Contacts of the helix formed by residues 123 - 132 (chain E) in PDB entry 1IES
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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7E ASN* 3.9 7.9 - - - +
121E ALA* 3.2 13.0 - - + +
122E ASP* 1.3 84.4 - - - +
124E HIS* 1.3 56.9 + - - +
126E CYS* 3.5 8.1 + - + +
127E ASP* 2.8 29.8 + - - +
111F LEU* 3.8 26.9 - - + +
114F HIS* 3.5 46.4 - - + +
130F GLU* 4.1 4.5 - - - +
134F LEU* 3.7 11.2 - - + -
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Residues in contact with HIS 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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68E MET* 4.5 15.3 - - + +
71E GLN* 5.0 3.8 - - - -
72E ARG* 3.5 27.9 + - + +
122E ASP* 3.2 8.6 + - - +
123E PRO* 1.3 79.1 - - + +
125E LEU* 1.3 63.7 + - - +
127E ASP* 3.3 9.8 + - - +
128E PHE* 2.8 36.3 + + + +
111F LEU* 6.2 1.8 - - + -
134F LEU* 4.0 15.8 - - + +
135F ASP* 3.3 38.0 + - + -
138F VAL* 3.8 37.6 - - + +
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Residues in contact with LEU 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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8E TYR* 5.0 2.2 - - + -
12E VAL* 3.5 33.7 - - + -
16E VAL* 4.2 5.8 - - + -
68E MET* 3.6 32.8 - - + -
72E ARG* 5.7 1.1 - - - +
113E LEU* 3.9 25.6 - - + +
114E HIS* 5.4 0.2 - - - -
117E GLY* 3.7 26.2 - - - +
122E ASP* 3.2 21.5 + - + +
124E HIS* 1.3 77.6 + - - +
126E CYS* 1.3 68.1 + - - +
128E PHE* 3.1 6.1 + - + +
129E LEU* 2.9 33.3 + - + +
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Residues in contact with CYS 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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114E HIS* 3.8 36.1 + - + +
117E GLY* 3.7 4.3 - - - -
118E SER* 3.5 35.0 - - - -
122E ASP 3.2 15.3 + - - +
123E PRO* 3.6 11.7 - - + +
125E LEU* 1.3 79.7 - - - +
127E ASP* 1.3 61.9 + - - +
129E LEU* 3.4 2.7 + - - +
130E GLU* 3.0 31.4 + - - +
130F GLU* 5.2 4.3 - - - +
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Residues in contact with ASP 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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204D CD 4.1 11.1 - - - -
123E PRO 2.8 21.2 + - - +
124E HIS* 3.6 10.3 - - - +
126E CYS* 1.3 73.2 - - - +
128E PHE* 1.3 54.7 + - - +
130E GLU* 3.2 6.8 + - - +
131E SER* 2.7 53.9 + - - -
130F GLU* 3.7 50.3 + - + +
131F SER* 4.8 1.7 + - - -
134F LEU* 5.8 1.1 - - + +
135F ASP* 4.9 9.5 - - - +
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Residues in contact with PHE 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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64E ARG* 3.7 22.2 - - + -
65E LEU* 3.7 9.2 - - + -
68E MET* 3.6 55.6 - - + -
71E GLN* 6.2 1.1 - - - -
124E HIS* 2.8 31.4 + + + +
125E LEU* 3.4 7.6 - - - +
127E ASP* 1.3 75.1 + - - +
129E LEU* 1.3 68.2 + - + +
131E SER* 3.4 1.7 + - - -
132E HIS* 2.9 60.2 + + - +
133E PHE* 3.4 28.7 - + - -
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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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65E LEU* 4.7 3.8 - - + -
110E LEU* 3.9 28.3 - - + +
113E LEU* 3.7 30.1 - - + -
114E HIS* 3.7 42.0 - - + +
125E LEU* 2.9 22.6 + - + +
126E CYS 3.7 3.1 - - - +
128E PHE* 1.3 98.5 - - + +
130E GLU* 1.3 57.4 + - - +
133E PHE* 2.8 33.4 + - + -
134E LEU* 3.0 15.1 + - + -
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Residues in contact with GLU 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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123D PRO* 4.1 8.0 - - - +
126D CYS* 5.4 2.6 - - - +
127D ASP* 3.8 44.7 - - + +
130D GLU* 3.8 5.0 - - - +
203D CD 2.7 28.5 - - - -
114E HIS* 2.8 32.7 + - - +
126E CYS* 3.0 20.9 + - - +
127E ASP* 3.6 6.2 - - - +
129E LEU* 1.3 76.4 - - - +
131E SER* 1.3 64.1 + - - +
134E LEU* 3.7 26.1 + - + +
135E ASP* 4.1 6.9 + - - +
130F GLU* 3.9 4.2 - - - +
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Residues in contact with SER 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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127D ASP* 5.3 2.0 - - - -
127E ASP* 2.7 41.1 + - - -
128E PHE* 3.8 3.6 - - - -
130E GLU* 1.3 74.6 - - - +
132E HIS* 1.3 77.8 + - - +
135E ASP* 5.7 2.8 - - - +
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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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64E ARG* 3.7 38.6 + - - +
128E PHE* 2.9 51.5 + + - -
130E GLU 4.7 0.4 - - - -
131E SER* 1.3 91.4 + - - +
133E PHE* 1.3 76.6 + - + +
135E ASP 5.3 0.7 - - - -
136E GLU* 3.6 25.7 - - - +
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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