Contacts of the helix formed by residues 112 - 121 (chain R) in PDB entry 5IYB
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 GLY 112 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109R LEU 4.0 4.1 + - - -
110R ASP* 3.1 5.8 + - - +
111R ILE* 1.3 81.6 - - - +
113R LEU* 1.3 55.0 + - - -
114R LYS* 3.3 3.8 - - - -
115R GLN* 3.2 5.2 + - - -
116R LYS* 2.8 35.9 + - - +
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Residues in contact with LEU 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112R GLY* 1.3 71.4 - - - -
114R LYS* 1.3 59.4 + - + +
116R LYS* 3.6 20.6 - - + +
117R GLN* 2.9 66.5 + - + +
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Residues in contact with LYS 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112R GLY* 3.3 1.3 - - - -
113R LEU* 1.3 78.5 - - + +
115R GLN* 1.3 60.3 + - + +
117R GLN* 3.5 8.4 + - - +
118R TRP* 3.0 28.6 + - - +
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Residues in contact with GLN 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R PHE 6.3 0.7 - - - -
111R ILE* 3.0 47.2 - - + +
112R GLY* 3.2 2.0 + - - -
114R LYS* 1.3 76.1 - - + +
116R LYS* 1.3 66.3 + - - +
118R TRP* 3.3 10.1 + - + +
119R LEU* 2.9 36.5 + - + +
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Residues in contact with LYS 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99R LEU* 3.6 22.8 - - + +
100R ASP* 2.7 36.8 + - - +
103R LEU* 3.6 19.1 - - + -
109R LEU* 3.6 15.7 - - + +
111R ILE* 4.1 12.9 - - + +
112R GLY 2.8 21.5 + - - +
113R LEU* 3.6 23.5 - - + +
115R GLN* 1.3 72.6 - - - +
117R GLN* 1.3 57.5 - - + +
119R LEU* 3.5 7.9 + - - +
120R MET* 3.0 30.2 + - + +
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Residues in contact with GLN 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113R LEU* 2.9 52.5 + - + +
114R LYS* 3.8 7.1 - - - +
116R LYS* 1.3 74.9 - - + +
118R TRP* 1.3 59.6 + - - +
120R MET* 3.1 5.5 + - - -
121R THR* 2.8 46.5 + - + +
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Residues in contact with TRP 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R PHE* 4.9 28.3 - + + -
78R LEU* 6.0 0.4 - - + -
114R LYS 3.0 18.5 + - - +
115R GLN* 3.7 9.4 - - + +
117R GLN* 1.3 75.2 - - - +
119R LEU* 1.3 93.9 + - + +
121R THR* 4.8 2.0 - - - -
122R GLU* 2.9 71.0 + - + +
123R ALA* 3.5 8.6 + - + -
192T GLU* 5.6 6.3 - - - -
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Residues in contact with LEU 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R PHE* 4.9 8.7 - - - +
77R VAL* 5.0 12.8 - - + -
78R LEU* 3.6 45.1 - - + +
81R ILE* 5.3 5.8 - - + -
99R LEU* 4.2 13.2 - - + -
103R LEU* 6.2 2.7 - - + -
111R ILE* 4.9 15.7 - - + -
115R GLN* 2.9 27.4 + - + +
116R LYS* 3.6 7.4 - - - +
118R TRP* 1.3 99.1 - - + +
120R MET* 1.3 57.2 + - - +
123R ALA* 3.3 7.0 + - + +
124R LEU* 3.0 32.2 + - - +
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Residues in contact with MET 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98R THR* 5.6 3.6 - - - -
99R LEU* 3.5 38.6 - - + +
116R LYS* 3.0 19.8 + - + +
117R GLN* 3.1 6.9 + - - +
119R LEU* 1.3 79.4 - - - +
121R THR* 1.3 71.0 + - + +
122R GLU 3.4 1.0 + - - -
124R LEU* 4.2 2.3 - - - +
125R VAL* 3.5 14.6 - - - +
135R GLY* 4.8 13.7 - - - +
137R TYR* 2.7 54.6 + - + +
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Residues in contact with THR 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117R GLN* 2.8 28.9 + - + +
118R TRP* 4.1 1.6 - - - -
120R MET* 1.3 89.2 - - + +
122R GLU* 1.3 58.2 + - - +
125R VAL* 3.8 14.5 - - + +
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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