Contacts of the helix formed by residues 119 - 141 (chain E) in PDB entry 4GTU
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 PHE 119 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113E VAL* 4.7 9.2 - - + -
114E CYS* 4.5 11.4 - - - -
116E SER 3.4 4.9 + - - -
117E PRO 3.0 8.2 + - - +
118E ASP* 1.3 71.6 - - - +
120E GLU* 1.3 88.0 + - - +
122E LEU* 2.9 6.1 + - - +
123E LYS* 2.8 72.2 + - + +
169E PHE* 4.2 10.1 - + - -
213E VAL* 3.6 35.2 - - + -
214E TRP* 3.3 41.7 - + + -
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Residues in contact with GLU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E PRO 5.2 1.4 - - - +
118E ASP 3.3 0.6 - - - -
119E PHE* 1.3 106.3 + - - +
121E LYS* 1.3 61.9 + - + +
123E LYS* 4.8 2.8 - - - +
124E PRO* 2.9 26.7 - - - +
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Residues in contact with LYS 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E ASP* 3.0 32.3 + - + +
120E GLU* 1.3 80.7 - - + +
122E LEU* 1.3 69.6 + - + +
124E PRO* 3.5 10.2 - - - +
125E GLU* 3.1 21.8 - - - +
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Residues in contact with LEU 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E ARG 5.6 0.2 - - - -
113E VAL* 3.6 31.0 - - + +
116E SER* 3.7 29.2 - - - +
118E ASP* 3.2 27.8 + - - +
119E PHE* 2.9 5.6 + - - +
121E LYS* 1.3 86.8 - - + +
123E LYS* 1.3 63.7 + - - +
125E GLU* 3.3 11.7 - - + +
126E TYR* 3.2 23.0 + - - +
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Residues in contact with LYS 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E VAL* 4.3 6.4 - - - +
119E PHE* 2.8 55.5 + - + +
120E GLU* 4.4 2.7 - - - +
122E LEU* 1.3 75.0 - - - +
124E PRO* 1.3 74.2 - - + +
126E TYR* 3.3 3.6 + - - +
127E LEU* 3.0 48.6 + - + +
169E PHE* 3.6 34.5 + - + -
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Residues in contact with PRO 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E GLU 2.9 28.5 - - - +
121E LYS* 3.5 9.2 - - - +
123E LYS* 1.3 88.3 - - + +
125E GLU* 1.3 64.8 + - + +
127E LEU* 3.1 13.4 + - + +
128E GLU* 2.9 26.9 + - - +
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Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E LYS 3.1 23.8 - - - +
122E LEU* 3.3 17.0 - - + +
123E LYS 3.2 0.2 - - - -
124E PRO* 1.3 80.6 - - + +
126E TYR* 1.3 62.9 + - - +
128E GLU* 3.2 23.7 + - - +
129E GLU* 3.4 11.3 + - - +
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Residues in contact with TYR 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E VAL* 4.3 6.2 + - - +
109E GLN* 3.5 33.1 + - + -
110E LEU* 3.8 31.0 - - + -
113E VAL* 4.8 13.7 - - + -
122E LEU 3.2 9.4 + - - +
123E LYS* 3.7 7.0 - - - +
125E GLU* 1.3 75.9 - - - +
127E LEU* 1.3 57.0 + - + +
128E GLU 3.0 4.5 - - - -
129E GLU* 2.8 13.4 + - + +
130E LEU* 2.7 43.8 + - + +
133E MET* 3.1 29.5 - - + +
166E HIS* 2.8 37.7 + + - -
169E PHE* 4.5 10.8 - + + -
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Residues in contact with LEU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E LYS* 3.0 49.9 + - + +
124E PRO* 3.5 13.0 - - + +
126E TYR* 1.3 76.9 - - + +
128E GLU* 1.3 58.5 + - - +
129E GLU 3.3 0.2 - - - -
130E LEU* 3.8 26.2 - - + +
131E PRO* 3.4 16.1 - - - +
169E PHE* 4.4 21.3 - - + +
170E GLU* 4.0 30.4 - - + +
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Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E PRO 2.9 10.8 + - - +
125E GLU* 3.4 18.2 - - - +
126E TYR 3.0 0.2 - - - -
127E LEU* 1.3 76.9 - - - +
129E GLU* 1.3 64.9 + - - +
131E PRO* 3.8 12.4 - - - +
132E THR* 6.0 0.2 - - - +
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Residues in contact with GLU 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E GLU 3.4 9.4 + - - +
126E TYR* 2.8 16.0 + - + +
128E GLU* 1.3 81.9 - - - +
130E LEU* 1.3 66.3 + - - +
131E PRO* 3.3 5.4 - - - -
132E THR* 3.6 21.8 + - + +
133E MET* 3.5 22.3 + - + +
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Residues in contact with LEU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E TYR* 2.7 27.5 + - + +
127E LEU* 3.8 19.3 - - + +
129E GLU* 1.3 76.0 - - - +
131E PRO* 1.3 67.1 - - + +
133E MET* 3.2 34.2 - - + +
134E MET* 3.1 28.9 + - + +
166E HIS* 4.1 18.6 - - + -
169E PHE* 5.7 1.1 - - + -
170E GLU* 3.9 29.6 - - + -
173E CYS* 4.0 19.7 - - + -
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Residues in contact with PRO 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E LEU 3.4 17.7 - - - +
128E GLU* 3.8 12.6 - - - +
129E GLU 3.3 2.5 - - - -
130E LEU* 1.3 86.7 - - + +
132E THR* 1.3 59.7 + - + +
133E MET 3.0 4.9 - - - -
134E MET* 2.9 23.4 + - + +
135E GLN* 3.0 9.9 + - - +
173E CYS* 6.0 2.7 - - + -
177E PHE* 3.7 16.2 - - + -
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Residues in contact with THR 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E GLU 6.0 0.2 - - - +
129E GLU* 3.7 25.1 - - + +
131E PRO* 1.3 81.5 - - + +
133E MET* 1.3 57.5 + - + +
135E GLN* 3.1 36.6 + - - +
136E HIS* 2.8 32.3 + - + +
50F PHE* 4.8 15.3 - - + -
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Residues in contact with MET 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E VAL* 4.5 19.1 - - + -
109E GLN* 3.9 10.8 - - - +
126E TYR* 3.1 41.3 - - - +
129E GLU* 3.5 11.4 - - + +
130E LEU* 3.2 34.8 - - + +
132E THR* 1.3 82.2 - - + +
134E MET* 1.3 70.1 + - + +
135E GLN 3.1 0.9 - - - -
136E HIS* 3.1 30.8 + - + +
137E PHE* 3.8 14.9 + - + +
162E VAL* 6.0 0.9 - - + -
166E HIS* 4.1 12.1 - - + -
56F PHE* 4.5 0.7 - - - -
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Residues in contact with MET 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E LEU* 3.1 29.1 + - + +
131E PRO* 2.9 9.7 + - + +
133E MET* 1.3 83.3 - - + +
135E GLN* 1.3 63.9 + - - +
137E PHE* 3.3 19.5 - - - +
138E SER 3.2 15.4 + - - -
162E VAL* 6.0 0.2 - - - -
163E LEU* 4.0 23.1 - - + -
166E HIS* 4.4 15.9 - - + +
173E CYS* 3.5 33.4 - - + +
174E LEU* 3.8 22.0 - - + -
177E PHE* 3.7 21.6 - - + -
180E LEU* 3.7 11.0 - - + +
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Residues in contact with GLN 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PRO 3.0 7.2 + - - +
132E THR* 3.1 31.7 + - - +
133E MET 3.1 0.4 - - - -
134E MET* 1.3 75.7 - - - +
136E HIS* 1.3 73.6 - - - +
138E SER* 3.0 6.9 + - - -
139E GLN* 2.9 51.2 + - + +
177E PHE* 3.7 16.3 - - + -
50F PHE* 5.9 4.8 - - - -
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Residues in contact with HIS 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E THR* 2.8 34.1 + - + +
133E MET* 3.1 24.7 + - + +
135E GLN* 1.3 82.3 - - + +
137E PHE* 1.3 53.2 + - - +
139E GLN* 3.0 18.8 + - - +
140E PHE* 2.7 36.9 + - - +
50F PHE* 5.0 6.4 - + - -
55F ASP 2.8 25.8 - - - +
56F PHE* 3.3 19.8 - + + -
57F PRO* 3.9 31.4 - - + +
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Residues in contact with PHE 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 4.6 12.1 - - + -
102E GLN* 4.8 9.4 - - + -
103E ALA* 4.7 14.8 - - + -
106E VAL* 4.9 7.2 - - + -
133E MET* 3.8 9.2 + - + -
134E MET* 3.3 24.7 + - - +
136E HIS* 1.3 77.1 - - - +
138E SER* 1.3 62.9 + - - +
140E PHE* 3.1 4.7 + - - +
141E LEU* 3.1 23.6 + - - +
147E PHE* 3.9 19.2 - + - -
159E ALA* 4.8 5.6 - - - -
162E VAL* 4.0 28.7 - - + -
163E LEU* 3.6 35.4 - - + -
180E LEU* 4.0 8.3 - - + -
56F PHE* 3.3 32.8 - + - -
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Residues in contact with SER 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E MET 3.2 1.5 + - - -
135E GLN 3.0 9.0 + - - -
137E PHE* 1.3 79.0 - - - +
139E GLN* 1.3 58.9 + - - +
142E GLY* 3.0 23.9 + - - -
177E PHE* 3.7 30.8 - - - +
178E PRO* 5.4 0.9 - - - +
179E ASN* 2.6 40.5 + - - +
180E LEU* 3.9 6.5 - - - +
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Residues in contact with GLN 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ARG* 5.5 0.2 + - - -
135E GLN* 2.9 47.0 + - + +
136E HIS* 3.0 18.4 + - - +
138E SER* 1.3 76.7 - - - +
140E PHE* 1.3 64.1 + - - +
142E GLY* 3.8 10.0 + - - -
144E ARG* 5.0 3.1 + - - -
55F ASP* 5.3 11.7 - - + +
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Residues in contact with PHE 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ARG* 3.0 79.0 + - + +
98E ILE* 3.6 30.3 - - + -
99E LEU* 3.7 22.2 - - + -
136E HIS 2.7 19.3 + - - +
137E PHE* 3.1 5.8 + - - +
139E GLN* 1.3 72.9 - - - +
141E LEU* 1.3 64.8 + - - +
144E ARG* 3.6 4.0 + - - -
147E PHE* 4.0 19.3 - + + -
55F ASP* 3.5 35.6 - - + +
56F PHE* 3.3 21.1 - + + -
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Residues in contact with LEU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E PHE 3.1 13.1 + - - +
140E PHE* 1.3 75.4 - - - +
142E GLY* 1.3 67.7 + - - +
144E ARG* 3.0 53.9 - - - +
145E PRO 4.0 6.5 - - - +
146E TRP 3.8 2.7 - - - -
147E PHE* 3.3 62.1 - - + +
179E ASN* 3.5 40.6 - - + +
180E LEU* 3.9 6.1 - - + -
183E PHE* 3.9 9.6 - - + -
186E ARG* 4.2 2.9 - - - +
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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