Contacts of the helix formed by residues 103 - 111 (chain A) in PDB entry 40ER
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 LEU 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLU* 1.3 69.6 - - - +
104A PHE* 1.3 52.7 + - - +
106A TYR* 2.9 25.7 + - + +
107A ILE* 2.7 43.8 + - + +
121A LEU* 3.9 20.4 - - + -
125A ILE* 4.5 12.3 - - + -
144A PRO* 2.9 27.5 + - + +
147A VAL* 2.8 34.4 + - + +
149A LEU* 3.7 15.7 - - + -
205A ILE* 4.7 4.3 - - + -
209A LEU* 4.0 23.3 - - + -
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLU* 3.2 8.2 - - - +
103A LEU* 1.3 76.0 - - - +
105A ASP* 1.3 62.6 + - - +
107A ILE* 4.3 13.7 - - + -
108A CYS* 3.2 32.6 + - + +
144A PRO* 3.2 27.1 + - + -
145A GLU* 3.4 46.9 - - + +
181A TYR* 4.8 1.6 - - - -
208A ALA* 6.2 1.6 - - + -
214A LEU* 4.5 21.5 - - + -
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLY 5.3 5.4 - - - +
101A GLY* 5.0 2.3 - - - -
102A GLU* 3.2 43.3 + - - +
103A LEU 3.1 0.2 - - - -
104A PHE* 1.3 80.9 - - - +
106A TYR* 1.3 56.4 + - - +
108A CYS* 4.3 1.7 - - - +
109A LYS* 3.1 35.0 + - + +
601A STU 6.1 0.5 - - - -
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLY 5.9 1.8 - - - +
102A GLU 3.4 4.2 + - - +
103A LEU* 2.9 33.7 + - + +
105A ASP* 1.3 78.1 - - - +
107A ILE* 1.3 64.4 + - - +
109A LYS* 4.3 7.4 - - + +
110A ASN* 3.0 44.3 + - + +
113A LEU* 3.8 35.2 - - + +
117A GLU* 3.2 25.7 + - - -
121A LEU* 4.3 8.3 - - + -
149A LEU* 4.3 14.8 - - + -
153A MET* 4.6 26.1 - - + +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 2.7 35.7 + - + +
104A PHE* 4.0 18.2 - - + +
106A TYR* 1.3 73.0 - - - +
108A CYS* 1.3 54.0 + - - +
110A ASN 3.4 0.3 - - - -
111A GLY 2.7 51.6 + - - +
113A LEU* 3.6 23.1 - - + -
144A PRO* 4.7 6.3 - - + -
208A ALA* 3.6 32.3 - - + +
209A LEU* 3.7 22.9 - - + -
212A GLY* 4.4 13.9 - - - +
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Residues in contact with CYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.2 25.7 + - + +
105A ASP* 4.3 2.5 - - - +
107A ILE* 1.3 81.0 - - + +
109A LYS* 1.3 63.5 + - - +
111A GLY* 3.2 11.8 + - - -
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASP 3.1 19.9 + - - +
106A TYR* 4.3 7.4 - - + +
108A CYS* 1.3 80.6 - - - +
110A ASN* 1.3 62.0 + - + +
111A GLY 3.3 0.4 + - - -
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 3.0 40.6 + - + +
107A ILE 3.4 0.7 - - - +
109A LYS* 1.3 78.5 + - + +
111A GLY* 1.3 63.1 + - - +
112A ARG* 3.2 10.6 + - - +
113A LEU* 3.4 26.7 - - + +
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Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ILE* 2.7 38.7 + - - +
108A CYS* 3.2 12.2 + - - -
109A LYS 3.3 1.0 + - - -
110A ASN* 1.3 71.2 - - - +
112A ARG* 1.3 80.9 + - - -
113A LEU* 4.3 1.1 + - - +
212A GLY* 4.0 5.5 - - - +
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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