Contacts of the helix formed by residues 119 - 130 (chain E) in PDB entry 4P5O
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 LYS 119 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69E TYR* 3.1 37.6 - - + +
78E GLU* 6.1 0.9 - - + -
79E ASN* 2.3 39.0 + - + +
118E SER* 1.3 68.3 - - - +
120E GLN* 1.3 58.5 + - - +
122E PHE* 3.2 1.4 + - - +
123E MET* 2.8 35.8 + - + +
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Residues in contact with GLN 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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79E ASN* 5.6 1.5 - - - +
118E SER* 3.2 7.9 + - - +
119E LYS* 1.3 77.8 - - - +
121E GLU* 1.3 57.8 + - + +
123E MET* 4.6 2.9 - - - -
124E ASP* 3.0 59.2 + - - +
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Residues in contact with GLU 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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109E PHE* 3.6 28.1 - - - +
110E ARG 4.2 4.4 - - - +
111E ALA* 3.6 13.2 - - - -
112E ALA* 2.9 29.5 + - - +
116E GLU* 3.4 7.4 - - - +
117E PHE* 3.3 24.3 - - + -
118E SER* 3.0 42.1 + - - +
120E GLN* 1.3 77.4 - - - +
122E PHE* 1.3 57.5 + - - +
124E ASP* 4.6 0.4 - - - +
125E GLY* 2.9 28.9 + - - -
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Residues in contact with PHE 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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65E LEU* 3.5 29.6 - - + -
68E LEU* 4.4 18.4 - - + -
69E TYR* 4.1 22.0 - + + -
72E TYR* 4.0 28.0 - + - -
81E ILE* 3.5 26.0 - - + -
89E PHE* 4.4 17.9 - + - -
109E PHE* 4.5 18.5 - + - -
117E PHE* 5.0 8.0 - + + -
118E SER 3.0 11.9 + - - +
119E LYS 3.6 6.5 - - - +
121E GLU* 1.3 75.8 - - - +
123E MET* 1.3 60.5 + - - +
125E GLY* 3.7 0.2 - - - -
126E MET* 2.9 53.7 + - + +
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Residues in contact with MET 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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62E ARG* 3.4 53.2 - - + +
65E LEU* 3.5 36.6 - - + -
66E GLU* 3.9 20.2 - - - +
69E TYR* 6.0 3.6 - - - -
119E LYS* 2.8 22.5 + - + +
120E GLN* 4.0 3.4 - - - +
122E PHE* 1.3 79.1 - - + +
124E ASP* 1.3 65.3 + - - +
126E MET* 3.3 1.7 + - - +
127E THR* 2.9 36.4 + - + +
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Residues in contact with ASP 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 GLN* 3.0 43.2 + - - +
121E GLU* 5.3 0.2 - - - -
123E MET* 1.3 83.0 - - - +
125E GLY* 1.3 62.4 + - - +
127E THR* 2.8 19.9 + - - +
128E GLU* 3.0 24.4 + - - +
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Residues in contact with GLY 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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108E LYS 4.5 4.4 - - - +
109E PHE* 3.7 28.7 + - - -
121E GLU 2.9 20.5 + - - -
124E ASP* 1.3 78.6 - - - +
126E MET* 1.3 56.6 + - - +
128E GLU* 3.8 2.0 - - - +
129E LEU* 2.9 32.6 + - - +
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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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65E LEU* 3.9 16.8 - - + -
68E LEU* 5.2 4.7 - - + -
89E PHE* 5.7 1.6 - - + -
109E PHE* 3.6 24.8 - - + -
122E PHE* 2.9 47.1 + - + +
123E MET 3.9 2.7 - - - +
125E GLY* 1.3 75.8 - - - +
127E THR* 1.3 53.6 + - - +
129E LEU* 3.2 3.0 + - - -
130E GLY 2.7 28.2 + - - -
131E CYS* 3.1 47.5 + - + +
132E ASP 5.0 0.7 - - - -
133E SER* 3.8 19.5 - - - +
134E ILE* 5.4 0.4 - - + -
137E LEU* 3.8 22.0 - - + -
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Residues in contact with THR 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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62E ARG* 4.2 21.8 - - - +
65E LEU* 3.9 18.8 - - + -
123E MET* 2.9 24.3 + - + +
124E ASP* 2.8 25.3 + - - +
126E MET* 1.3 77.0 - - - +
128E GLU* 1.3 59.4 + - - +
130E GLY* 3.2 15.6 + - - +
131E CYS 5.6 0.4 - - - -
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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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110E ARG* 5.9 0.9 + - - -
124E ASP* 3.0 22.7 + - - +
125E GLY* 4.4 1.6 - - - +
127E THR* 1.3 74.5 + - - +
129E LEU* 1.3 62.2 + - - +
130E GLY 3.1 5.2 - - - -
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Residues in contact with LEU 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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105E ILE* 4.5 0.2 - - + -
108E LYS* 4.1 37.5 - - + +
109E PHE* 3.6 28.7 - - + -
125E GLY 2.9 16.8 + - - +
126E MET* 3.4 6.7 - - - +
128E GLU* 1.3 79.6 - - - +
130E GLY* 1.3 63.7 + - - +
131E CYS* 3.4 16.8 - - - -
137E LEU* 3.6 20.0 - - + -
140E GLN* 4.2 31.0 + - + +
144E MET* 4.3 12.3 - - + -
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Residues in contact with GLY 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 2.7 8.6 + - - -
127E THR* 3.2 11.3 + - - -
128E GLU 3.1 4.6 - - - -
129E LEU* 1.3 79.5 - - - +
131E CYS* 1.3 58.5 + - - -
132E ASP* 4.1 7.2 - - - +
136E LYS* 5.4 1.4 - - - +
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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