Contacts of the helix formed by residues 107 - 116 (chain A) in PDB entry 2XZ0
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 ALA 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ILE 3.2 2.4 + - - +
104A THR 3.0 11.9 + - - +
106A GLU* 1.3 76.0 - - - +
108A LEU* 1.3 62.5 + - - +
109A PRO* 3.2 4.9 - - - -
110A THR* 3.0 27.5 + - - +
111A TYR* 3.6 14.8 - - + +
169A ILE* 5.4 1.3 - - + +
172A LEU* 3.7 33.0 - - + -
173A ILE* 3.9 17.7 - - + -
266A PRO 5.9 0.2 - - - +
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Residues in contact with LEU 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 GLU 3.6 13.3 + - - +
106A GLU 2.9 6.2 + - - +
107A ALA* 1.3 76.9 - - - +
109A PRO* 1.3 61.2 - - + +
111A TYR* 2.7 36.5 + - + +
112A GLN 3.2 9.4 + - - +
139A TRP* 4.3 11.9 - - + -
140A THR* 3.7 29.6 - - + +
143A GLU* 3.5 29.2 - - + -
144A ASN* 3.6 39.0 - - + +
109B PRO* 4.1 12.8 - - + -
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Residues in contact with PRO 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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106A GLU 3.7 7.9 - - - +
107A ALA* 3.2 7.4 - - - +
108A LEU* 1.3 93.6 - - + +
110A THR* 1.3 59.8 + - - +
112A GLN* 3.6 2.2 + - - +
113A THR* 3.1 17.8 + - - -
173A ILE* 4.3 13.5 - - + -
108B LEU* 4.0 22.4 - - + -
109B PRO* 4.2 33.1 - - + +
112B GLN* 2.9 26.4 - - - +
140B THR* 3.9 13.7 - - + -
144B ASN* 5.2 2.5 - - - +
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Residues in contact with THR 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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107A ALA* 3.0 17.6 + - - +
109A PRO* 1.3 78.3 - - - +
111A TYR* 1.3 58.5 + - + +
113A THR* 3.1 8.2 + - - +
114A MET* 2.7 32.7 + - + +
172A LEU 4.7 0.9 + - - -
173A ILE* 4.1 19.8 + - - +
176A GLY* 4.0 16.1 - - - -
177A MET* 3.8 43.5 - - + +
266A PRO 5.5 0.4 - - - +
112B GLN* 3.7 7.0 + - - +
126B GLY* 5.8 1.8 - - - +
137B ARG* 6.0 0.3 - - - +
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Residues in contact with TYR 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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104A THR* 2.9 47.6 + - + +
105A GLU* 4.6 4.9 - - - -
107A ALA* 3.6 19.7 - - + +
108A LEU* 2.7 32.8 + - + +
110A THR* 1.3 85.1 - - + +
112A GLN* 1.3 62.3 + - - +
114A MET* 3.6 10.2 - - + +
115A LEU* 3.2 26.7 + - - +
139A TRP* 3.9 24.2 - + + -
177A MET* 4.0 10.1 - - + -
266A PRO* 3.5 37.8 + - + +
267A ALA* 4.7 0.5 - - - +
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Residues in contact with GLN 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 LEU 3.2 7.5 + - - +
109A PRO 4.2 5.4 - - - +
111A TYR* 1.3 73.8 - - - +
113A THR* 1.3 66.4 + - - +
115A LEU* 3.2 6.5 + - - +
116A ASN* 3.1 24.4 + - - +
136A THR* 3.9 14.2 - - + +
137A ARG* 3.9 29.7 - - - +
139A TRP* 4.7 2.5 - - - -
140A THR* 3.1 38.4 + - + +
109B PRO* 2.9 38.1 - - + +
110B THR* 3.6 5.4 + - - +
113B THR* 3.6 17.8 + - - +
173B ILE* 4.9 4.1 + - - +
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Residues in contact with THR 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 PRO 3.1 8.9 + - - -
110A THR* 3.1 10.4 + - - +
112A GLN* 1.3 76.1 - - - +
114A MET* 1.3 57.8 + - - +
116A ASN* 2.9 25.5 + - + +
117A THR* 3.4 15.1 + - + +
112B GLN* 3.4 26.8 + - - +
113B THR* 4.1 12.3 + - - -
116B ASN* 3.2 33.9 + - + +
123B ASP* 5.5 1.8 - - + +
126B GLY* 4.6 20.6 - - - +
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Residues in contact with MET 114 (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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110A THR* 2.7 19.7 + - + +
111A TYR* 3.6 9.4 - - - +
112A GLN 3.2 0.2 - - - -
113A THR* 1.3 74.7 - - - +
115A LEU* 1.3 75.4 + - + +
117A THR* 2.6 28.0 + - - +
118A LEU* 3.9 10.1 + - + +
177A MET* 3.6 29.4 - - + -
179A PRO* 3.8 14.6 - - + -
181A THR* 3.7 35.0 - - + +
188A GLY* 4.5 12.1 - - - +
191A TYR* 4.3 14.6 - - + -
192A THR* 4.7 6.5 - - + -
125B THR 6.0 2.5 - - - +
126B GLY* 6.3 1.6 - - - -
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Residues in contact with LEU 115 (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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111A TYR 3.2 14.9 + - - +
112A GLN* 3.2 7.4 + - - +
114A MET* 1.3 85.1 - - - +
116A ASN* 1.3 58.7 - - - +
117A THR 3.2 4.3 + - - -
118A LEU* 3.5 38.9 + - + +
121A VAL* 3.7 13.6 - - + +
122A ARG* 4.3 0.9 - - - -
135A TRP* 4.9 2.5 - - + +
136A THR* 3.9 31.4 + - + +
139A TRP* 4.0 26.2 - - + -
189A PHE* 4.7 7.0 - - + -
192A THR* 4.0 24.7 - - + -
236A TYR* 3.8 20.9 - - + +
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Residues in contact with ASN 116 (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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112A GLN* 3.1 20.0 + - - +
113A THR* 2.9 15.8 + - - +
115A LEU* 1.3 79.0 - - - +
117A THR* 1.3 58.7 + - - +
118A LEU 3.6 0.2 - - - -
122A ARG* 3.6 25.4 - - + +
123A ASP* 3.0 38.4 + - - +
136A THR* 4.0 13.7 + - - +
113B THR* 3.0 40.9 + - + +
116B ASN* 5.5 6.6 - - + +
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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