Contacts of the helix formed by residues 118 - 133 (chain E) in PDB entry 1M54
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 VAL 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110E GLU* 3.3 32.3 - - + -
113E ASN* 4.2 0.9 - - - +
117E SER* 1.3 73.3 - - - +
119E LYS* 1.3 90.9 + - + +
120E ASP 3.1 2.2 - - - -
121E ARG* 3.2 18.8 + - - +
122E ILE* 4.0 2.1 + - - +
232E HIS* 3.6 28.6 - - + +
236E THR* 6.0 1.1 - - + -
260E THR* 3.9 12.8 - - + -
373E ILE* 5.5 5.4 - - + -
375E PRO* 3.1 29.3 + - + +
1510E PLP 4.3 5.8 - - + +
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Residues in contact with LYS 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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117E SER* 3.4 3.9 - - - +
118E VAL* 1.3 85.2 - - - +
120E ASP* 1.3 57.6 + - - +
121E ARG 2.8 1.2 + - - -
122E ILE* 2.9 34.4 + - + +
123E SER* 2.6 36.8 + - - -
149E ASN* 3.3 18.2 - - + +
150E THR* 3.0 53.4 - - + +
222E GLN* 4.0 2.9 - - - +
257E THR* 4.8 2.9 - - - -
260E THR* 5.9 0.7 - - - -
1510E PLP 1.5 66.4 + - + +
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Residues in contact with ASP 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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84E ILE* 3.4 32.4 - - + +
113E ASN* 3.3 11.9 - - + +
114E ALA 3.8 0.2 + - - -
115E GLY* 2.6 41.6 + - - +
117E SER* 3.2 24.7 + - - +
119E LYS* 1.3 74.6 - - - +
121E ARG* 1.3 55.5 + - - +
123E SER* 3.3 8.8 - - - -
124E LEU* 2.9 29.6 + - - +
149E ASN 4.9 0.2 - - - +
152E ILE* 4.9 0.9 - - - +
153E GLY* 3.8 18.5 + - - -
156E LEU* 5.5 2.2 - - - -
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Residues in contact with ARG 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E ILE* 3.4 19.2 + - + +
85E GLY* 3.4 14.9 - - - -
87E THR* 3.0 12.7 + - - +
108E LYS* 4.0 2.0 - - - +
110E GLU* 2.7 37.3 + - - +
113E ASN* 4.8 0.9 - - - +
118E VAL 3.2 9.3 + - - +
119E LYS 2.8 4.2 + - - -
120E ASP* 1.3 70.0 - - - +
122E ILE* 1.3 51.7 + - + +
123E SER 2.8 4.5 + - - -
124E LEU* 2.6 26.7 + - - +
125E ARG* 2.8 18.7 + - - +
231E ALA* 4.6 6.3 - - + -
232E HIS* 3.5 16.3 + - + +
235E THR* 3.7 14.1 + - - +
236E THR* 2.6 33.8 + - - +
239E GLU* 2.9 43.2 + - - -
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Residues in contact with ILE 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 VAL 4.4 2.5 - - - +
119E LYS* 2.9 47.8 + - + +
121E ARG* 1.3 71.7 - - + +
123E SER* 1.3 62.4 + - - +
124E LEU 3.3 0.2 - - - -
125E ARG* 4.3 8.5 - - - -
126E MET* 3.0 47.8 + - + +
150E THR* 4.0 6.5 - - + -
222E GLN* 4.1 4.0 - - + -
228E ASN* 3.0 58.1 - - - +
231E ALA* 4.4 2.9 - - + +
232E HIS* 3.4 26.2 - - + +
1510E PLP 5.7 0.2 - - - +
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Residues in contact with SER 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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119E LYS* 2.6 23.5 + - - -
120E ASP* 3.3 10.8 - - - -
122E ILE* 1.3 82.9 - - - +
124E LEU* 1.3 58.1 + - - +
126E MET* 4.2 1.8 - - - -
127E ILE* 2.8 29.8 + - - +
150E THR* 3.7 4.3 + - - +
153E GLY* 2.9 8.2 - - - -
154E LEU* 2.7 45.6 + - - +
157E ALA* 4.9 3.3 - - - +
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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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81E LEU* 3.5 46.2 - - + +
84E ILE* 4.4 20.9 - - + +
120E ASP 2.9 14.1 + - - +
121E ARG* 2.6 12.2 + - - +
123E SER* 1.3 70.0 - - - +
125E ARG* 1.3 55.3 + - - +
126E MET 3.0 0.7 - - - -
127E ILE* 2.8 8.6 + - + -
128E GLU* 2.6 68.0 + - + +
157E ALA* 5.2 7.2 - - + -
161E ARG* 4.8 7.0 - - - +
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Residues in contact with ARG 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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66E HIS* 2.5 36.8 + - - +
67E HIS* 4.1 0.8 - - - +
68E THR* 3.6 18.9 + - - -
121E ARG 2.8 13.2 + - - +
122E ILE* 4.3 2.5 - - - -
124E LEU* 1.3 76.2 - - - +
126E MET* 1.3 52.1 + - - +
128E GLU* 2.9 15.5 + - - -
129E ASP* 2.4 70.9 + - - +
132E ARG* 4.3 4.2 - - - +
227E SER* 3.3 19.0 + - - +
230E LEU* 2.9 37.4 - - - +
231E ALA* 3.6 20.8 - - + +
234E ASP* 4.0 10.0 + - - -
235E THR* 6.3 2.0 - - - -
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Residues in contact with MET 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 ILE* 3.0 50.2 + - + +
123E SER* 4.2 5.6 - - - +
124E LEU 2.9 0.4 + - - -
125E ARG* 1.3 74.9 - - - +
127E ILE* 1.4 55.3 + - - +
128E GLU 2.8 13.0 + - - -
129E ASP* 3.0 10.4 + - - +
130E ALA* 3.2 17.2 + - - +
144E GLU* 5.9 0.2 - - - +
150E THR* 4.8 4.0 - - + -
154E LEU* 4.9 5.8 - - + -
220E LEU* 3.1 49.2 - - + +
222E GLN* 4.4 16.8 - - + -
225E ASN* 3.7 16.4 + - + +
227E SER* 3.6 22.0 - - - -
228E ASN* 4.1 13.5 - - + -
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Residues in contact with ILE 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 SER 2.8 25.8 - - - +
124E LEU* 2.8 11.0 + - + +
126E MET* 1.4 70.1 - - - +
128E GLU* 1.3 57.1 + - - +
131E GLU* 2.9 38.1 - - - +
136E LEU* 3.7 9.2 - - + -
142E ILE* 2.8 38.1 - - + -
154E LEU* 3.6 36.3 - - + +
157E ALA* 4.6 11.2 - - + -
158E ALA 4.6 5.8 - - - +
161E ARG* 5.5 5.8 - - - -
163E TYR* 3.6 20.9 - - + -
220E LEU* 4.1 3.4 - - + -
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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 LEU* 2.6 49.5 + - + +
125E ARG* 3.2 15.9 - - - +
126E MET 2.8 1.0 - - - -
127E ILE* 1.3 78.5 - - - +
129E ASP* 1.3 60.8 + - - +
130E ALA 3.5 0.4 - - - -
131E GLU* 4.2 10.5 - - - +
132E ARG* 3.6 34.3 + - - +
161E ARG* 5.0 10.3 + - - +
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Residues in contact with ASP 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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66E HIS* 4.4 8.3 - - - +
125E ARG* 2.4 57.1 + - - -
126E MET 3.0 0.2 + - - -
128E GLU* 1.3 69.0 - - - +
130E ALA* 1.3 66.0 + - - +
131E GLU 3.3 0.2 - - - -
132E ARG* 3.3 32.3 + - - +
133E ASP* 3.0 31.7 + - - +
227E SER* 2.8 32.0 + - - +
230E LEU* 4.0 5.0 - - - +
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Residues in contact with ALA 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 MET 3.2 14.7 + - - +
129E ASP* 1.3 76.2 - - - +
131E GLU* 1.3 68.0 + - - +
133E ASP* 3.2 13.3 + - - -
135E THR* 3.3 38.6 + - - +
136E LEU* 3.9 17.5 - - + -
218E HIS* 6.6 0.2 - - + -
220E LEU* 4.4 14.8 - - + -
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Residues in contact with GLU 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 ILE* 2.9 28.3 + - - +
128E GLU* 4.2 12.4 - - - +
129E ASP 3.3 0.2 - - - -
130E ALA* 1.3 78.7 - - - +
132E ARG* 1.3 65.3 + - - +
134E GLY* 3.0 14.9 + - - -
136E LEU* 3.4 30.6 - - + +
161E ARG* 4.4 15.9 - - - +
163E TYR* 2.6 37.4 + - - +
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Residues in contact with ARG 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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66E HIS* 4.1 16.2 + - + +
68E THR* 3.0 38.3 - - - +
125E ARG* 4.3 3.8 - - - +
128E GLU* 3.6 24.1 + - - +
129E ASP* 3.3 30.5 + - - +
130E ALA 3.2 0.4 - - - -
131E GLU* 1.3 79.7 - - - +
133E ASP* 1.3 64.0 + - - +
134E GLY* 3.2 1.6 + - - -
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Residues in contact with ASP 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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66E HIS* 3.8 27.5 + - - -
129E ASP* 3.0 19.6 + - - +
130E ALA* 3.2 5.2 + - - +
132E ARG* 1.3 76.0 - - - +
134E GLY* 1.3 58.8 + - - +
135E THR* 3.4 21.2 - - + +
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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