Contacts of the helix formed by residues 116 - 124 (chain B) 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 LYS 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B LEU* 1.3 80.4 - - - +
117B LYS* 1.3 65.4 + - - +
118B ASP* 3.8 22.6 + - + +
119B GLU* 3.3 35.0 + - + +
120B LEU* 3.3 22.7 + - - +
135B LYS* 3.8 2.2 - - - +
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LYS* 1.3 73.7 - - - +
118B ASP* 1.3 64.7 + - - +
120B LEU* 3.6 3.5 + - - +
121B SER* 3.3 22.7 + - - -
133B LEU 3.0 28.8 + - - -
134B ARG* 3.5 16.7 - - - +
135B LYS* 3.7 40.8 - - + +
138B LEU* 4.7 8.5 - - + -
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LYS* 3.2 23.3 + - + +
117B LYS* 1.3 81.2 - - - +
119B GLU* 1.3 66.2 + - + +
121B SER* 3.4 10.0 + - - -
122B GLN* 3.7 15.8 + - - +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ARG* 2.9 40.3 + - - -
115B LEU* 3.8 21.6 - - + +
116B LYS* 3.3 43.6 + - + +
117B LYS 3.5 0.4 - - - -
118B ASP* 1.3 77.7 - - + +
120B LEU* 1.3 64.4 + - - +
121B SER 3.5 0.3 + - - -
122B GLN* 3.5 7.6 + - - +
123B LEU* 3.5 15.1 + - - +
156B GLN* 5.4 8.1 + - - +
159B PHE* 3.8 12.8 - - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 3.8 19.3 - - + +
112B PHE* 3.5 67.5 - - + -
115B LEU* 3.7 18.8 - - + +
116B LYS 3.3 18.6 + - - +
117B LYS* 4.0 4.3 - - + +
118B ASP 3.2 0.8 - - - -
119B GLU* 1.3 79.4 - - - +
121B SER* 1.3 64.4 + - - +
123B LEU* 2.8 18.0 + - + +
124B PHE* 3.2 29.9 + - + -
135B LYS* 3.9 12.8 - - + -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LYS* 3.3 17.3 + - - -
118B ASP* 3.4 4.2 + - - -
120B LEU* 1.3 76.9 - - - +
122B GLN* 1.3 55.2 + - - +
124B PHE* 3.5 3.1 - - - +
125B ARG* 2.7 40.2 + - - +
128B LEU 5.2 5.5 + - - -
138B LEU* 6.0 5.1 - - - +
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ASP 3.7 11.1 + - - +
119B GLU* 3.5 9.7 + - - +
120B LEU 3.2 0.6 - - - -
121B SER* 1.3 77.8 - - - +
123B LEU* 1.3 57.0 + - - +
125B ARG* 3.0 48.9 + - + +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU* 3.8 18.6 - - + -
115B LEU* 5.4 5.8 - - + -
119B GLU 3.5 9.0 + - - +
120B LEU* 2.8 14.9 + - + +
122B GLN* 1.3 79.8 - - - +
124B PHE* 1.3 87.9 + - + +
125B ARG* 3.3 9.3 + - - +
126B ASP 5.1 0.5 + - - -
155B TRP* 3.1 40.4 - - + +
156B GLN* 3.4 31.6 - - + +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU* 3.5 20.0 - - + -
111B LEU* 4.1 2.2 - - + -
112B PHE* 4.2 3.4 - + - -
120B LEU* 3.2 33.8 + - + +
121B SER* 3.5 3.8 - - - +
123B LEU* 1.3 94.0 - - + +
125B ARG* 1.3 65.5 + - - +
126B ASP* 2.9 5.8 + - - -
127B HIS* 2.9 17.3 + - + +
128B LEU 3.6 10.8 + - - +
142B LEU* 3.3 44.2 - - + -
146B PHE* 3.6 25.8 - + - -
155B TRP* 3.4 41.5 - + - -
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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