Contacts of the helix formed by residues 123 - 135 (chain E) in PDB entry 4F2N
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 PRO 123 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121E PRO 3.3 8.7 - - - +
122E MET* 1.3 90.4 - - + +
124E LYS* 1.3 67.7 + - - +
125E THR* 3.3 3.4 - - - +
126E LEU* 3.2 4.2 + - + -
127E GLU* 3.0 19.3 + - - +
218E TRP* 3.4 20.4 - - + +
219E GLU* 4.3 14.6 - - + -
222E CYS* 3.8 31.2 - - + -
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Residues in contact with LYS 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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122E MET 3.8 1.4 + - - +
123E PRO* 1.3 69.6 - - - +
125E THR* 1.3 59.9 + - - +
127E GLU* 3.2 36.3 + - - +
128E ASN* 2.8 55.6 + - - +
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Residues in contact with THR 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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123E PRO* 4.6 1.8 - - - +
124E LYS* 1.3 79.6 - - - +
126E LEU* 1.3 60.9 + - - +
128E ASN* 3.5 8.6 + - - +
129E ALA* 3.1 22.0 + - - +
222E CYS* 4.1 19.1 - - - -
225E TYR* 4.4 19.2 - - + -
226E GLU* 4.5 12.1 + - + +
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Residues in contact with LEU 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 MET* 3.9 8.1 - - + -
123E PRO* 3.2 8.9 + - + +
125E THR* 1.3 76.8 - - - +
127E GLU* 1.3 66.3 + - - +
129E ALA* 3.2 4.4 + - + +
130E ILE* 2.9 45.6 + - + +
168E LEU* 5.2 0.2 - - + -
187E ILE* 4.3 12.3 - - + -
218E TRP* 3.6 46.2 - - + +
221E VAL* 3.6 13.5 - - + -
222E CYS* 3.9 17.9 - - + +
225E TYR* 4.2 28.9 - - + -
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Residues in contact with GLU 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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122E MET* 3.5 26.0 - - + +
123E PRO 3.0 13.2 + - - +
124E LYS* 3.2 45.2 + - - +
126E LEU* 1.3 75.8 - - - +
128E ASN* 1.3 61.8 + - - +
130E ILE* 3.8 1.2 - - - +
131E ALA* 2.9 31.1 + - + +
137E VAL* 3.7 20.1 - - + +
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Residues in contact with ASN 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 LYS* 2.8 45.4 + - - +
125E THR* 3.6 7.3 - - - +
127E GLU* 1.3 82.0 - - - +
129E ALA* 1.3 56.7 + - - +
131E ALA* 3.4 5.8 + - - +
132E LYS* 3.0 30.4 + - - +
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Residues in contact with ALA 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 THR 3.1 16.1 + - - +
126E LEU* 3.2 5.8 + - + +
128E ASN* 1.3 72.7 - - - +
130E ILE* 1.3 66.2 + - - +
132E LYS* 3.5 7.0 + - - +
133E GLN* 3.1 23.9 + - - +
168E LEU* 3.7 8.2 - - + +
225E TYR* 3.3 42.8 - - + +
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Residues in contact with ILE 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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122E MET* 4.3 16.2 - - + -
126E LEU* 2.9 48.3 + - + +
127E GLU 3.9 2.9 - - - +
129E ALA* 1.3 73.9 - - - +
131E ALA* 1.3 62.6 + - - +
133E GLN 3.3 0.2 + - - -
134E PHE* 2.9 35.0 + - + +
137E VAL* 4.0 17.5 - - + -
140E PHE* 3.5 37.5 - - + -
159E LEU* 4.3 18.4 - - + -
168E LEU* 4.0 15.0 - - + -
218E TRP* 4.5 5.8 - - + -
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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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127E GLU* 2.9 20.5 + - + +
128E ASN* 3.9 5.6 - - - +
130E ILE* 1.3 77.3 - - - +
132E LYS* 1.3 56.4 + - - +
135E GLY* 3.0 33.2 + - - +
136E SER* 3.9 23.3 - - - +
137E VAL* 4.3 7.2 - - + +
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Residues in contact with LYS 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 ASN 3.0 17.8 + - - +
129E ALA* 3.8 7.4 - - - +
130E ILE 3.2 0.2 - - - -
131E ALA* 1.3 80.3 - - - +
133E GLN* 1.3 61.5 + - - +
135E GLY* 4.4 2.1 + - - -
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Residues in contact with GLN 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 ALA 3.1 17.3 + - - +
132E LYS* 1.3 80.9 - - - +
134E PHE* 1.3 84.0 + - + +
135E GLY 3.5 0.2 - - - -
167E GLU* 3.3 29.1 + - - +
168E LEU* 3.0 47.5 + - + +
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Residues in contact with PHE 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 ILE* 2.9 24.0 + - + +
133E GLN* 1.3 98.2 - - + +
135E GLY* 1.3 56.0 + - - +
136E SER 3.3 4.0 - - - +
139E ASP* 3.3 20.0 - - - +
140E PHE* 3.8 42.4 - + + +
143E SER* 5.4 3.1 - - - -
159E LEU* 3.7 22.4 - - + -
168E LEU* 3.8 25.8 - - + -
169E LEU* 4.0 4.0 - - - -
170E ILE* 3.8 32.1 - - + -
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Residues in contact with GLY 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 ALA* 3.0 18.7 + - - +
132E LYS 4.4 1.9 + - - -
133E GLN 3.5 2.2 - - - -
134E PHE* 1.3 75.7 - - - +
136E SER* 1.3 62.0 + - - +
139E ASP* 4.4 4.0 - - - -
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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