Contacts of the helix formed by residues 114 - 122 (chain A) in PDB entry 3PU3
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 THR 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A SER 3.5 12.8 - - - +
112A GLN* 2.6 28.3 + - - +
113A LEU* 1.3 72.0 - - - +
115A LEU* 1.3 63.0 + - - +
116A GLY* 2.8 16.7 + - - -
117A TYR* 3.0 10.6 + - - +
118A MET* 2.9 24.9 + - - +
211A ILE* 3.6 6.3 - - - -
214A LYS* 6.0 0.9 - - - -
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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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5A EDO 6.3 2.0 - - - -
114A THR* 1.3 74.4 - - - +
116A GLY* 1.3 56.5 + - - +
118A MET* 3.5 2.3 + - + +
119A GLU* 2.8 56.7 + - + +
211A ILE* 3.7 12.1 - - + +
214A LYS* 4.0 42.4 - - + +
215A LEU* 3.6 34.8 - - + -
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Residues in contact with GLY 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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114A THR* 2.8 8.8 + - - -
115A LEU* 1.3 76.2 - - - +
117A TYR* 1.3 52.0 + - - -
119A GLU* 3.2 11.1 + - - +
120A GLU* 2.8 37.9 + - - +
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Residues in contact with TYR 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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106A ALA* 4.0 13.7 - - - +
108A VAL* 3.5 31.1 - - + +
112A GLN* 3.3 32.3 - - + +
113A LEU* 3.9 15.5 - - + -
114A THR* 3.0 12.4 + - + +
116A GLY* 1.3 73.2 - - - +
118A MET* 1.3 69.4 + - - +
120A GLU* 3.1 5.4 + - - +
121A HIS* 2.9 70.6 + + + +
127A ILE* 3.9 23.5 - - + +
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Residues in contact with MET 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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113A LEU* 3.9 20.6 - - + -
114A THR 2.9 19.4 + - - +
115A LEU* 3.8 6.5 - - + +
117A TYR* 1.3 78.3 - - - +
119A GLU* 1.3 55.8 + - - +
121A HIS* 5.1 0.7 - - - -
122A GLY* 2.6 37.2 + - - +
123A PHE* 3.6 40.7 + - + +
127A ILE* 4.0 15.3 - - + -
211A ILE* 3.7 25.1 - - + -
215A LEU* 3.5 29.4 - - + -
314A PHE* 5.5 4.9 - - + -
336A PHE* 5.8 0.7 - - + -
340A LEU* 3.6 16.6 - - + +
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Residues in contact with GLU 119 (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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33A EDO 3.2 36.0 + - - -
115A LEU* 2.8 53.2 + - + +
116A GLY* 3.8 7.9 - - - +
118A MET* 1.3 74.0 - - + +
120A GLU* 1.3 63.5 + - - +
122A GLY* 3.9 5.5 + - - -
215A LEU* 6.2 0.4 - - + -
340A LEU* 4.5 17.2 - - + +
394A HIS* 6.0 3.8 - - + -
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Residues in contact with GLU 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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33A EDO 4.6 5.8 + - - -
116A GLY 2.8 18.8 + - - +
117A TYR* 3.4 6.7 - - - +
119A GLU* 1.3 79.3 - - - +
121A HIS* 1.3 71.0 + - + +
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Residues in contact with HIS 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 TYR* 2.9 64.0 + + + +
118A MET* 4.3 1.1 - - - +
120A GLU* 1.3 88.2 - - + +
122A GLY* 1.3 62.7 + - - +
123A PHE* 3.4 4.9 + - - +
124A THR* 4.3 12.9 + - - +
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Residues in contact with GLY 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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14A EDO 4.7 1.7 + - - -
33A EDO 6.4 0.2 - - - -
118A MET 2.6 19.5 + - - -
119A GLU 3.9 5.1 + - - -
120A GLU 3.6 1.4 - - - -
121A HIS* 1.3 72.0 - - - +
123A PHE* 1.3 69.8 + - - +
124A THR* 3.1 15.9 + - - +
340A LEU* 4.2 25.7 - - - +
341A SER* 5.0 1.0 + - - -
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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