Contacts of the helix formed by residues 118 - 129 (chain E) in PDB entry 2P1N
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 THR 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E TYR* 5.9 1.2 - - - -
94E TYR* 5.1 3.5 - - + +
116E VAL* 4.8 9.9 + - - +
117E VAL* 1.3 74.1 - - - +
119E ASP* 1.3 67.2 + - - +
120E ASP* 2.8 38.8 - - + +
121E CYS* 3.1 29.5 + - - +
122E LEU* 3.3 12.0 + - - +
142E GLY 3.6 10.8 + - - -
143E PHE* 4.0 1.8 - - - -
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Residues in contact with ASP 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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118E THR* 1.3 70.5 - - - +
120E ASP* 1.3 65.7 + - - +
122E LEU* 2.8 18.6 + - - +
123E GLU* 2.9 27.0 + - - +
142E GLY 4.2 2.6 + - - -
143E PHE* 3.3 6.3 - - - +
144E SER* 2.7 50.2 + - - +
146E ASP* 3.2 10.3 - - + +
147E GLY* 3.1 21.5 + - - +
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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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94E TYR* 4.3 17.0 - - + -
118E THR* 2.8 17.9 - - + +
119E ASP* 1.3 79.0 - - - +
121E CYS* 1.3 60.5 + - - +
122E LEU 3.0 0.2 + - - -
123E GLU* 3.2 14.9 + - - +
124E LEU* 3.1 21.1 + - - +
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Residues in contact with CYS 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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93E VAL* 3.9 12.3 - - + -
94E TYR* 3.8 45.9 - - - -
97E ILE* 4.3 10.5 - - + +
116E VAL 4.9 0.9 - - - -
117E VAL* 4.3 10.5 - - + -
118E THR* 3.1 40.1 + - - +
120E ASP* 1.3 72.5 - - - +
122E LEU* 1.3 59.5 + - + +
124E LEU* 3.5 5.4 + - - +
125E ILE* 2.8 34.5 + - + +
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Residues in contact with LEU 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 VAL* 4.2 16.4 - - + -
118E THR 3.6 8.3 - - - +
119E ASP* 2.8 12.0 + - - +
121E CYS* 1.3 75.4 - - + +
123E GLU* 1.3 62.6 + - - +
125E ILE* 3.2 10.8 + - + +
126E ALA* 2.9 29.3 + - - +
135E LEU* 3.8 31.4 - - + -
137E LEU* 4.4 4.7 - - + -
143E PHE* 3.8 42.6 - - + -
147E GLY* 3.9 33.2 - - - +
148E LEU* 4.4 3.1 - - + +
150E ALA* 5.1 1.1 - - - -
151E ILE* 3.5 12.9 - - + +
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Residues in contact with GLU 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 ASP* 2.9 30.8 + - - +
120E ASP* 3.5 21.1 - - - +
122E LEU* 1.3 77.1 - - - +
124E LEU* 1.3 51.3 + - - +
126E ALA* 3.0 8.2 + - - +
127E LYS* 2.8 38.5 + - - +
146E ASP* 5.0 8.3 - - - +
147E GLY* 5.7 1.3 - - - -
150E ALA* 4.0 20.8 - - + +
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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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94E TYR* 4.1 23.6 - - + +
97E ILE* 3.4 26.7 - - + +
98E GLU* 4.0 20.9 - - - +
101E SER* 4.3 8.5 - - - +
120E ASP 3.1 13.8 + - - +
121E CYS* 3.7 4.5 - - - +
123E GLU* 1.3 75.0 - - - +
125E ILE* 1.3 65.5 + - - +
126E ALA 3.1 1.1 - - - -
127E LYS* 4.5 13.0 - - + +
128E SER* 2.6 47.5 + - - +
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Residues in contact with ILE 125 (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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97E ILE* 3.7 23.3 - - + +
110E ILE* 3.1 33.0 - - + -
121E CYS* 2.8 33.8 + - + +
122E LEU* 3.4 16.8 - - + +
124E LEU* 1.3 70.1 - - - +
126E ALA* 1.3 71.8 + - - +
128E SER 3.1 8.3 + - - -
129E PHE* 3.2 36.2 + - + +
132E PHE* 3.7 33.7 - - + +
135E LEU* 5.4 4.5 - - + -
151E ILE* 4.3 6.1 - - + -
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Residues in contact with ALA 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 LEU 2.9 13.9 + - - +
123E GLU* 3.0 12.3 + - - +
125E ILE* 1.3 82.7 - - - +
127E LYS* 1.3 61.9 + - + +
128E SER 3.4 0.3 + - - -
129E PHE 4.0 11.4 - - - +
130E LYS* 5.4 0.9 - - - -
150E ALA* 4.0 14.6 - - + +
151E ILE* 4.0 8.7 - - + -
154E THR* 3.5 34.6 - - + +
155E CYS* 4.3 15.1 - - - -
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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 GLU 2.8 16.1 + - - +
124E LEU* 4.7 11.4 - - + +
126E ALA* 1.3 79.7 - - + +
128E SER* 1.3 61.7 + - - +
129E PHE 5.5 0.2 - - - -
154E THR* 4.4 10.1 - - + -
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Residues in contact with SER 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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101E SER* 3.1 40.3 - - - +
105E THR* 3.9 20.4 - - - +
124E LEU* 2.6 35.5 + - - +
125E ILE 3.1 0.9 + - - -
127E LYS* 1.3 81.6 - - - +
129E PHE* 1.3 71.5 + - - +
130E LYS 4.1 1.5 + - - -
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Residues in contact with PHE 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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97E ILE* 5.0 5.4 - - + -
100E MET* 4.1 26.2 - - + -
101E SER* 4.2 14.6 - - - -
104E TYR 3.3 27.1 - - - -
105E THR* 4.0 5.4 - - - +
107E LEU* 3.5 52.9 - - + +
110E ILE* 4.2 0.4 - - + -
124E LEU 4.9 0.2 - - - -
125E ILE* 3.2 55.0 + - + +
126E ALA 4.0 10.3 - - - +
127E LYS 5.5 0.2 - - - -
128E SER* 1.3 81.6 - - - +
130E LYS* 1.3 66.6 + - - +
131E ASN 3.1 0.8 + - - -
132E PHE* 3.4 20.4 + + + +
155E CYS* 5.4 2.6 - - - -
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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