Contacts of the helix formed by residues 113 - 134 (chain E) in PDB entry 3UDB
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 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E ARG 4.2 0.6 + - - -
112E PHE* 1.3 77.8 - - - +
114E GLU* 1.3 64.6 + - - +
115E ASP* 3.5 8.2 + - - +
116E GLU* 3.1 24.7 + - - +
117E ALA* 3.0 19.8 + - - +
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Residues in contact with GLU 114 (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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112E PHE 3.6 1.2 + - - -
113E SER* 1.3 73.4 - - - +
115E ASP* 1.3 62.4 + - - +
117E ALA* 3.2 8.0 + - - +
118E ARG* 3.0 45.7 + - + +
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Residues in contact with ASP 115 (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 SER* 3.2 8.6 + - - +
114E GLU* 1.3 79.0 - - - +
116E GLU* 1.3 57.7 + - - +
118E ARG* 2.7 39.4 + - - +
119E PHE* 3.1 24.9 + - - +
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Residues in contact with GLU 116 (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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105E ARG* 2.6 32.9 + - - -
109E ALA* 5.8 1.2 - - - +
112E PHE* 2.8 42.4 - - + -
113E SER* 3.1 23.5 + - - +
115E ASP* 1.3 74.6 - - - +
117E ALA* 1.3 65.5 + - - +
119E PHE* 3.3 24.7 + - - +
120E PHE* 3.3 17.5 + - + -
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Residues in contact with ALA 117 (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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112E PHE* 4.1 16.1 - - + +
113E SER 3.0 12.9 + - - +
114E GLU* 3.7 10.5 - - - +
116E GLU* 1.3 75.5 - - - +
118E ARG* 1.3 58.5 + - - +
120E PHE* 3.3 4.7 + - - +
121E PHE* 2.9 32.7 + - - +
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Residues in contact with ARG 118 (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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114E GLU* 3.0 34.0 + - + +
115E ASP* 2.7 38.1 + - - +
117E ALA* 1.3 75.2 - - - +
119E PHE* 1.3 58.3 + - - +
121E PHE* 4.2 8.5 - - + -
122E GLN* 2.9 66.4 + - + +
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Residues in contact with PHE 119 (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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115E ASP 3.1 12.2 + - - +
116E GLU* 3.3 17.0 - - - +
117E ALA 3.2 0.2 - - - -
118E ARG* 1.3 81.1 - - - +
120E PHE* 1.3 83.0 + + - +
122E GLN* 4.0 12.5 - - - +
123E GLN* 3.1 45.1 + - - +
153E ALA* 4.7 15.0 - - + -
154E PRO* 3.5 24.2 - - + -
155E ARG* 3.7 22.0 - - - -
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Residues in contact with PHE 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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102E LEU* 4.3 17.3 - - + -
105E ARG* 3.9 21.8 - - - -
112E PHE* 3.3 34.3 - + - -
116E GLU* 3.3 23.4 + - - -
117E ALA* 3.3 6.1 + - - +
118E ARG 3.2 0.4 - - - -
119E PHE* 1.3 89.2 - + - +
121E PHE* 1.3 62.4 + - - +
122E GLN 3.2 1.6 - - - -
123E GLN* 3.1 11.9 + - - +
124E LEU* 2.9 28.6 + - - +
148E LEU* 3.7 26.0 - - + -
154E PRO* 3.7 31.9 - - + -
156E LEU* 4.3 15.3 - - + +
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Residues in contact with PHE 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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117E ALA 2.9 18.5 + - - +
118E ARG* 3.7 9.6 - - + +
120E PHE* 1.3 77.6 - - - +
122E GLN* 1.3 59.5 + - + +
124E LEU* 3.2 21.1 + - + +
125E ILE* 2.9 60.0 + - + +
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Residues in contact with GLN 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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118E ARG* 2.9 48.0 + - + +
119E PHE* 4.0 14.8 + - - +
121E PHE* 1.3 79.1 - - + +
123E GLN* 1.3 59.3 + - + +
125E ILE* 3.9 4.0 - - - +
126E SER* 2.9 31.1 + - - -
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Residues in contact with GLN 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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76E ASN* 2.9 36.7 + - - +
119E PHE* 3.1 53.2 + - - +
120E PHE* 3.1 11.8 + - - +
122E GLN* 1.3 76.2 - - + +
124E LEU* 1.3 65.8 + - - +
126E SER* 3.3 0.4 + - - -
127E GLY* 2.9 21.1 + - - -
154E PRO 4.0 3.2 + - - -
155E ARG* 3.4 24.4 + - - +
156E LEU* 2.8 37.0 + - + -
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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 PHE 2.9 14.0 + - - +
121E PHE* 3.5 29.6 - - + +
123E GLN* 1.3 76.1 - - - +
125E ILE* 1.3 62.3 + - + +
127E GLY* 3.3 0.9 + - - -
128E VAL* 2.9 50.4 + - + +
143E LEU* 5.5 8.7 - - + +
146E THR* 4.5 15.7 - - + -
156E LEU* 3.5 23.5 - - + +
158E ILE* 4.1 11.1 - - + +
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Residues in contact with ILE 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 PHE* 2.9 57.4 + - + +
122E GLN* 4.0 4.3 - - - +
124E LEU* 1.3 79.2 - - + +
126E SER* 1.3 61.3 + - - +
128E VAL* 4.1 10.2 - - + +
129E SER* 2.9 32.7 + - - -
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Residues in contact with SER 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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74E HIS* 3.0 24.4 + - - -
76E ASN* 3.5 12.8 + - - -
122E GLN 2.9 18.4 + - - -
125E ILE* 1.3 79.8 - - - +
127E GLY* 1.3 61.7 + - - +
129E SER* 3.6 5.1 - - - -
130E TYR* 3.1 19.1 + - - +
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Residues in contact with GLY 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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74E HIS* 3.5 21.5 - - - -
76E ASN* 3.9 5.4 - - - -
77E ILE* 3.9 8.1 - - - +
123E GLN 2.9 15.3 + - - -
124E LEU 3.7 1.6 - - - -
126E SER* 1.3 78.4 + - - +
128E VAL* 1.3 55.2 + - - +
130E TYR* 3.4 4.2 + - - +
131E ALA* 3.1 25.8 + - - +
158E ILE* 4.0 13.0 - - - -
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Residues in contact with VAL 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 LEU* 2.9 33.1 + - + +
125E ILE* 4.1 11.4 - - + +
127E GLY* 1.3 73.8 - - - +
129E SER* 1.3 64.0 + - - +
131E ALA* 3.4 5.6 + - - +
132E HIS* 3.0 50.7 + - + +
143E LEU* 4.6 16.8 - - + -
158E ILE* 4.0 15.3 - - + -
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Residues in contact with SER 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 ILE* 2.9 23.4 + - - -
126E SER* 3.6 7.0 - - - -
128E VAL* 1.3 77.4 - - - +
130E TYR* 1.3 63.5 + - - +
132E HIS* 3.3 10.2 + - - +
133E ALA* 3.1 22.2 + - - +
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Residues in contact with TYR 130 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71E SER 3.6 8.7 + - - -
72E LEU* 3.7 25.4 - - + -
73E ARG* 2.9 45.4 + - - +
74E HIS* 3.6 31.6 - + + -
77E ILE* 5.4 3.1 - - + -
126E SER 3.1 11.0 + - - +
127E GLY 3.5 9.6 - - - +
129E SER* 1.3 77.0 - - - +
131E ALA* 1.3 70.5 + - + +
133E ALA* 3.0 18.4 + - + +
134E MET* 3.1 37.2 + - + +
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Residues in contact with ALA 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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72E LEU* 4.8 7.6 - - + -
77E ILE* 4.1 17.0 - - + -
127E GLY 3.1 11.4 + - - +
128E VAL* 3.8 10.5 - - - +
129E SER 3.4 0.2 - - - -
130E TYR* 1.3 85.6 - - - +
132E HIS* 1.3 65.8 + - + +
134E MET* 3.3 12.8 + - - +
135E GLN 3.4 17.3 + - - +
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Residues in contact with HIS 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 VAL* 3.0 42.9 + - + +
129E SER* 3.5 9.8 - - - +
130E TYR 3.1 0.2 - - - -
131E ALA* 1.3 81.9 - - + +
133E ALA* 1.3 60.6 + - - +
134E MET 3.1 2.5 + - - -
135E GLN* 3.5 25.0 + - - +
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Residues in contact with ALA 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 SER 3.1 11.2 + - - +
130E TYR* 3.0 12.2 + - + +
132E HIS* 1.3 76.7 - - - +
134E MET* 1.3 64.2 + - - +
135E GLN* 3.3 10.0 + - - +
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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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68E ASN* 5.6 1.9 - - - +
71E SER* 3.4 35.8 + - - +
72E LEU* 3.6 30.2 - - + +
130E TYR* 3.1 36.3 + - + +
131E ALA 3.7 5.4 - - - +
132E HIS 3.1 0.8 - - - -
133E ALA* 1.3 84.4 - - - +
135E GLN* 1.3 72.4 + - - +
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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
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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