Contacts of the helix formed by residues 125 - 134 (chain G) in PDB entry 4UIS
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 ARG 125 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119G ARG* 4.8 2.5 - - - +
120G MET* 2.6 26.1 + - + +
123G GLN* 2.3 50.8 + - + +
124G LYS* 1.3 70.1 - - - +
126G TRP* 1.3 58.6 + - - +
127G ASP* 3.1 3.7 + - - -
128G GLU* 3.3 24.6 + - + +
129G ALA* 2.8 27.7 + - - +
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Residues in contact with TRP 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G SER 4.1 2.5 - - - -
91G LEU* 3.3 24.2 - - + -
95G ARG* 3.2 53.9 - - - +
121G LEU* 3.5 34.4 - - + +
124G LYS* 3.0 71.3 + - + +
125G ARG* 1.3 76.3 - - - +
127G ASP* 1.3 62.8 + - - +
129G ALA* 3.6 4.4 - - - +
130G ALA* 2.9 29.8 + - - +
153G PHE* 3.7 14.8 - - + +
154G ARG* 5.0 10.6 + - - +
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Residues in contact with ASP 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G ARG 3.1 1.2 + - - -
126G TRP* 1.3 81.0 - - - +
128G GLU* 1.3 61.1 + - + +
130G ALA* 3.1 8.3 + - - +
131G VAL* 2.9 32.5 + - + +
154G ARG* 4.7 15.1 - - - +
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Residues in contact with GLU 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G MET* 3.4 24.9 - - + +
125G ARG* 3.3 22.3 + - + +
127G ASP* 1.3 78.9 - - + +
129G ALA* 1.3 58.5 + - - +
130G ALA 3.1 0.4 - - - -
131G VAL* 3.6 11.2 - - + -
132G ASN* 2.3 44.5 + - - +
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Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G SER* 3.5 16.2 - - - +
120G MET* 3.5 25.4 - - + -
121G LEU* 3.5 23.6 - - + -
125G ARG 2.8 19.2 + - - +
126G TRP* 3.6 5.2 - - - +
128G GLU* 1.3 77.5 - - - +
130G ALA* 1.3 57.7 + - - +
133G LEU* 2.9 36.7 + - - +
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Residues in contact with ALA 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G TRP 2.9 18.2 + - - +
127G ASP* 3.3 7.9 - - - +
129G ALA* 1.3 75.3 - - - +
131G VAL* 1.3 60.5 + - + +
132G ASN 3.2 1.3 - - - -
133G LEU* 4.4 2.7 - - - -
134G ALA* 2.9 27.9 + - - +
150G ILE* 3.5 36.1 - - + +
153G PHE* 5.7 2.0 - - + +
154G ARG* 4.9 13.5 - - + +
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Residues in contact with VAL 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ASP* 2.9 24.1 + - + +
128G GLU* 3.3 13.9 + - + +
130G ALA* 1.3 77.4 - - + +
132G ASN* 1.3 59.4 + - - +
134G ALA* 3.2 20.3 - - + +
135G LYS* 3.7 25.3 - - + +
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Residues in contact with ASN 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G PHE* 4.2 8.3 - - - -
116G ASN* 3.6 20.8 + - + +
117G SER* 3.0 26.3 + - - +
120G MET* 3.0 24.0 - - - +
128G GLU* 2.3 37.9 + - - +
129G ALA 4.0 0.9 - - - +
131G VAL* 1.3 80.4 - - - +
133G LEU* 1.3 57.3 + - - +
134G ALA 3.1 1.3 - - - -
135G LYS* 2.6 52.3 + - - +
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Residues in contact with LEU 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G MET* 3.7 27.1 - - + -
114G PHE* 4.5 15.8 - - + -
117G SER* 3.0 20.8 + - - +
118G LEU* 5.6 1.6 - - + -
121G LEU* 4.5 15.0 - - + -
129G ALA 2.9 27.9 + - - +
130G ALA* 3.9 4.0 - - - +
132G ASN* 1.3 76.1 - - - +
134G ALA* 1.3 61.9 + - - +
135G LYS 4.2 0.5 + - - -
136G SER* 4.5 2.1 + - - -
138G TRP* 3.5 10.2 - - + -
139G TYR* 3.4 13.2 - - - +
150G ILE* 3.4 27.9 - - + +
153G PHE* 3.9 36.6 - - + -
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Residues in contact with ALA 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ALA 2.9 14.3 + - - +
131G VAL* 3.2 19.7 - - + +
132G ASN 3.1 1.4 - - - -
133G LEU* 1.3 82.1 - - - +
135G LYS* 3.1 31.5 - - - +
136G SER 3.5 4.8 + - - +
139G TYR* 3.4 38.4 - - + +
150G ILE* 3.6 13.0 - - + -
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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