Contacts of the helix formed by residues 121 - 145 (chain D) in PDB entry 3GTU
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 SER 121 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D TYR 3.5 2.0 + - - -
120D SER* 1.3 69.2 + - - +
122D ASP* 1.3 69.6 + - - +
123D HIS* 3.0 11.6 + - - +
124D GLU* 4.5 1.9 + - - +
125D LYS* 4.1 5.9 + - - -
217D GLN* 3.9 20.0 - - - +
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Residues in contact with ASP 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D SER* 3.1 13.9 + - - +
121D SER* 1.3 84.5 + - - +
123D HIS* 1.3 63.3 + - - -
124D GLU 2.8 5.1 + - - -
125D LYS* 2.9 49.3 + - + +
126D LEU* 2.9 25.3 + - + +
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Residues in contact with HIS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D LEU* 2.7 53.3 + - + +
118D CYS* 3.9 2.0 - - - -
120D SER* 3.1 19.7 + - - +
121D SER 3.0 2.4 - - - +
122D ASP* 1.3 75.7 - - - +
124D GLU* 1.3 64.3 + - + +
126D LEU* 4.6 0.9 - - - -
127D LYS* 2.8 35.8 + - + +
173D PHE* 3.7 20.1 - + - -
217D GLN* 3.4 35.0 + - + -
218D TRP* 3.7 24.8 - - + +
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D SER 4.5 1.7 + - - +
122D ASP 2.8 4.9 + - - -
123D HIS* 1.3 80.5 - - + +
125D LYS* 1.3 74.1 + - - +
127D LYS* 3.1 26.4 + - - +
128D PRO* 3.1 23.7 - - - +
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D SER 4.1 4.8 + - - -
122D ASP* 2.9 61.0 + - + +
124D GLU* 1.3 84.4 - - - +
126D LEU* 1.3 67.7 + - + +
128D PRO* 3.3 12.2 - - - +
129D GLN* 4.2 12.0 + - - +
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ARG* 5.5 5.2 - - + +
117D LEU* 3.7 22.8 - - + +
120D SER* 3.9 27.1 - - - +
122D ASP* 2.9 21.4 + - + +
125D LYS* 1.3 94.5 - - + +
127D LYS* 1.3 66.1 + - - +
128D PRO 3.4 0.2 - - - -
129D GLN* 3.0 24.7 + - + +
130D TYR* 3.2 9.7 + - - +
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Residues in contact with LYS 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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117D LEU* 3.5 10.1 - - + +
123D HIS* 2.8 22.8 + - + +
124D GLU* 3.1 36.3 + - - +
126D LEU* 1.3 75.5 - - - +
128D PRO* 1.4 64.1 - - + +
130D TYR* 3.2 5.4 + - - +
131D LEU* 3.0 48.5 + - + +
173D PHE* 3.7 39.4 + - + -
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Residues in contact with PRO 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 GLU* 3.1 22.0 - - - +
125D LYS* 3.3 13.0 - - - +
127D LYS* 1.4 88.6 - - + +
129D GLN* 1.3 65.7 + - - +
131D LEU* 3.2 12.6 + - + +
132D GLU* 2.8 36.2 + - - +
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Residues in contact with GLN 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 LYS 4.2 12.8 + - - +
126D LEU* 3.0 18.5 + - + +
128D PRO* 1.3 83.5 - - - +
130D TYR* 1.3 65.0 + - - +
132D GLU* 3.0 46.6 + - - +
133D GLU* 3.0 25.2 + - - +
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Residues in contact with TYR 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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110D PHE* 3.2 21.2 - + - -
113D GLN* 4.1 20.6 - - + -
114D LEU* 3.5 46.0 - - + +
117D LEU* 3.9 26.2 - - + -
126D LEU 3.2 4.6 + - - +
127D LYS 3.2 7.6 + - - +
129D GLN* 1.3 77.7 - - - +
131D LEU* 1.3 59.9 + - + +
133D GLU* 3.2 8.1 + - + +
134D LEU* 2.8 40.6 + - + +
170D ASN* 3.1 34.2 + - - -
173D PHE* 3.9 24.9 - + - -
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Residues in contact with LEU 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 LYS* 3.0 49.1 + - + +
128D PRO* 3.5 11.0 - - + +
130D TYR* 1.3 76.8 - - + +
132D GLU* 1.3 56.7 + - - +
133D GLU 3.1 0.2 - - - -
134D LEU* 3.3 19.2 + - + +
135D PRO* 3.0 27.7 - - - +
173D PHE* 3.9 28.5 - - + +
174D ASP* 4.4 17.5 - - + +
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Residues in contact with GLU 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 PRO* 2.8 16.5 + - - +
129D GLN* 3.0 55.3 + - - +
131D LEU* 1.3 74.4 - - - +
133D GLU* 1.3 66.7 + - + +
135D PRO* 4.1 6.6 - - - +
136D GLY 5.6 0.2 + - - -
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Residues in contact with GLU 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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113D GLN* 5.4 3.5 - - - +
129D GLN* 3.0 34.1 + - - +
130D TYR* 3.8 6.0 + - + +
131D LEU 3.1 0.6 - - - -
132D GLU* 1.3 87.3 - - + +
134D LEU* 1.3 65.8 + - - +
135D PRO* 3.5 1.8 - - - -
136D GLY* 3.4 11.7 + - - -
137D GLN* 3.6 10.2 + - - +
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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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110D PHE* 3.5 28.7 - - + -
130D TYR* 2.8 25.7 + - + +
131D LEU* 3.5 25.4 - - + +
133D GLU* 1.3 75.2 - - - +
135D PRO* 1.4 71.7 - - + +
137D GLN* 3.0 14.6 + - - +
138D LEU* 3.1 26.7 + - + +
170D ASN* 3.1 34.3 - - + +
173D PHE* 5.4 1.1 - - + -
174D ASP* 5.0 5.6 - - + +
177D CYS* 4.2 23.1 - - + -
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Residues in contact with PRO 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 LEU 3.0 26.5 - - - +
132D GLU 4.1 6.7 - - - +
133D GLU 3.6 3.1 - - - -
134D LEU* 1.4 81.9 - - + +
136D GLY* 1.3 52.0 + - - +
138D LEU* 3.4 6.8 + - + -
139D LYS* 2.8 37.1 + - - +
177D CYS 5.9 0.4 - - - +
180D GLU* 4.8 15.0 - - - +
181D PHE* 3.6 12.7 - - + -
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Residues in contact with GLY 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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132D GLU 5.6 0.2 + - - -
133D GLU 3.4 6.7 + - - -
134D LEU 3.1 1.4 + - - -
135D PRO* 1.3 77.7 - - - +
137D GLN* 1.3 62.1 + - - +
139D LYS* 3.1 14.8 - - - +
140D GLN* 3.1 28.5 + - - +
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Residues in contact with GLN 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* 4.2 0.7 - - - -
106D GLN* 3.4 22.4 + - - +
109D ASP* 6.2 0.6 - - - +
110D PHE* 3.8 45.5 - - + +
113D GLN* 4.4 16.5 - - - +
133D GLU 3.6 9.6 + - - +
134D LEU* 3.0 9.0 + - - +
136D GLY* 1.3 74.8 - - - +
138D LEU* 1.3 63.1 + - - +
140D GLN* 3.0 40.0 + - - +
141D PHE* 3.2 29.3 + - + -
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Residues in contact with LEU 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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110D PHE* 3.9 12.3 - - + -
134D LEU* 3.1 55.0 + - + +
135D PRO* 3.7 7.6 - - + +
137D GLN* 1.3 71.8 - - - +
139D LYS* 1.3 66.6 + - - +
141D PHE* 3.0 8.6 + - + +
142D SER* 2.9 22.7 + - - -
167D LEU* 3.5 32.1 - - + -
170D ASN* 5.0 4.7 - - + -
177D CYS* 4.5 14.8 - - + +
178D LEU* 4.4 13.7 - - + -
181D PHE* 3.8 18.4 - - + -
184D LEU* 3.7 16.0 - - + +
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Residues in contact with LYS 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 PRO 2.8 18.2 + - - +
136D GLY* 3.1 17.7 - - - +
138D LEU* 1.3 73.6 - - - +
140D GLN* 1.3 59.0 + - + +
142D SER* 3.4 3.1 + - - -
143D MET* 3.0 29.5 + - + +
181D PHE* 3.4 22.1 - - + -
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Residues in contact with GLN 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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50C PHE* 5.2 5.9 - - - -
55C ASP 4.3 6.7 - - - +
56C PHE* 3.6 27.2 - - + +
57C PRO* 3.1 31.0 - - - +
106D GLN* 4.6 2.0 - - - +
136D GLY 3.1 13.4 + - - +
137D GLN* 3.0 35.0 + - - +
139D LYS* 1.3 75.0 - - + +
141D PHE* 1.3 61.4 + - - +
143D MET* 3.4 10.3 + - - +
144D PHE* 2.9 30.1 + - - +
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Residues in contact with PHE 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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56C PHE* 4.3 9.4 - + - -
103D ILE* 4.3 13.7 - - + -
106D GLN* 4.0 19.7 - - + -
107D VAL* 4.1 26.2 - - + -
110D PHE* 3.8 28.3 - + - -
137D GLN* 3.2 41.9 + - + -
138D LEU* 3.0 11.0 + - - +
140D GLN* 1.3 75.3 - - - +
142D SER* 1.3 60.6 + - - +
144D PHE* 3.3 5.3 + - - +
145D LEU* 2.8 32.1 + - - +
151D PHE* 3.6 24.8 - + + -
163D THR* 4.1 11.9 - - + -
166D ILE* 5.4 1.8 - - + -
167D LEU* 5.0 6.7 - - + -
184D LEU* 4.1 16.8 - - + -
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Residues in contact with SER 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 LEU 2.9 11.9 + - - -
139D LYS 3.6 8.5 - - - -
141D PHE* 1.3 77.3 - - - +
143D MET* 1.3 62.1 + - - +
145D LEU 3.3 0.5 + - - -
146D GLY* 3.0 10.4 + - - -
181D PHE* 3.8 25.9 - - - +
183D ASN* 2.8 48.4 + - - +
184D LEU* 3.9 13.1 - - - +
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Residues in contact with MET 143 (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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54C LEU 5.3 0.9 - - - +
55C ASP* 3.1 52.5 - - - +
139D LYS* 3.0 19.1 + - + +
140D GLN* 3.6 7.4 - - - +
141D PHE 3.3 0.2 - - - -
142D SER* 1.3 77.4 - - - +
144D PHE* 1.3 75.2 + - - +
146D GLY* 3.6 9.4 + - - -
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Residues in contact with PHE 144 (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* 3.5 39.0 - - + -
56C PHE* 3.7 18.4 - + + -
99D ARG* 3.0 86.1 + - + -
102D ILE* 5.1 9.4 - - + -
103D ILE* 3.4 37.2 - - + -
140D GLN 2.9 18.7 + - - +
141D PHE 3.7 2.9 - - - +
143D MET* 1.3 84.6 - - - +
145D LEU* 1.3 61.8 + - - +
151D PHE* 3.7 17.0 - + - -
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Residues in contact with LEU 145 (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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99D ARG* 4.6 1.3 - - - +
141D PHE 2.8 20.4 + - - +
142D SER 3.3 3.3 + - - +
144D PHE* 1.3 76.0 - - - +
146D GLY* 1.3 65.1 + - - +
148D PHE* 3.2 49.6 + - + +
149D SER 4.6 0.2 - - - -
150D TRP* 3.5 35.2 - - - +
151D PHE* 3.8 32.1 - - + +
183D ASN* 3.8 19.5 - - - +
184D LEU* 4.3 9.4 - - + -
187D PHE* 4.0 22.2 - - + -
190D ARG* 4.9 2.5 - - - +
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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