Contacts of the helix formed by residues 118 - 142 (chain D) in PDB entry 1C72
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D SER* 3.1 5.9 + - - +
117D PRO* 1.3 80.4 - - - +
119D PHE* 1.3 63.5 + - - +
120D GLU 3.3 2.5 - - - -
121D LYS* 3.0 27.1 + - + +
122D LEU* 3.0 38.3 - - + +
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Residues in contact with PHE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 3.4 39.9 - - + +
114D CYS* 3.9 16.2 - - - -
116D SER* 3.0 16.2 + - - +
117D PRO 3.0 3.2 + - - +
118D ASP* 1.3 74.8 - - - +
120D GLU* 1.3 80.3 + - + +
122D LEU* 3.0 6.4 + - - +
123D LYS* 2.9 44.4 + - + +
169D PHE* 4.5 10.3 - + - -
213D LEU* 4.1 26.2 - - + -
214D TRP* 3.6 41.1 - + + -
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Residues in contact with GLU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D PRO 4.8 0.8 + - - -
118D ASP 3.3 1.0 - - - -
119D PHE* 1.3 96.7 - - + +
121D LYS* 1.3 63.6 + - + +
123D LYS* 2.9 34.5 + - - +
124D PRO* 3.5 16.5 - - - +
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ASP* 3.0 23.8 + - + +
120D GLU* 1.3 81.2 - - + +
122D LEU* 1.3 69.2 + - + +
124D PRO* 3.6 13.7 - - - +
125D ALA* 5.1 1.7 + - - +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ARG 6.0 0.2 - - - -
113D LEU* 4.0 18.8 - - + -
116D SER* 3.6 32.3 - - - +
118D ASP* 3.0 28.9 - - + +
119D PHE 3.0 4.7 + - - +
121D LYS* 1.3 84.9 - - + +
123D LYS* 1.3 64.6 + - - +
124D PRO* 3.4 2.0 - - - -
125D ALA* 3.2 18.6 + - + +
126D TYR* 3.2 12.8 + - - +
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 4.2 9.6 - - + -
119D PHE* 2.9 29.1 + - + +
120D GLU* 2.9 42.9 + - - +
122D LEU* 1.3 76.5 - - - +
124D PRO* 1.3 72.1 - - + +
126D TYR* 3.2 6.4 + - - +
127D LEU* 3.1 35.6 + - + +
169D PHE* 4.3 23.3 - - + -
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Residues in contact with PRO 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D GLU 3.5 13.2 - - - +
121D LYS* 3.6 12.1 - - - +
122D LEU 3.4 2.2 - - - -
123D LYS* 1.3 101.2 - - + +
125D ALA* 1.3 62.6 + - + +
127D LEU* 3.2 9.3 + - + +
128D GLU* 3.2 32.1 + - - +
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Residues in contact with ALA 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LYS 5.3 1.1 - - - +
122D LEU* 3.2 14.2 + - + +
124D PRO* 1.3 80.2 - - + +
126D TYR* 1.3 63.2 + - - +
128D GLU* 3.3 26.3 + - - +
129D LEU* 3.4 16.8 - - + +
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Residues in contact with TYR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU 5.0 2.0 + - - -
109D ALA* 4.8 13.2 - - + -
110D PHE* 3.3 44.2 - + - +
113D LEU* 3.4 27.8 - - + -
122D LEU 3.2 5.6 + - - +
123D LYS 3.2 8.1 + - - +
125D ALA* 1.3 79.4 - - - +
127D LEU* 1.3 59.7 + - + +
128D GLU 3.1 0.5 + - - -
129D LEU* 3.3 29.3 - - + +
130D LEU* 3.0 44.4 + - + +
166D GLN* 2.8 30.0 + - - -
169D PHE* 3.9 17.5 - + - -
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Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LYS* 3.1 33.0 + - + +
124D PRO* 3.2 9.1 + - + +
126D TYR* 1.3 79.5 - - + +
128D GLU* 1.3 58.0 + - - +
130D LEU* 3.9 13.5 - - + +
131D PRO* 3.2 20.4 - - - +
169D PHE* 3.4 35.9 - - + -
170D VAL* 5.0 16.4 - - + -
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D PRO* 3.2 24.2 + - - +
125D ALA* 3.4 13.6 - - - +
126D TYR 3.1 0.6 - - - -
127D LEU* 1.3 78.9 - - - +
129D LEU* 1.3 57.8 + - + +
130D LEU 3.2 1.1 - - - -
131D PRO* 3.2 21.9 - - - +
132D GLY 4.8 0.5 + - - -
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ALA* 3.4 16.8 - - + +
126D TYR* 3.3 41.7 - - + +
128D GLU* 1.3 77.1 - - - +
130D LEU* 1.3 64.6 + - - +
131D PRO 3.6 0.2 - - - -
132D GLY* 3.5 4.4 + - - -
133D LYS* 3.3 35.4 + - + +
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Residues in contact with LEU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR* 3.0 43.7 + - + +
127D LEU* 3.9 13.5 - - + +
129D LEU* 1.3 78.3 - - - +
131D PRO* 1.3 74.1 - - + +
133D LYS* 3.0 12.1 + - + +
134D LEU* 3.0 49.7 + - + +
166D GLN* 4.4 17.7 - - + +
169D PHE* 5.1 0.2 - - + -
170D VAL* 3.9 26.9 - - + -
173D CYS* 5.0 4.5 - - - -
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Residues in contact with PRO 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D LEU 3.2 19.1 - - - +
128D GLU* 3.2 15.3 - - - +
130D LEU* 1.3 91.4 - - + +
132D GLY* 1.3 55.6 + - - +
134D LEU* 3.7 7.6 - - + +
135D ARG* 2.9 49.2 + - - +
173D CYS* 5.0 6.3 - - - -
175D GLU* 3.3 33.4 - - + +
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Residues in contact with GLY 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D GLU 4.8 0.2 + - - -
129D LEU* 3.5 6.9 + - - -
130D LEU 3.1 1.0 - - - -
131D PRO* 1.3 78.9 - - - +
133D LYS* 1.3 65.4 + - - +
135D ARG* 3.2 20.5 + - - +
136D GLN* 3.1 24.9 + - - +
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Residues in contact with LYS 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS* 4.7 13.9 - - - +
57C PRO 4.6 10.9 + - - -
58C ASN* 5.1 7.5 - - - +
222C EPY 5.4 1.2 + - - -
102D HIS* 4.9 5.1 + - + -
106D LEU* 4.5 29.2 - - + -
129D LEU* 3.3 26.8 + - + +
130D LEU* 3.0 15.1 + - + +
132D GLY* 1.3 74.8 - - - +
134D LEU* 1.3 59.2 + - + +
136D GLN* 3.1 56.1 + - - +
137D LEU* 3.3 13.0 + - - +
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D LEU* 3.0 41.7 + - + +
131D PRO* 3.7 5.2 - - + +
133D LYS* 1.3 78.0 - - - +
135D ARG* 1.3 56.1 + - - +
137D LEU* 3.5 9.0 + - + +
138D SER* 3.1 26.5 + - - -
163D LEU* 4.0 26.7 - - + -
166D GLN* 4.5 10.5 - - + -
173D CYS* 4.0 21.3 - - - -
175D GLU* 4.1 18.1 - - + +
176D LEU* 3.9 30.1 - - + -
180D LEU* 3.6 11.5 - - + +
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Residues in contact with ARG 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PRO* 2.9 30.1 + - - +
132D GLY* 3.2 22.5 + - - +
134D LEU* 1.3 73.0 - - - +
136D GLN* 1.3 64.7 + - - +
138D SER* 3.5 5.3 + - - -
139D ARG* 3.0 62.7 + - - +
175D GLU* 3.6 36.4 + - - -
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Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS* 5.4 4.2 - - - -
50C GLU* 5.4 1.6 - - - +
55C ASP 3.9 16.3 - - - +
56C PHE* 3.6 22.5 - - + +
57C PRO* 3.7 17.4 - - + +
102D HIS* 3.4 31.1 + - - +
132D GLY 3.1 11.2 + - - +
133D LYS* 3.1 41.0 + - - +
135D ARG* 1.3 78.8 - - - +
137D LEU* 1.3 57.2 + - - +
139D ARG* 3.2 8.7 + - - +
140D PHE* 3.0 26.9 + - - +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C PHE* 3.3 30.1 - - + -
99D LEU* 4.7 5.2 - - + -
102D HIS* 3.9 14.8 - - + +
103D LEU* 4.5 12.3 - - + -
106D LEU* 3.8 26.9 - - + -
133D LYS 3.3 12.0 + - - +
134D LEU* 3.8 13.7 - - + +
136D GLN* 1.3 77.5 - - - +
138D SER* 1.3 65.0 + - - +
140D PHE* 3.8 1.3 - - - +
141D LEU* 3.1 25.6 + - - +
147D PHE* 3.9 22.6 - - + -
159D ALA* 6.5 0.2 - - + -
162D VAL* 5.7 1.8 - - + -
163D LEU* 5.0 16.4 - - + -
180D LEU* 4.4 13.2 - - + +
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Residues in contact with SER 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D LEU 3.1 18.0 + - - -
135D ARG* 3.5 11.2 - - - -
137D LEU* 1.3 76.1 - - - +
139D ARG* 1.3 69.5 + - - +
142D GLY* 3.2 19.1 + - - -
175D GLU 4.8 5.1 + - - -
177D GLN 5.6 1.6 + - - -
179D ASN* 2.7 35.2 + - - +
180D LEU* 3.9 13.0 - - - +
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Residues in contact with ARG 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ARG* 3.0 56.3 + - - +
136D GLN* 3.2 11.0 + - - +
138D SER* 1.3 82.1 - - - +
140D PHE* 1.3 65.9 + - - +
142D GLY* 3.5 9.6 + - - -
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Residues in contact with PHE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ASP* 3.2 42.6 - - + +
56C PHE* 3.4 27.8 - + + -
95D ARG* 3.5 35.0 - - + -
98D VAL* 6.4 0.7 - - + -
99D LEU* 3.8 20.0 - - + -
136D GLN 3.0 14.6 + - - +
137D LEU* 3.8 4.9 - - - +
138D SER 3.4 0.2 - - - -
139D ARG* 1.3 79.6 - - - +
141D LEU* 1.3 58.8 + - - +
142D GLY* 4.3 0.2 - - - -
144D ARG* 2.9 31.0 + - - -
147D PHE* 3.6 37.7 - + - -
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU 3.1 14.7 + - - +
140D PHE* 1.3 78.9 - - - +
142D GLY* 1.3 62.0 + - - +
144D ARG* 2.9 53.5 + - - +
145D SER 4.5 3.1 - - - +
146D TRP 3.5 31.2 - - - +
147D PHE* 3.9 28.2 - - + +
179D ASN* 3.5 38.4 - - + +
180D LEU* 4.5 5.4 - - + -
183D PHE* 4.1 17.3 - - + -
186D ARG* 5.0 3.8 - - - +
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Residues in contact with GLY 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D SER 3.2 12.4 + - - -
139D ARG 3.5 9.6 + - - -
140D PHE 3.3 2.0 - - - -
141D LEU* 1.3 81.2 - - - +
143D SER* 1.3 57.7 + - - -
144D ARG* 3.6 3.3 + - - +
179D ASN* 3.3 24.7 + - - +
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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
------------------------------------------------------------
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