Contacts of the helix formed by residues 104 - 112 (chain A) in PDB entry 1Z10
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 GLN 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLY 4.4 0.2 + - - -
103A GLU* 1.3 75.1 - - - +
105A ALA* 1.3 57.7 + - - +
106A THR* 3.0 6.2 + - - -
107A PHE* 3.0 34.7 + - + -
108A ASP* 2.8 34.3 + - - -
118A PHE* 3.7 22.8 - - + -
212A THR* 4.0 18.8 - - - +
217A GLY 5.5 0.4 + - - -
218A GLN* 4.6 1.4 + - - -
221A GLU* 3.3 28.2 + - - +
370A LEU* 4.3 5.2 - - + -
371A ALA 6.1 0.4 - - - +
480A PHE* 3.9 37.2 - - + +
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Residues in contact with ALA 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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103A GLU* 4.0 14.5 + - - +
104A GLN* 1.3 73.4 - - - +
106A THR* 1.3 62.5 + - - +
108A ASP* 3.8 8.1 - - - +
109A TRP* 3.1 18.7 + - - +
220A TYR* 3.5 27.3 + - + +
221A GLU* 2.8 26.3 + - - +
224A SER* 3.8 19.7 - - - +
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Residues in contact with THR 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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104A GLN* 3.0 9.7 + - - -
105A ALA* 1.3 74.1 - - - +
107A PHE* 1.3 67.8 + - + +
109A TRP* 3.2 19.8 - - - +
208A ILE* 5.4 4.3 - - + +
211A PHE* 3.1 33.9 - - + -
212A THR* 3.7 24.1 - - + +
217A GLY 4.5 1.7 + - - -
220A TYR* 3.4 18.7 - - - +
221A GLU* 3.2 6.6 + - - -
237A ALA* 4.8 6.3 - - + -
238A PHE* 4.9 4.5 - - + -
241A LEU* 3.3 22.2 - - + +
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Residues in contact with PHE 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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104A GLN* 3.0 35.9 + - + +
106A THR* 1.3 78.5 - - + +
108A ASP* 1.3 62.1 + - - +
109A TRP 3.1 0.7 + - - -
110A VAL* 3.1 5.7 + - - +
111A PHE* 3.0 42.7 + + + -
118A PHE* 3.6 30.7 - + + -
208A ILE* 4.1 25.6 - - + -
209A PHE* 4.2 14.6 - + - -
212A THR* 4.1 14.8 - - + -
241A LEU* 4.3 14.4 - - + -
300A ILE* 4.8 3.1 - - + -
480A PHE* 3.7 33.9 - + - -
501A COU 3.7 20.9 - + - -
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Residues in contact with ASP 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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103A GLU* 2.9 35.2 - - - +
104A GLN 2.8 25.2 + - - +
105A ALA* 3.3 7.3 + - - +
106A THR 3.3 0.2 - - - -
107A PHE* 1.3 73.0 - - - +
109A TRP* 1.3 62.3 + - - +
110A VAL 3.2 0.2 - - - -
111A PHE* 4.2 1.1 - - - +
112A LYS* 2.8 36.1 + - - +
113A GLY 5.2 3.4 + - - +
118A PHE* 3.3 33.3 - - - +
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Residues in contact with TRP 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 ALA 3.1 11.7 + - - +
106A THR 3.2 14.4 - - - +
107A PHE 3.0 0.6 - - - -
108A ASP* 1.3 78.3 - - - +
110A VAL* 1.3 76.6 + - + +
112A LYS* 3.8 16.9 - - - +
220A TYR* 4.1 7.6 - - - +
228A LYS* 4.5 15.3 + - + +
235A GLN* 5.8 0.2 - - - -
238A PHE* 3.4 83.8 - + + -
239A GLN* 5.3 2.7 - - - -
241A LEU* 4.2 3.4 - - + -
242A GLN* 3.9 25.8 - - + -
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Residues in contact with VAL 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 THR 4.2 0.2 + - - -
107A PHE 3.1 11.5 + - - +
109A TRP* 1.3 94.8 - - + +
111A PHE* 1.3 94.1 + - + +
112A LYS* 3.5 12.5 + - - +
241A LEU* 3.9 33.0 - - + +
242A GLN* 5.1 0.2 - - - -
245A GLU* 3.1 41.5 - - + +
293A MET* 3.2 23.4 - - + +
296A LEU* 4.6 5.8 - - + -
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Residues in contact with PHE 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 PHE* 3.0 36.6 + + + +
108A ASP* 4.6 1.6 - - - -
110A VAL* 1.3 84.5 - - + +
112A LYS* 1.3 73.0 + - - +
113A GLY 4.2 3.8 - - - +
114A TYR* 2.9 33.2 + - - +
118A PHE* 3.3 37.2 - + + -
289A LYS* 4.7 1.0 - - - -
293A MET* 3.7 35.0 - - + +
296A LEU* 3.8 30.5 - - + -
297A ASN* 3.0 29.4 - - - -
300A ILE* 4.4 5.6 - - + -
501A COU 3.9 9.9 - - - -
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Residues in contact with LYS 112 (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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108A ASP* 2.8 30.4 + - - +
109A TRP* 3.8 14.4 - - - +
110A VAL* 3.7 15.5 - - - +
111A PHE* 1.3 72.8 - - - +
113A GLY* 1.3 57.2 + - - +
114A TYR* 3.2 25.1 - - + -
123A ARG* 4.9 0.3 + - - -
245A GLU* 6.0 1.1 - - - -
289A LYS* 4.3 20.5 - - - +
293A MET* 5.6 0.2 - - - -
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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