.0 12.1 + - - -
127A VAL* 3.0 29.0 + - + +
140A LEU* 5.7 2.7 - - + -
145A ILE* 3.6 39.9 - - + -
157A ILE* 4.0 21.7 - - + +
159A ILE* 4.6 6.8 - - + +
203A ILE* 4.7 11.2 - - + -
206A ILE* 4.5 12.1 - - + -
210A LEU* 6.1 1.1 - - + -
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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 LEU* 2.9 39.3 + - + +
121A LYS* 3.5 8.7 - - - +
123A ILE* 1.3 77.0 - - + +
125A ASN* 1.3 51.6 + - - +
127A VAL* 3.4 1.5 + - - -
128A TYR* 2.7 36.7 + - - +
203A ILE* 3.8 38.8 - - + -
251A PHE* 4.4 4.9 - - + -
266A ILE* 3.5 8.7 - - + +
269A SER* 4.0 20.2 - - - +
270A LEU* 3.7 26.9 - - + -
275A ILE* 4.2 23.8 - - + -
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Residues in contact with ASN 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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73A HIS* 4.4 10.1 + - + +
75A ASN* 3.8 12.2 - - - +
121A LYS* 3.0 29.2 + - - +
122A GLN* 3.0 13.7 + - - +
124A LEU* 1.3 73.7 - - - +
126A GLY* 1.3 57.8 + - - +
128A TYR* 2.8 13.1 + - + +
129A TYR* 2.7 34.7 + - - +
270A LEU* 4.4 16.2 - - - +
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Residues in contact with GLY 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* 4.5 3.6 - - - -
75A ASN* 3.9 21.1 - - - +
76A VAL* 4.6 4.5 - - - -
122A GLN 3.1 4.2 + - - -
123A ILE 3.0 6.2 + - - -
125A ASN* 1.3 78.2 - - - +
127A VAL* 1.3 62.3 + - - +
129A TYR* 3.3 8.0 + - - +
130A LEU* 2.9 27.5 + - - +
159A ILE* 4.3 14.1 - - - -
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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* 3.0 25.9 + - + +
124A LEU 3.7 5.2 - - - +
126A GLY* 1.3 75.3 - - - +
128A TYR* 1.3 53.2 + - - +
130A LEU* 3.2 8.9 + - + +
131A HIS* 2.7 69.4 + - + +
137A HIS* 6.2 0.4 - - + -
140A LEU* 4.1 21.3 - - + -
159A ILE* 4.3 10.0 - - + +
199A ASP* 4.5 1.1 - - + +
203A ILE* 3.9 22.4 - - + -
266A ILE* 3.9 13.2 - - + -
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Residues in contact with TYR 128 (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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124A LEU 2.7 19.6 + - - +
125A ASN* 2.8 18.8 + - - +
127A VAL* 1.3 73.2 - - - +
129A TYR* 1.3 62.6 + - - -
131A HIS* 3.8 0.5 - - - -
132A SER* 2.8 41.1 + - - -
266A ILE* 3.4 33.0 - - + +
267A GLN* 3.2 34.5 + - + -
270A LEU* 3.8 21.1 - - + -
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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 GLU 3.9 5.0 + - - -
71A ILE* 3.4 24.4 - - + -
72A GLN* 3.0 43.5 + - - +
73A HIS* 3.4 41.7 - + + +
76A VAL* 4.7 2.2 - - + -
125A ASN 2.7 11.0 + - - +
126A GLY 3.4 7.2 - - - +
128A TYR* 1.3 74.8 - - - +
130A LEU* 1.3 85.2 + - + +
132A SER* 2.9 24.0 + - - -
133A LEU* 3.2 35.4 + - + +
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Residues in contact with LEU 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 ILE* 3.6 31.9 - - + -
76A VAL* 4.2 9.0 - - + -
126A GLY 2.9 17.2 + - - +
127A VAL* 3.5 10.8 - - + +
129A TYR* 1.3 87.9 - - + +
131A HIS* 1.3 62.0 + - + +
133A LEU* 3.1 9.8 + - - -
135A ILE* 2.9 48.3 + - + +
137A HIS* 4.3 18.8 - - + -
159A ILE* 4.5 7.0 - - + -
162A PHE* 3.7 35.0 - - + -
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Residues in contact with HIS 131 (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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127A VAL* 2.7 43.0 + - + +
128A TYR 3.8 2.9 - - - +
130A LEU* 1.3 74.3 - - + +
132A SER* 1.3 55.6 + - - +
134A GLN* 2.6 36.8 + - - +
135A ILE 3.4 18.2 - - - +
196A LEU* 3.5 49.9 + - + +
199A ASP* 3.2 22.3 + - + +
200A MET* 3.8 16.6 - - + -
266A ILE* 3.8 26.3 + - + +
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Residues in contact with SER 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 TYR* 2.8 41.2 + - - -
129A TYR* 2.9 12.2 + - - -
131A HIS* 1.3 75.8 - - - +
133A LEU* 1.3 67.6 + - - +
134A GLN* 3.1 11.5 + - - +
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Residues in contact with LEU 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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70A GLU* 3.6 26.0 - - + +
71A ILE* 6.1 0.7 - - + -
129A TYR* 3.3 47.6 - - + +
130A LEU* 3.1 9.0 + - - +
132A SER* 1.3 82.6 - - - +
134A GLN* 1.3 63.1 + - - +
135A ILE* 3.2 11.2 + - + -
167A LYS* 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
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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