Contacts of the helix formed by residues 119 - 141 (chain C) 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 PHE 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.5 44.4 - - + -
114C CYS* 3.9 7.0 - - - -
116C ASP 3.0 16.0 + - - +
117C PRO 3.0 2.8 + - - +
118C ASP* 1.3 74.8 - - - +
120C GLU* 1.3 64.2 + - + +
122C LEU* 4.4 4.5 - - - -
123C LYS* 2.8 56.5 + - + +
169C PHE* 3.6 17.3 - + - -
213C VAL* 3.7 26.2 - - + -
214C TRP* 3.5 42.2 - + + -
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PRO 5.4 5.0 - - - +
118C ASP 3.1 0.6 + - - -
119C PHE* 1.3 88.2 - - + +
121C LYS* 1.3 80.4 + - - +
123C LYS* 3.8 4.6 - - - +
124C PRO* 3.2 19.8 - - - +
213C VAL* 6.5 0.4 - - + -
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ASP* 3.3 40.5 + - + +
120C GLU* 1.3 100.8 + - + +
122C LEU* 1.3 75.4 + - + +
123C LYS 3.4 0.2 - - - -
124C PRO* 3.4 13.8 - - - +
125C GLU* 4.3 6.6 + - - +
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 3.5 20.7 - - + +
116C ASP* 3.4 40.6 - - + +
118C ASP* 3.0 31.6 + - + +
119C PHE 4.0 0.2 - - - +
121C LYS* 1.3 87.9 - - + +
123C LYS* 1.3 64.7 + - - +
125C GLU* 3.1 31.7 + - - +
126C TYR* 3.1 12.5 + - - +
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Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASP* 3.2 33.7 + - - -
113C LEU* 3.9 8.7 - - - +
119C PHE* 2.8 42.1 + - + +
120C GLU* 3.8 4.0 - - - +
122C LEU* 1.3 74.7 - - - +
124C PRO* 1.4 68.9 - - + +
126C TYR* 3.0 7.1 + - - +
127C LEU* 2.9 40.8 + - + +
169C PHE* 3.8 41.9 + - + -
170C GLU* 5.5 3.7 + - - -
214C TRP* 5.7 3.8 - - - +
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Residues in contact with PRO 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C GLU 3.2 18.2 - - - +
121C LYS* 3.4 14.4 - - - +
123C LYS* 1.4 93.1 - - + +
125C GLU* 1.3 60.9 - - - +
127C LEU* 3.2 12.1 + - + +
128C GLN* 3.0 34.1 + - - +
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LYS 4.3 3.3 + - - +
122C LEU* 3.1 29.3 + - - +
124C PRO* 1.3 79.7 - - - +
126C TYR* 1.3 64.6 + - - +
128C GLN* 3.4 26.6 - - - +
129C ALA* 3.4 12.2 + - + +
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Residues in contact with TYR 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C SER 4.7 1.9 + - - -
109C GLN* 3.5 51.6 - - + -
110C LEU* 3.9 25.1 + - + +
113C LEU* 4.1 16.4 - - + -
122C LEU 3.1 6.8 + - - +
123C LYS* 3.0 9.1 + - - +
125C GLU* 1.3 78.9 + - - +
127C LEU* 1.3 68.4 + - + +
129C ALA* 3.0 6.6 + - - +
130C LEU* 2.9 44.6 + - + +
133C MET* 4.0 6.3 - - - +
166C ASN* 2.8 35.3 + - - -
169C PHE* 4.0 23.3 - + - -
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A SER* 6.1 4.7 - - - -
123C LYS* 2.9 43.5 + - + +
124C PRO* 3.2 11.9 + - + +
126C TYR* 1.3 75.6 - - + +
128C GLN* 1.3 63.0 + - - +
130C LEU* 3.1 27.9 + - + +
131C PRO* 3.1 11.8 - - - +
169C PHE* 4.1 15.5 - - + -
170C GLU* 4.0 39.3 - - + +
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Residues in contact with GLN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C PRO* 3.0 20.0 + - - +
125C GLU* 3.4 29.3 + - - +
127C LEU* 1.3 76.5 - - - +
129C ALA* 1.3 58.8 + - + +
130C LEU 3.4 0.2 - - - -
131C PRO* 3.4 12.5 - - - +
132C GLU 5.4 0.3 + - - -
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLN* 5.2 9.0 - - - +
125C GLU* 3.4 12.3 + - + +
126C TYR* 3.0 10.8 + - - +
128C GLN* 1.3 79.0 - - + +
130C LEU* 1.3 66.1 + - - +
131C PRO 3.3 0.9 - - - -
132C GLU* 3.4 17.3 + - - +
133C MET* 3.8 7.5 + - - +
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Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLN* 5.8 1.1 + - - -
126C TYR* 2.9 36.8 + - + +
127C LEU* 3.2 29.4 - - + +
129C ALA* 1.3 75.8 - - - +
131C PRO* 1.4 64.0 - - + +
133C MET* 3.0 38.9 + - + +
134C LEU* 3.1 39.4 - - + +
166C ASN* 3.7 14.8 - - - +
169C PHE* 5.8 0.7 - - + -
170C GLU* 5.2 2.7 - - + -
173C CYS* 3.7 30.1 - - + -
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Residues in contact with PRO 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LEU 3.1 15.5 - - - +
128C GLN* 3.4 15.5 - - - +
129C ALA 3.4 0.7 - - - -
130C LEU* 1.4 89.4 - - + +
132C GLU* 1.3 55.4 + - - +
134C LEU* 3.4 1.2 + - + -
135C LYS* 2.8 33.2 + - - +
177C PHE* 3.3 26.3 - - + -
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Residues in contact with GLU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLN 5.4 0.2 + - - -
129C ALA* 3.4 10.1 + - - +
130C LEU 3.3 1.0 - - - -
131C PRO* 1.3 77.8 - - - +
133C MET* 1.3 64.7 + - - +
135C LYS* 3.3 28.9 + - - +
136C LEU* 3.2 41.1 + - + +
54D PHE* 5.6 10.7 - - + -
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Residues in contact with MET 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLN* 6.1 1.6 - - - +
106C SER* 3.6 29.2 - - - +
109C GLN* 4.2 27.1 - - - +
126C TYR* 4.0 6.1 - - - +
129C ALA 3.8 4.9 + - - +
130C LEU* 3.0 35.1 + - + +
132C GLU* 1.3 81.8 - - - +
134C LEU* 1.3 69.6 + - + +
136C LEU* 3.2 15.9 + - - +
137C TYR* 3.1 35.8 + - + -
163C LEU* 6.1 1.1 - - + -
166C ASN* 3.5 24.9 - - - +
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU* 3.1 56.0 + - + +
131C PRO* 3.9 1.6 - - + +
133C MET* 1.3 84.1 - - + +
135C LYS* 1.3 59.8 + - - +
137C TYR* 3.1 10.7 + - + +
138C SER* 2.8 27.5 + - - -
163C LEU* 3.6 31.2 - - + -
166C ASN* 5.2 3.6 - - + +
173C CYS* 5.1 2.2 - - + +
174C LEU* 4.0 21.5 - - + -
177C PHE* 3.7 27.4 - - + -
180C LEU* 3.5 16.7 - - + +
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Residues in contact with LYS 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C PRO* 2.8 20.7 + - - +
132C GLU* 3.3 34.3 - - - +
133C MET 3.2 0.4 - - - -
134C LEU* 1.3 76.0 - - - +
136C LEU* 1.3 56.9 + - - +
138C SER* 3.2 3.3 + - - -
139C GLN* 2.9 54.3 + - + +
177C PHE* 3.6 23.7 - - + -
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLN* 6.1 0.9 - - - +
132C GLU* 3.4 34.8 - - + +
133C MET* 3.2 10.9 + - - +
135C LYS* 1.3 74.5 - - - +
137C TYR* 1.3 57.8 + - - +
139C GLN* 3.3 17.5 + - - +
140C PHE* 2.9 30.7 + - - +
54D PHE* 6.2 2.9 - - + -
59D ASP 3.6 19.1 - - - +
60D PHE* 3.7 31.3 - - + -
61D PRO* 4.6 15.5 - - + -
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LEU* 4.4 5.6 - - + -
102C GLN* 3.2 33.1 + - + +
103C PHE* 3.3 40.4 - + - -
106C SER* 2.7 30.5 + - - -
133C MET* 3.1 38.5 + - + -
134C LEU* 3.1 17.6 + - + +
136C LEU* 1.3 77.7 - - - +
138C SER* 1.3 61.3 + - - +
140C PHE* 3.5 5.4 + - - +
141C LEU* 3.0 24.6 + - - +
147C PHE* 3.9 8.8 - + + -
162C VAL* 6.1 0.4 - - + -
163C LEU* 4.7 5.8 - - + -
180C LEU* 4.0 14.8 - - + +
60D PHE* 3.7 25.6 - + - -
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Residues in contact with SER 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LEU 2.8 12.6 + - - -
135C LYS 3.5 7.6 - - - -
137C TYR* 1.3 74.2 - - - +
139C GLN* 1.3 68.7 + - - +
141C LEU 3.2 1.2 + - - -
142C GLY* 2.9 19.9 + - - -
177C PHE* 4.1 20.8 - - - +
179C ASN* 2.9 35.7 + - - +
180C LEU* 3.7 19.0 - - - +
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Residues in contact with GLN 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LYS* 2.9 49.2 + - + +
136C LEU* 3.7 20.4 - - - +
138C SER* 1.3 77.2 - - - +
140C PHE* 1.3 62.4 + - - +
142C GLY* 3.1 14.7 + - - -
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Residues in contact with PHE 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ARG* 3.1 71.4 + - + -
98C ILE* 5.6 6.7 - - + -
99C LEU* 3.3 34.3 - - + -
136C LEU 2.9 17.3 + - - +
137C TYR* 3.6 4.7 - - - +
139C GLN* 1.3 78.6 - - - +
141C LEU* 1.3 62.1 + - - +
142C GLY* 4.4 0.3 - - - -
144C GLN* 3.3 13.0 + - - -
147C PHE* 3.9 15.9 - + + -
59D ASP* 3.5 33.0 - - + -
60D PHE* 3.6 27.6 - + + -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C TYR 3.0 16.0 + - - +
138C SER 3.6 4.0 - - - +
140C PHE* 1.3 76.6 - - - +
142C GLY* 1.3 64.7 + - - +
144C GLN* 2.9 57.3 + - - +
145C PRO 4.5 1.8 - - - +
146C TRP* 3.8 27.8 - - - +
147C PHE* 3.9 22.9 - - + +
179C ASN* 3.6 36.3 - - - +
180C LEU* 3.9 15.0 - - + -
183C PHE* 4.3 17.5 - - + -
186C ARG* 4.8 1.6 - - - +
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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