Contacts of the helix formed by residues 106 - 116 (chain Y) in PDB entry 2W4T
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 ILE 106 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104Y LEU 3.2 4.2 + - - -
105Y ASN* 1.3 66.2 - - - +
107Y GLU* 1.3 82.6 + - + +
109Y ILE* 2.3 47.5 - - + +
110Y LYS* 3.1 22.0 + - + +
129Y PHE* 4.5 24.2 - - + -
134Y VAL* 4.6 13.9 - - + -
137Y GLY* 2.7 36.5 + - - +
139Y PHE* 4.5 1.8 - - + -
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Residues in contact with GLU 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Y ASN* 2.4 54.8 + - - +
106Y ILE* 1.3 80.5 + - + +
108Y TYR* 1.3 69.4 + - + +
110Y LYS* 3.8 5.8 - - - +
111Y ASP* 3.0 30.0 + - - +
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Residues in contact with TYR 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Y PHE* 3.5 37.7 - + + -
105Y ASN* 2.6 63.4 + - + +
107Y GLU* 1.3 86.5 - - + +
109Y ILE* 1.3 64.6 + - - +
111Y ASP* 2.8 18.7 + - - +
112Y LEU* 2.8 17.5 + - - +
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Residues in contact with ILE 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Y PHE* 4.7 3.1 - - + -
96Y PHE* 4.9 0.4 - - - -
104Y LEU* 3.1 48.7 - - + -
105Y ASN 3.7 2.9 - - - +
106Y ILE* 2.3 63.7 - - + +
108Y TYR* 1.3 72.6 - - + +
110Y LYS* 1.3 75.5 + - - +
112Y LEU* 2.9 22.2 + - - +
113Y LEU* 3.0 18.9 + - + +
139Y PHE* 4.2 19.3 - - + -
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Residues in contact with LYS 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Y ILE* 3.1 28.4 + - + +
107Y GLU* 3.8 5.6 - - - +
109Y ILE* 1.3 83.9 - - - +
111Y ASP* 1.3 54.9 + - - +
113Y LEU* 4.1 3.3 - - - +
114Y GLU* 2.4 52.6 + - + +
125Y MET* 1.5 63.1 - - + +
129Y PHE* 6.2 1.0 - - - +
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Residues in contact with ASP 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Y GLU 3.0 15.8 + - - +
108Y TYR* 2.8 15.8 + - - +
110Y LYS* 1.3 75.3 - - - +
112Y LEU* 1.3 62.2 + - - +
114Y GLU* 4.3 2.7 - - - -
115Y ASN* 2.4 53.0 + - - +
116Y MET* 4.1 9.2 - - - +
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Residues in contact with LEU 112 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804C GLN* 3.3 23.8 - - - +
808C LEU* 3.5 36.8 - - + -
96Y PHE* 4.1 32.1 - - + -
104Y LEU* 5.8 2.2 - - + -
108Y TYR 2.8 12.9 + - - +
109Y ILE* 2.9 13.4 + - - +
111Y ASP* 1.3 78.2 + - + +
113Y LEU* 1.3 58.0 + - + +
116Y MET* 2.9 61.3 + - + +
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Residues in contact with LEU 113 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808C LEU* 5.7 1.1 - - + -
811C ILE* 2.9 30.3 - - + -
812C GLN* 4.0 0.9 - - + -
815C ILE* 4.9 8.5 - - + -
109Y ILE* 3.0 12.6 + - + +
110Y LYS* 4.1 4.0 - - - +
112Y LEU* 1.3 81.3 - - + +
114Y GLU* 1.3 62.6 - - - +
116Y MET 4.3 2.6 + - - +
119Y ASN* 3.7 4.0 - - - -
120Y PHE* 1.5 97.9 + - + -
128Y THR* 5.2 15.7 - - + +
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Residues in contact with GLU 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y LYS* 2.4 41.0 + - + +
111Y ASP* 3.7 4.9 - - - +
113Y LEU* 1.3 81.3 - - + +
115Y ASN* 1.3 65.1 + - + +
119Y ASN* 3.4 16.1 - - - +
120Y PHE* 3.5 15.2 + - - +
121Y ASN 4.0 6.4 - - - +
122Y LYS* 5.2 1.6 - - - -
125Y MET* 2.7 53.1 - - - +
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Residues in contact with ASN 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111Y ASP* 2.4 47.9 + - - +
114Y GLU* 1.3 79.6 - - + +
116Y MET* 1.3 76.8 + - - +
119Y ASN* 4.3 9.2 - - - -
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Residues in contact with MET 116 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808C LEU* 4.8 10.3 - - + +
812C GLN* 5.5 2.4 - - - +
111Y ASP* 3.6 10.1 - - - +
112Y LEU* 2.9 44.3 + - + +
113Y LEU* 4.3 4.4 + - - +
114Y GLU 3.8 1.0 - - - -
115Y ASN* 1.3 109.2 - - - +
117Y GLY* 1.3 63.4 - - - +
118Y ASP 3.3 5.2 + - - -
119Y ASN* 4.1 5.3 + - - +
21Z TRP* 5.4 16.8 - - + -
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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