Contacts of the helix formed by residues 118 - 142 (chain A) in PDB entry 1HNA
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 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASP* 3.0 16.7 + - - +
117A PRO* 1.3 82.8 - - + +
119A PHE* 1.3 63.3 + - - +
120A GLU* 3.2 4.9 - - - +
121A LYS* 3.1 49.3 + - + +
122A LEU* 3.8 7.7 + - + +
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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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113A LEU* 3.3 41.1 - - + -
116A ASP* 3.3 9.5 + - + +
117A PRO 3.1 7.0 + - - +
118A ASP* 1.3 73.9 - - - +
120A GLU* 1.3 64.8 + - - +
121A LYS 3.0 1.0 + - - -
122A LEU* 3.2 4.7 + - - +
123A LYS* 3.0 47.5 + - + +
169A PHE* 4.0 24.7 - + - -
213A VAL* 3.5 32.8 - - + -
214A PHE* 4.6 17.9 - + + -
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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
----------------------------------------------------------
118A ASP* 4.8 3.8 - - + -
119A PHE* 1.3 82.7 - - - +
121A LYS* 1.3 63.8 + - + +
123A LYS* 4.7 3.9 - - - +
124A PRO* 3.6 15.8 - - - +
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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
----------------------------------------------------------
118A ASP* 3.1 42.3 + - + +
119A PHE 3.0 0.2 + - - -
120A GLU* 1.3 83.6 - - + +
122A LEU* 1.3 70.1 + - + +
124A PRO* 3.4 16.3 - - - +
125A GLU* 4.2 9.9 - - - +
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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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112A LYS* 4.0 21.3 - - - +
113A LEU* 3.1 38.5 - - + +
116A ASP* 4.6 8.1 - - - +
118A ASP* 3.9 14.6 - - + +
119A PHE 3.2 3.3 + - - +
121A LYS* 1.3 89.5 - - + +
123A LYS* 1.3 67.1 + - - +
124A PRO 3.3 0.9 - - - -
125A GLU* 2.9 20.1 + - + +
126A TYR 3.0 9.7 + - - -
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Residues in contact with LYS 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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113A LEU* 3.4 11.3 - - - +
119A PHE* 3.0 32.9 + - + +
120A GLU* 4.7 4.3 - - - +
122A LEU* 1.3 73.1 - - - +
124A PRO* 1.3 89.1 - - + +
125A GLU 3.0 1.7 + - - -
126A TYR* 3.0 12.9 + - - +
127A LEU* 3.0 30.7 + - + +
169A PHE* 3.7 27.1 - - + -
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Residues in contact with PRO 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 3.6 11.0 - - - +
121A LYS 3.4 19.5 - - - +
123A LYS* 1.3 113.2 - - + +
125A GLU* 1.3 67.9 + - - +
127A LEU* 3.7 10.3 - - + +
128A GLN* 3.2 27.0 + - - +
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Residues in contact with GLU 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 LYS 4.2 9.5 - - - +
122A LEU* 2.9 14.5 + - + +
124A PRO* 1.3 88.1 - - - +
126A TYR* 1.3 66.6 + - - +
127A LEU 3.1 1.6 - - - -
128A GLN* 2.6 51.7 + - - +
129A ALA* 3.3 7.1 + - - +
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Residues in contact with TYR 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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106A SER 4.7 1.6 + - - -
109A GLN* 4.0 48.5 - - + -
110A LEU* 3.8 22.0 + - + +
113A LEU* 3.5 28.0 - - + -
122A LEU 3.0 4.8 + - - -
123A LYS* 3.0 5.5 + - - +
125A GLU* 1.3 75.8 - - - +
127A LEU* 1.3 56.6 + - - +
129A ALA* 3.1 9.4 + - + +
130A LEU* 2.9 45.0 + - + +
133A MET* 4.2 7.3 - - - -
166A ASN* 2.9 37.3 + - - -
169A PHE* 3.6 30.1 - + - -
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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 LYS* 3.0 44.6 + - + +
124A PRO* 3.7 9.4 - - + +
125A GLU 3.1 0.2 - - - -
126A TYR* 1.3 78.7 - - - +
128A GLN* 1.3 56.8 + - - +
130A LEU* 3.8 11.8 - - + +
131A PRO* 3.1 23.4 - - - +
169A PHE* 3.2 30.3 - - + -
170A GLU* 3.9 31.6 - - + +
173A CYS* 4.5 6.2 - - - -
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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 PRO* 3.2 14.4 + - - +
125A GLU* 2.6 48.6 + - - +
127A LEU* 1.3 78.7 - - - +
129A ALA* 1.3 58.8 + - - +
130A LEU 3.5 0.2 - - - -
131A PRO* 3.7 9.7 - - - +
132A GLU* 5.1 1.7 + - - +
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Residues in contact with ALA 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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109A GLN* 5.2 12.3 - - - +
125A GLU 3.3 6.1 + - - +
126A TYR* 3.1 11.7 + - + +
128A GLN* 1.3 78.3 - - - +
130A LEU* 1.3 66.2 + - - +
131A PRO 3.4 0.9 - - - -
132A GLU* 3.1 20.5 + - - +
133A MET* 3.3 12.0 + - - +
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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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126A TYR* 2.9 31.7 + - + +
127A LEU* 3.8 8.3 - - + +
129A ALA* 1.3 76.4 - - - +
131A PRO* 1.3 68.9 - - + +
133A MET* 3.2 38.6 + - + +
134A LEU* 2.9 35.1 + - + +
166A ASN* 3.7 31.4 - - + +
169A PHE* 4.3 12.1 - - + -
170A GLU* 5.1 0.9 - - + -
173A CYS* 3.9 26.7 - - + -
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Residues in contact with PRO 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 3.1 19.1 - - - +
128A GLN* 3.7 9.0 - - - +
129A ALA 3.6 3.1 - - - -
130A LEU* 1.3 90.0 - - + +
132A GLU* 1.3 55.9 + - - +
134A LEU* 3.4 2.6 + - + -
135A LYS* 2.8 35.0 + - - +
173A CYS* 5.3 9.6 - - + -
177A PHE* 3.6 17.9 - - + -
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Residues in contact with GLU 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 5.1 1.1 + - - +
129A ALA* 3.1 14.6 + - - +
131A PRO* 1.3 78.6 - - - +
133A MET* 1.3 62.7 + - - +
135A LYS* 3.4 14.2 + - - +
136A LEU* 3.2 48.9 + - + +
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Residues in contact with MET 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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102A GLN* 6.1 0.9 - - - +
106A SER* 3.8 32.8 - - - +
109A GLN* 4.7 16.8 - - - +
126A TYR* 4.2 8.1 - - - +
129A ALA 3.3 8.8 + - - +
130A LEU* 3.2 29.5 + - + +
132A GLU* 1.3 81.5 - - - +
134A LEU* 1.3 76.3 + - + +
136A LEU* 3.5 8.7 + - - +
137A TYR* 3.2 43.4 + - + -
162A VAL* 5.3 4.3 - - + -
163A LEU* 5.3 1.6 - - + -
166A ASN* 3.4 25.4 - - - +
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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 LEU* 2.9 24.5 + - + +
131A PRO* 3.8 0.7 - - + +
133A MET* 1.3 99.8 - - + +
135A LYS* 1.3 61.1 + - - +
137A TYR* 3.2 3.4 + - + -
138A SER* 2.8 29.8 + - - -
163A LEU* 4.2 18.8 - - + -
166A ASN* 5.0 3.1 - - + +
173A CYS* 3.7 43.1 - - + +
174A LEU* 4.0 14.4 - - + -
177A PHE* 3.4 19.5 - - + -
180A LEU* 3.5 18.2 - - + +
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Residues in contact with LYS 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 PRO* 2.8 20.9 + - - +
132A GLU* 3.6 13.9 - - - +
133A MET 3.3 0.2 - - - -
134A LEU* 1.3 76.8 - - - +
136A LEU* 1.3 62.9 + - + +
138A SER* 3.6 1.7 - - - -
139A GLN* 2.9 31.7 + - + +
177A PHE* 3.6 22.8 - - + -
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Residues in contact with LEU 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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102A GLN* 6.4 0.9 - - - +
132A GLU* 3.2 38.0 + - + +
133A MET* 3.8 7.9 - - - +
134A LEU 3.3 0.4 - - - -
135A LYS* 1.3 79.4 - - + +
137A TYR* 1.3 67.4 + - + +
139A GLN* 3.0 34.3 + - + +
140A PHE* 3.1 12.1 + - - +
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Residues in contact with TYR 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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99A LEU* 4.6 10.3 - - + -
102A GLN* 3.2 40.8 + - + +
103A PHE* 3.4 43.9 - + - -
106A SER* 2.5 30.1 + - - -
133A MET* 3.2 37.5 + - + -
134A LEU* 3.2 7.9 + - - +
136A LEU* 1.3 75.4 - - + +
138A SER* 1.3 59.5 + - - +
140A PHE* 3.3 4.8 + - + +
141A LEU* 2.9 31.2 + - - +
147A PHE* 4.1 9.4 - + + -
162A VAL* 5.1 0.4 - - + -
163A LEU* 4.4 13.9 - - + -
180A LEU* 4.2 13.9 - - + -
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Residues in contact with SER 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 17.4 + - - -
135A LYS* 3.6 4.7 - - - -
137A TYR* 1.3 74.2 - - - +
139A GLN* 1.3 65.0 + - - +
142A GLY* 2.9 9.7 + - - -
177A PHE* 3.8 23.9 - - - +
179A ASN* 2.8 45.5 + - - +
180A LEU* 3.9 13.6 - - - +
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Residues in contact with GLN 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 LYS* 2.9 18.4 + - + +
136A LEU* 3.0 39.1 + - + +
138A SER* 1.3 76.8 - - - +
140A PHE* 1.3 93.5 + - - +
142A GLY* 3.4 10.3 + - - -
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Residues in contact with PHE 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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95A ARG* 3.4 67.1 + - + -
98A ILE* 5.8 10.1 - - + -
99A LEU* 3.7 44.0 - - + -
136A LEU 3.1 15.4 + - - +
137A TYR* 3.6 7.4 - - + +
139A GLN* 1.3 95.0 - - - +
141A LEU* 1.3 67.4 + - - +
142A GLY* 3.3 0.9 + - - -
144A GLN* 3.8 8.0 + - - -
147A PHE* 4.3 7.4 - + + -
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Residues in contact with LEU 141 (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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137A TYR 2.9 19.9 + - - +
140A PHE* 1.3 73.4 - - - +
142A GLY* 1.3 67.1 + - - +
144A GLN* 3.0 56.9 + - - +
145A PRO 4.5 1.1 - - - +
146A TRP* 3.6 29.6 - - - +
147A PHE* 3.9 25.7 - - + +
179A ASN* 3.8 33.7 - - - +
180A LEU* 4.1 12.3 - - + -
183A PHE* 4.0 18.8 - - + -
186A ARG* 5.0 1.8 - - - +
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Residues in contact with GLY 142 (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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138A SER 2.9 13.2 + - - -
139A GLN 3.7 8.5 - - - -
140A PHE 3.2 2.5 - - - -
141A LEU* 1.3 76.0 - - - +
143A LYS* 1.3 66.0 + - - +
144A GLN 3.8 0.2 + - - -
179A ASN* 2.6 34.9 + - - +
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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