Contacts of the helix formed by residues 113 - 120 (chain J) in PDB entry 5XTD
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 113 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111J ARG 3.9 1.4 + - - -
112J ASP* 1.3 71.8 - - - +
114J ASP* 1.3 60.9 + - - +
115J SER 3.2 2.5 - - - -
116J ILE* 3.0 26.5 + - - +
117J ARG* 3.1 17.0 + - + +
151J ALA* 3.3 28.3 - - + +
154J GLN* 5.1 6.9 + - - +
155J LEU* 3.5 27.8 - - + -
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Residues in contact with ASP 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ASP* 3.6 3.7 - - + +
113J LYS* 1.3 76.2 - - - +
115J SER* 1.3 65.9 + - - +
117J ARG* 3.0 31.7 + - - +
118J ARG* 2.9 20.3 + - - +
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Residues in contact with SER 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J TRP* 3.8 21.4 - - - +
109J ASP 3.0 31.3 + - - -
112J ASP* 3.5 14.2 + - - +
113J LYS 4.5 0.4 - - - +
114J ASP* 1.3 77.6 - - - +
116J ILE* 1.3 65.9 + - - +
118J ARG* 3.0 23.0 + - - +
119J VAL* 3.0 24.5 + - - +
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Residues in contact with ILE 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J PHE* 3.9 24.7 - - + -
108J TRP* 4.3 21.1 - - + -
109J ASP 4.7 0.2 - - - +
110J ALA* 4.2 10.8 - - - +
112J ASP 3.5 22.0 - - - +
113J LYS* 3.0 14.1 + - - +
115J SER* 1.3 85.7 + - - +
117J ARG* 1.3 59.8 + - - +
119J VAL* 3.1 18.7 - - - +
120J VAL* 3.1 21.9 - - + +
148J ILE* 5.3 7.9 - - + -
151J ALA* 4.7 15.9 - - + -
152J ILE* 4.3 17.5 - - + -
155J LEU* 4.0 14.4 - - + -
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Residues in contact with ARG 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LYS* 3.3 17.8 - - - +
114J ASP* 3.0 35.7 + - - +
116J ILE* 1.3 78.9 - - - +
118J ARG* 1.3 61.8 + - - +
120J VAL* 3.2 19.4 - - - +
121J GLN* 3.2 17.7 - - - +
155J LEU* 3.5 32.0 - - + +
158J GLU* 4.3 13.4 + - - -
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Residues in contact with ARG 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J LEU* 5.6 8.8 - - + +
107J GLU 3.6 22.4 + - - -
108J TRP* 5.1 1.2 - - - +
114J ASP* 2.9 12.9 + - - +
115J SER* 3.0 23.4 + - - +
117J ARG* 1.3 77.6 - - - +
119J VAL* 1.3 64.0 + - - +
121J GLN* 3.2 37.2 + - - +
54T ILE* 4.4 7.6 - - - +
57T VAL* 3.7 31.1 - - + +
58T GLY* 5.6 7.2 - - - +
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Residues in contact with VAL 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J THR* 3.4 23.1 + - + -
59J PHE* 3.7 22.2 - - + -
81J ILE* 3.9 13.0 - - + +
83J PRO* 3.5 29.4 - - + -
106J LEU* 3.7 28.4 - - + +
108J TRP* 5.2 7.0 - - + -
115J SER 3.0 15.4 + - - +
116J ILE* 3.1 24.5 - - - +
118J ARG* 1.3 79.1 - - - +
120J VAL* 1.3 60.1 + - + +
121J GLN 3.4 0.6 + - - -
123J SER* 3.5 0.9 + - - -
54T ILE* 5.0 1.4 - - - +
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Residues in contact with VAL 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J THR* 4.5 6.1 - - + -
59J PHE* 4.3 14.1 - - + -
116J ILE* 3.1 26.2 - - + +
117J ARG* 3.2 15.3 - - - +
119J VAL* 1.3 87.1 - - + +
121J GLN* 1.3 67.1 + - - +
123J SER* 3.2 25.8 - - - +
126J VAL* 4.6 17.7 - - + -
152J ILE* 5.3 1.3 - - + +
155J LEU* 4.4 24.2 - - + +
156J SER* 5.0 5.4 - - - +
159J ALA* 3.7 14.9 - - + +
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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