Contacts of the helix formed by residues 105 - 113 (chain A) in PDB entry 1Q2L
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 ASP 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU* 3.0 19.1 + - - +
96A MET* 3.3 10.3 - - - +
104A ALA* 1.3 76.3 - - - +
106A SER* 1.3 63.3 + - - +
107A LEU 3.3 2.9 - - - -
108A ALA* 3.3 14.3 + - + +
109A GLU* 2.9 37.2 + - + +
161A ARG* 3.1 40.5 + - - -
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Residues in contact with SER 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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95A LEU 4.4 2.6 + - - -
101A TYR* 3.5 26.0 - - - +
103A GLN* 3.6 20.4 + - - -
104A ALA 3.1 3.9 - - - -
105A ASP* 1.3 76.5 - - - +
107A LEU* 1.3 62.7 + - - +
109A GLU* 3.5 5.8 + - - +
110A TYR* 3.1 24.3 + - - +
144A ARG* 3.4 23.6 + - - +
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Residues in contact with LEU 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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95A LEU* 5.2 19.5 - - + -
105A ASP 3.3 0.8 - - - -
106A SER* 1.3 78.6 - - - +
108A ALA* 1.3 58.8 + - - +
110A TYR* 3.3 2.5 + - + +
111A LEU* 2.9 58.7 + - + +
118A HIS* 4.7 13.9 - - + +
130A TYR 6.5 0.2 - - - -
131A LEU* 4.0 11.2 - - + -
141A ALA* 3.6 27.4 - - - +
144A ARG* 4.0 23.2 - - + +
145A LEU* 4.2 30.1 - - + -
148A ALA* 6.1 1.8 - - + -
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Residues in contact with ALA 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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105A ASP* 3.3 19.7 + - + +
107A LEU* 1.3 76.7 - - - +
109A GLU* 1.3 66.8 + - + +
111A LEU* 4.0 2.4 - - - +
112A LYS* 3.0 31.2 + - - +
118A HIS* 3.5 34.9 + - + +
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Residues in contact with GLU 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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104A ALA 4.8 2.5 - - - +
105A ASP* 2.9 34.7 + - + +
106A SER* 3.9 4.9 - - - +
108A ALA* 1.3 76.0 - - + +
110A TYR* 1.3 62.6 + - - +
112A LYS* 3.5 21.8 + - - +
113A MET* 3.2 36.3 + - - +
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Residues in contact with TYR 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 SER 3.1 18.6 + - - +
107A LEU* 3.5 3.1 - - + +
109A GLU* 1.3 73.6 - - - +
111A LEU* 1.3 73.2 + - + +
113A MET* 3.0 7.1 + - - -
114A HIS* 2.6 63.6 + + + -
133A VAL* 4.8 0.2 - - + -
137A ALA* 2.7 40.8 + - + +
140A GLY* 3.6 14.1 + - - -
141A ALA* 3.4 26.9 - - + -
144A ARG* 3.5 39.0 - - - +
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Residues in contact with LEU 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 LEU* 2.9 32.5 + - + +
108A ALA* 4.0 3.6 - - - +
110A TYR* 1.3 78.4 - - + +
112A LYS* 1.3 59.4 + - - +
114A HIS 3.2 6.2 + - - +
116A GLY* 2.8 31.4 + - - -
117A SER* 3.5 32.5 - - - +
118A HIS* 3.5 23.6 - - + -
131A LEU* 3.7 11.0 - - + -
132A GLU 3.8 4.5 - - - +
133A VAL* 3.5 33.0 - - + -
141A ALA* 3.7 21.5 - - + -
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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 ALA* 3.0 23.0 + - - +
109A GLU* 3.5 24.2 + - - +
111A LEU* 1.3 79.5 - - - +
113A MET* 1.3 63.1 + - + +
114A HIS 3.2 1.1 + - - -
115A GLY* 4.0 6.8 + - - -
116A GLY 4.1 7.2 + - - -
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Residues in contact with MET 113 (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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109A GLU* 3.2 22.4 - - - +
110A TYR* 3.0 4.9 + - - +
112A LYS* 1.3 80.8 - - + +
114A HIS* 1.3 80.6 + - + +
115A GLY 3.7 1.1 - - - -
134A GLU* 5.0 0.9 - - - +
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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