Contacts of the helix formed by residues 134 - 143 (chain A) in PDB entry 5Y7G
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A LYS* 3.8 5.8 - - - +
133A LEU* 1.3 84.4 - - - +
135A LYS* 1.3 61.8 + - - +
136A ASP* 3.1 30.4 + - - +
137A ALA* 3.2 10.5 + - + +
138A LEU* 2.9 27.7 + - - +
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Residues in contact with LYS 135 (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 PHE* 3.0 59.1 + - + -
113A GLY 4.9 2.2 + - - -
115A LEU 3.2 14.9 + - - -
116A LYS* 4.5 1.0 - - - +
117A LYS* 3.9 42.3 - - + +
120A LEU* 3.8 17.0 - - + -
134A ARG* 1.3 71.2 - - - +
136A ASP* 1.3 67.9 + - - +
137A ALA 3.0 2.3 + - - -
138A LEU* 3.3 11.8 + - + -
139A LEU* 3.5 1.4 + - - +
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Residues in contact with ASP 136 (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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134A ARG* 3.1 46.5 + - - +
135A LYS* 1.3 73.9 + - - +
137A ALA* 1.3 58.8 + - - -
139A LEU* 4.0 6.3 + - - +
140A GLU* 3.6 24.0 + - - +
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Residues in contact with ALA 137 (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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133A LEU* 3.4 24.8 - - + +
134A ARG* 3.2 21.0 + - + +
135A LYS 3.0 0.8 - - - -
136A ASP* 1.3 80.1 + - - +
138A LEU* 1.3 63.8 + - - +
139A LEU 3.3 0.2 - - - -
140A GLU* 3.0 11.5 + - - +
141A ARG* 3.0 22.7 + - - +
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Residues in contact with LEU 138 (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 PHE* 3.6 13.0 - - + -
117A LYS* 4.0 20.2 - - + +
120A LEU* 6.4 1.1 - - + -
121A SER* 6.0 5.6 - - - -
128A LEU* 3.2 44.2 - - + -
133A LEU* 3.9 15.9 - - + +
134A ARG 2.9 17.5 + - - +
135A LYS* 3.5 11.9 - - + +
137A ALA* 1.3 74.0 - - - +
139A LEU* 1.3 52.5 + - - +
141A ARG* 3.0 7.7 + - + -
142A LEU* 2.4 57.9 + - + +
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Residues in contact with LEU 139 (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* 3.5 32.1 - - + -
109A ALA* 3.7 29.8 - - + +
112A PHE* 3.5 39.0 - - + -
135A LYS 3.5 3.5 + - - +
136A ASP* 4.1 9.2 - - - +
137A ALA 3.3 0.6 - - - -
138A LEU* 1.3 77.8 - - - +
140A GLU* 1.3 58.4 + - - +
142A LEU* 4.2 2.5 - - - +
143A GLN* 2.7 42.5 + - + +
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Residues in contact with GLU 140 (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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136A ASP* 3.6 14.4 + - - +
137A ALA* 3.0 14.4 + - - +
139A LEU* 1.3 82.1 - - - +
141A ARG* 1.3 60.5 + - - +
143A GLN* 4.5 1.8 - - - +
144A PRO* 3.4 15.9 - - - +
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Residues in contact with ARG 141 (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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127A HIS 3.0 18.7 + - - -
128A LEU* 3.1 42.7 - - + +
129A GLY 3.1 11.1 - - - +
130A ARG* 3.2 27.7 - - - +
131A ALA 4.7 3.8 + - - +
133A LEU* 4.8 14.7 - - + +
137A ALA 3.0 10.1 + - - +
138A LEU* 3.0 11.1 + - + +
140A GLU* 1.3 76.7 - - - +
142A LEU* 1.3 63.5 + - + +
144A PRO* 3.5 15.7 - - - +
145A LEU* 4.8 8.5 + - - +
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Residues in contact with LEU 142 (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* 3.4 14.3 - - + +
112A PHE* 3.8 16.8 - - + -
124A PHE* 3.6 26.7 - - + -
127A HIS* 4.5 11.7 - - + +
128A LEU* 4.1 14.6 - - + -
138A LEU* 2.4 56.9 + - + +
139A LEU* 4.0 1.3 - - - +
141A ARG* 1.3 71.6 - - + +
143A GLN* 1.3 62.8 + - - +
144A PRO 3.5 0.2 - - - -
145A LEU* 3.4 5.9 + - + -
146A PHE* 3.2 53.0 + - + -
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Residues in contact with GLN 143 (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 GLU* 3.1 28.3 + - - +
108A LEU* 3.1 35.3 - - - +
109A ALA* 4.1 10.2 + - - +
139A LEU* 2.7 27.4 + - + +
140A GLU* 4.5 1.8 - - - +
142A LEU* 1.3 73.6 - - - +
144A PRO* 1.3 69.0 - - + +
146A PHE 2.9 25.7 + - - -
147A PRO* 3.3 12.1 + - + +
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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