Contacts of the helix formed by residues 112 - 124 (chain A) in PDB entry 3DZ8
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASN* 3.4 28.0 - - - +
108A GLU* 3.0 12.3 + - + +
109A SER 3.6 10.1 - - - +
110A PHE 3.1 0.6 - - - -
111A ASN* 1.3 76.5 - - - +
113A VAL* 1.3 62.8 + - - +
114A GLN 3.4 0.7 - - - -
115A ASP* 3.0 16.3 + - + +
116A TRP* 3.0 28.4 + - + +
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Residues in contact with VAL 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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100A LEU* 4.0 16.9 - - + +
101A MET 5.4 0.4 - - - +
102A TYR* 4.3 7.0 - - + -
109A SER 3.8 11.0 - - - +
110A PHE* 3.3 29.4 - - + +
111A ASN 3.2 2.6 - - - -
112A ALA* 1.3 73.9 - - - +
114A GLN* 1.3 61.5 + - - +
116A TRP* 3.1 8.3 + - - +
117A ALA* 2.9 27.2 + - - +
132A LEU* 3.9 30.1 - - + -
153A LEU* 3.4 25.4 - - + -
157A LEU* 4.1 11.7 - - + -
159A PHE* 4.9 0.7 - - + -
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Residues in contact with GLN 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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111A ASN 4.3 5.0 + - - +
112A ALA 3.4 0.2 - - - -
113A VAL* 1.3 77.3 - - - +
115A ASP* 1.3 64.2 + - - +
117A ALA* 3.1 10.5 + - - +
118A THR* 3.0 31.5 + - - -
153A LEU* 4.8 6.9 - - + +
157A LEU* 4.8 9.2 - - + -
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Residues in contact with ASP 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 ASN 3.6 18.4 - - - +
112A ALA* 3.0 12.7 + - + +
114A GLN* 1.3 82.2 - - - +
116A TRP* 1.3 62.0 + - + +
118A THR* 3.5 8.4 + - - -
119A GLN* 3.2 19.2 + - - +
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Residues in contact with TRP 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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28A ILE* 3.8 20.1 - - + +
29A GLY* 3.4 33.0 - - - -
30A ASN* 2.9 28.7 + - - +
78A THR* 3.6 32.3 - - + -
81A GLN* 3.4 29.4 - - + -
92A TYR* 3.4 8.7 - - - -
100A LEU* 3.9 23.8 - - + -
101A MET 5.3 0.7 - - - -
109A SER 5.1 2.2 - - - -
112A ALA* 3.0 34.0 + - + +
113A VAL* 3.1 8.3 + - + +
115A ASP* 1.3 75.3 - - + +
117A ALA* 1.3 60.3 + - - +
119A GLN* 3.1 13.7 - - + +
120A ILE* 3.0 31.7 + - - +
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Residues in contact with ALA 117 (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 LEU* 4.0 7.5 - - - +
113A VAL 2.9 12.6 + - - +
114A GLN 3.2 11.0 - - - +
116A TRP* 1.3 73.8 - - - +
118A THR* 1.3 63.7 + - - +
120A ILE* 3.3 7.4 + - - +
121A LYS* 3.3 27.4 + - + +
157A LEU* 3.7 32.1 - - + -
159A PHE* 3.9 17.3 - - + -
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Residues in contact with THR 118 (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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114A GLN 3.0 13.5 + - - -
115A ASP* 3.8 10.8 - - - -
116A TRP 3.3 0.2 - - - -
117A ALA* 1.3 72.9 - - - +
119A GLN* 1.3 66.7 + - - +
121A LYS* 3.2 7.9 + - + +
122A THR* 3.1 36.4 + - - +
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Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLN* 4.9 1.5 + - - -
88A THR* 4.6 7.1 - - - +
92A TYR* 3.3 45.2 - - + +
115A ASP 3.2 13.9 + - - +
116A TRP* 3.1 26.9 + - + +
118A THR* 1.3 77.8 - - - +
120A ILE* 1.3 59.7 + - - +
122A THR* 3.4 5.6 + - - +
123A TYR* 3.2 51.6 + - - +
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Residues in contact with ILE 120 (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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28A ILE* 3.1 21.3 - - + -
92A TYR* 4.1 2.7 - - + -
98A PHE* 3.1 64.4 - - + -
100A LEU* 4.8 5.8 - - + -
116A TRP 3.0 18.2 + - - +
117A ALA* 3.5 10.8 - - - +
118A THR 3.3 0.2 - - - -
119A GLN* 1.3 75.9 - - - +
121A LYS* 1.3 70.4 + - + +
124A SER* 3.3 28.0 + - - +
125A TRP 5.0 1.5 - - - +
128A ALA* 4.8 9.0 - - + +
130A VAL* 4.0 20.0 - - + -
159A PHE* 5.6 2.5 - - + -
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Residues in contact with LYS 121 (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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117A ALA* 3.3 15.7 + - + +
118A THR* 3.2 8.8 + - + +
120A ILE* 1.3 82.0 - - + +
122A THR* 1.3 67.1 + - - +
124A SER 3.9 10.2 - - - +
125A TRP 6.1 0.4 - - - -
126A ASP* 5.5 8.6 - - - +
159A PHE* 6.2 4.5 - - + -
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Residues in contact with THR 122 (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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93A ARG* 5.5 2.1 + - - -
118A THR* 3.1 28.4 + - - +
119A GLN* 3.7 8.0 - - - +
121A LYS* 1.3 80.8 - - - +
123A TYR* 1.3 81.5 + - + +
124A SER 4.7 1.0 - - - +
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Residues in contact with TYR 123 (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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89A THR* 4.5 23.8 - - + +
92A TYR* 3.3 24.0 - + + -
93A ARG* 3.6 39.5 + - - +
94A GLY 4.4 0.2 + - - -
119A GLN* 3.2 35.3 + - - +
122A THR* 1.3 98.3 - - + +
124A SER* 1.3 59.1 + - - +
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Residues in contact with SER 124 (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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92A TYR* 3.0 28.9 + - - -
94A GLY 4.4 1.8 - - - +
95A ALA 4.1 4.5 - - - -
98A PHE* 2.9 36.5 - - - -
120A ILE 3.3 17.6 + - - +
121A LYS* 3.9 11.6 - - - +
122A THR 4.7 1.0 - - - +
123A TYR* 1.3 78.9 - - - +
125A TRP* 1.3 70.8 + - - +
126A ASP* 3.5 2.4 + - - -
128A ALA* 4.6 0.4 - - - -
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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