Contacts of the helix formed by residues 117 - 139 (chain E) in PDB entry 3GHG
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 TYR 117 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E SER* 3.1 35.3 + - - -
114E SER* 4.5 9.7 + - - +
115E PHE 3.7 0.8 - - - -
116E GLN* 1.3 91.1 - - + +
118E MET* 1.3 65.6 + - - +
120E LEU* 4.7 3.1 - - - +
121E LEU* 3.3 43.9 - - + +
122E LYS 4.3 0.2 + - - -
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Residues in contact with MET 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D THR* 5.6 6.7 - - + +
90D ILE* 5.7 9.2 - - + -
114E SER 5.3 5.6 + - - +
115E PHE 3.9 14.8 + - - +
116E GLN 2.9 3.0 + - - -
117E TYR* 1.3 78.2 - - - +
119E TYR* 1.3 61.1 + - + +
122E LYS* 2.5 50.0 + - + +
57F VAL* 4.2 30.3 - - + +
60F LEU* 3.4 35.9 - - + -
61F ILE* 6.0 5.8 - - + -
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Residues in contact with TYR 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E PHE 6.1 0.4 - - - -
116E GLN 3.8 6.0 + - - +
118E MET* 1.3 85.5 - - + +
120E LEU* 1.3 58.0 + - - +
122E LYS* 3.8 10.8 - - + +
123E ASP* 2.9 42.4 + - - +
56F GLU* 4.8 18.5 + - + -
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Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E GLN 4.6 6.3 + - - +
117E TYR* 5.5 2.7 - - - +
118E MET 3.4 0.6 - - - -
119E TYR* 1.3 78.1 - - - +
121E LEU* 1.3 80.6 + - + +
123E ASP* 3.7 5.7 + - - +
124E LEU* 3.0 35.6 + - + +
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Residues in contact with LEU 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D MET* 6.4 2.2 - - - -
94D LEU* 5.7 0.9 - - - +
117E TYR* 3.3 40.1 + - + +
118E MET 3.4 1.4 + - - -
120E LEU* 1.3 99.1 - - + +
122E LYS* 1.3 60.3 + - - +
123E ASP 3.4 0.2 - - - -
124E LEU* 3.7 19.9 - - + +
125E TRP* 3.1 25.8 + - - +
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Residues in contact with LYS 122 (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 TYR 4.3 0.2 + - - -
118E MET* 2.5 35.2 + - + +
119E TYR* 3.8 9.6 - - + +
121E LEU* 1.3 72.2 - - - +
123E ASP* 1.3 58.0 + - - +
125E TRP* 3.4 4.4 + - + +
126E GLN* 2.6 69.3 + - + +
60F LEU* 4.0 37.0 - - + +
64F ILE* 5.2 8.9 - - - +
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Residues in contact with ASP 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E TYR* 2.9 27.1 + - - +
120E LEU* 3.8 6.4 - - - +
122E LYS* 1.3 79.1 - - - +
124E LEU* 1.3 59.0 + - - +
125E TRP 3.1 0.2 - - - -
126E GLN* 4.3 7.6 - - - +
127E LYS* 2.8 50.7 + - + +
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Residues in contact with LEU 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 LEU* 3.0 26.6 + - + +
121E LEU* 3.9 25.6 - - + +
122E LYS 3.3 0.4 - - - -
123E ASP* 1.3 75.2 - - - +
125E TRP* 1.3 56.7 + - - +
127E LYS* 5.2 0.4 - - - -
128E ARG* 3.3 20.4 + - - +
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Residues in contact with TRP 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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94D LEU* 3.0 54.0 - - + +
97D ASP* 5.6 6.3 + - - +
121E LEU 3.1 16.8 + - - +
122E LYS* 3.9 3.6 - - + +
124E LEU* 1.3 76.6 - - - +
126E GLN* 1.3 92.7 + - + +
127E LYS 3.1 1.3 - - - -
128E ARG* 2.8 11.6 + - + +
129E GLN* 2.5 58.7 + - + +
64F ILE* 5.1 6.1 - - + -
68F TYR* 3.4 59.2 - + + -
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Residues in contact with GLN 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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122E LYS* 2.6 60.6 + - + +
123E ASP* 4.3 6.7 - - - +
125E TRP* 1.3 92.9 - - + +
127E LYS* 1.3 52.5 + - - +
129E GLN* 3.1 8.9 + - - +
130E LYS* 2.3 66.8 + - - +
64F ILE* 5.2 2.6 - - - +
68F TYR* 3.5 26.6 + - - -
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Residues in contact with LYS 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 ASP* 2.8 36.0 + - + +
124E LEU* 5.2 0.7 - - - -
126E GLN* 1.3 75.1 - - - +
128E ARG* 1.3 60.1 + - - +
129E GLN 3.3 0.4 - - - -
130E LYS* 3.4 44.3 - - + +
131E GLN* 3.1 44.0 + - + +
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Residues in contact with ARG 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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98D PHE* 6.2 5.4 - - + -
101D ALA* 5.4 13.1 - - + +
124E LEU 3.3 19.4 + - - +
125E TRP* 2.8 18.1 + - + +
127E LYS* 1.3 76.2 + - - +
129E GLN* 1.3 58.4 + - - +
131E GLN* 3.6 28.7 + - - +
132E VAL* 3.0 61.2 + - - +
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Residues in contact with GLN 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 TRP* 2.5 51.5 + - + +
126E GLN* 3.4 13.9 - - - +
128E ARG* 1.3 73.8 - - - +
130E LYS* 1.3 66.4 + - - +
131E GLN 3.3 0.4 - - - -
132E VAL* 3.1 11.6 - - + +
133E LYS* 3.0 60.3 + - - +
68F TYR* 4.4 18.0 + - + -
79F ILE* 6.4 0.4 - - - +
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Residues in contact with LYS 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 GLN* 2.3 53.7 + - - +
127E LYS* 3.4 43.5 - - + +
129E GLN* 1.3 75.1 - - - +
131E GLN* 1.3 62.6 + - - +
133E LYS* 3.3 33.3 - - + +
134E ASP* 3.7 13.5 + - - +
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Residues in contact with GLN 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 LYS* 3.1 31.7 + - + +
128E ARG* 3.6 24.0 + - - +
130E LYS* 1.3 76.4 - - - +
132E VAL* 1.3 59.8 + - - +
134E ASP* 3.5 5.5 + - - +
135E ASN* 3.0 25.7 + - - +
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Residues in contact with VAL 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E ARG* 3.0 50.0 - - - +
129E GLN* 3.1 20.4 - - + +
131E GLN* 1.3 74.3 - - - +
133E LYS* 1.3 58.4 + - - +
134E ASP 3.3 0.2 - - - -
135E ASN* 3.5 12.2 - - + +
136E GLU* 2.9 19.2 + - - +
79F ILE* 3.3 45.0 - - + +
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Residues in contact with LYS 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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129E GLN* 3.0 45.1 + - - +
130E LYS* 3.3 28.0 - - + +
132E VAL* 1.3 75.5 - - - +
134E ASP* 1.3 72.0 + - - +
136E GLU* 2.8 50.8 - - - +
137E ASN* 3.8 4.5 + - - -
79F ILE* 4.7 1.8 - - - -
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Residues in contact with ASP 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 LYS 3.7 13.0 + - - +
131E GLN* 3.5 8.1 + - - +
132E VAL 3.3 0.2 - - - -
133E LYS* 1.3 86.7 - - - +
135E ASN* 1.3 57.3 + - - +
136E GLU 3.2 4.9 - - - -
137E ASN* 3.4 13.8 + - - +
138E VAL* 2.9 27.1 + - - +
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Residues in contact with ASN 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 GLN 3.0 17.9 + - - +
132E VAL* 3.5 15.7 - - + +
133E LYS 3.4 0.4 - - - -
134E ASP* 1.3 73.6 - - - +
136E GLU* 1.3 59.6 + - - +
137E ASN 3.2 0.7 - - - -
138E VAL* 3.1 24.8 - - - +
139E VAL* 3.1 33.9 + - - +
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Residues in contact with GLU 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 VAL 2.9 12.4 + - - +
133E LYS* 2.8 38.1 - - - +
134E ASP 3.2 0.4 - - - -
135E ASN* 1.3 78.9 - - - +
137E ASN* 1.3 75.8 + - - +
139E VAL* 4.9 1.1 - - - -
140E ASN* 3.0 22.7 - - - +
79F ILE* 4.9 9.9 - - + +
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Residues in contact with ASN 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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133E LYS 3.8 5.2 + - - +
134E ASP* 3.4 17.1 + - - +
136E GLU* 1.3 105.7 + - - +
138E VAL* 1.3 60.3 + - - +
139E VAL 3.4 2.0 - - - -
140E ASN* 3.9 23.7 + - - +
141E GLU* 4.7 8.1 + - - +
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Residues in contact with VAL 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 ASP 2.9 15.1 + - - +
135E ASN* 3.1 36.1 - - - +
137E ASN* 1.3 78.8 - - - +
139E VAL* 1.3 64.0 + - + +
140E ASN 3.6 0.2 - - - -
141E GLU* 4.8 4.8 + - - +
142E TYR* 3.6 16.3 - - - -
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Residues in contact with VAL 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E ASN* 3.1 32.5 + - - +
136E GLU* 4.9 0.9 - - - -
138E VAL* 1.3 81.2 - - + +
140E ASN* 1.3 60.0 + - - +
141E GLU 3.3 1.8 - - - -
142E TYR* 3.6 31.8 + - + +
143E SER* 5.0 4.0 + - - -
82F ALA* 5.5 13.0 - - + -
83F THR* 5.1 14.4 - - + -
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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
------------------------------------------------------------
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