Contacts of the helix formed by residues 116 - 132 (chain R) in PDB entry 5GJQ
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 ASP 116 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52R PRO* 4.2 17.8 - - + +
111R LEU* 2.7 25.9 + - + +
114R ILE* 2.9 11.9 + - + +
115R GLY* 1.3 70.7 - - - -
117R LYS* 1.3 75.0 + - - +
118R GLU* 3.7 21.7 - - - +
119R GLY* 4.6 4.9 + - - +
120R ALA* 3.4 19.1 + - - +
151R TYR* 4.2 1.7 + - - -
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Residues in contact with LYS 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116R ASP* 1.3 77.4 + - - +
118R GLU* 1.3 63.2 - - - +
119R GLY 3.0 0.5 + - - -
120R ALA* 3.9 2.2 - - - +
121R LEU* 2.7 51.4 + - + +
147R ILE* 4.8 14.7 - - + +
148R GLY* 5.2 0.4 - - - -
151R TYR* 3.2 52.9 + - + +
153R ASP* 2.7 34.5 + - - +
156R LEU* 4.2 20.8 - - - +
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Residues in contact with GLU 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116R ASP* 3.7 19.7 - - - +
117R LYS* 1.3 76.7 - - - +
119R GLY* 1.3 61.7 + - - +
121R LEU* 3.1 15.1 - - + +
122R THR* 2.9 31.0 + - - -
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Residues in contact with GLY 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111R LEU* 3.9 13.5 - - - -
116R ASP* 3.7 9.5 + - - -
117R LYS 3.0 1.6 + - - -
118R GLU* 1.3 82.2 - - - +
120R ALA* 1.3 61.0 + - - +
122R THR* 2.8 21.4 + - - -
123R ALA* 2.9 16.5 + - - +
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Residues in contact with ALA 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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108R ALA* 3.1 24.0 - - - +
111R LEU* 3.4 13.5 - - + +
112R CYS* 4.3 5.8 - - + +
116R ASP 3.4 12.6 + - - +
117R LYS* 4.1 2.7 - - - +
119R GLY* 1.3 71.3 - - - +
121R LEU* 1.3 53.9 + - - +
124R PHE* 1.6 81.5 + - + -
147R ILE* 5.4 7.2 - - + -
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Residues in contact with LEU 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 LYS* 2.7 54.3 + - + +
118R GLU* 3.1 20.4 - - + +
120R ALA* 1.3 79.1 - - - +
122R THR* 1.3 66.1 + - - +
124R PHE* 3.5 6.7 - - + +
125R ARG* 2.9 20.8 + - - +
144R LEU* 4.8 22.0 - - + +
147R ILE* 5.1 7.4 - - + -
156R LEU* 5.1 9.0 - - + -
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Residues in contact with THR 122 (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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118R GLU 2.9 11.9 + - - -
119R GLY* 2.8 22.7 + - - -
121R LEU* 1.3 75.6 - - - +
123R ALA* 1.3 64.4 + - - +
125R ARG* 3.1 9.6 + - - +
126R LYS* 3.0 28.0 + - - +
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Residues in contact with ALA 123 (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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104R MET* 4.9 3.1 - - + +
107R LYS* 4.6 11.0 - - + -
108R ALA* 3.1 36.6 - - + +
111R LEU* 5.5 0.2 - - + -
119R GLY 2.9 12.2 + - - +
122R THR* 1.3 81.3 + - - +
124R PHE* 1.3 49.8 + - - +
126R LYS* 2.7 33.1 - - + +
127R THR* 2.8 22.3 - - + +
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Residues in contact with PHE 124 (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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105R MET* 5.2 5.2 - - + -
108R ALA* 2.9 28.0 - - + -
109R GLU* 3.8 7.0 - - + -
112R CYS* 5.1 5.4 - - + -
120R ALA* 1.6 78.2 + - + -
121R LEU* 3.3 7.4 - - + +
123R ALA* 1.3 68.5 - - - +
125R ARG* 1.3 60.8 + - - +
127R THR* 2.1 41.9 + - - -
128R TYR* 3.0 5.9 + - - +
140R ILE* 3.5 25.9 - - + +
143R TYR* 4.0 17.7 - + + -
144R LEU* 3.7 26.5 - - + -
147R ILE* 5.7 6.7 - - + -
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Residues in contact with ARG 125 (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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121R LEU 2.9 13.1 + - - +
122R THR* 3.3 12.8 - - - +
124R PHE* 1.3 73.1 - - - +
126R LYS* 1.3 56.3 + - - +
128R TYR* 2.6 37.0 + - - +
129R ASP* 3.3 9.3 + - - +
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Residues in contact with LYS 126 (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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104R MET* 4.0 28.1 - - - +
122R THR* 3.0 10.7 + - - +
123R ALA* 2.7 33.7 - - + +
125R ARG* 1.3 76.7 - - - +
127R THR* 1.3 58.4 + - - +
129R ASP* 3.4 30.0 - - + +
130R LYS* 3.5 6.2 + - - +
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Residues in contact with THR 127 (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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101R ARG* 4.4 9.5 - - - +
104R MET* 3.3 41.7 - - + -
105R MET* 4.5 8.4 - - + +
108R ALA* 5.7 0.4 - - + -
123R ALA 2.8 23.8 - - - +
124R PHE* 2.1 37.9 + - - +
126R LYS* 1.3 73.1 - - + +
128R TYR* 1.3 52.9 + - - +
130R LYS* 3.1 6.8 - - - +
131R THR* 2.4 47.8 + - - +
140R ILE* 4.3 8.3 - - - +
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Residues in contact with TYR 128 (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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124R PHE 3.0 6.4 + - - +
125R ARG* 2.6 23.6 + - - +
127R THR* 1.3 68.4 + - - +
129R ASP* 1.3 61.9 + - - +
130R LYS 2.9 6.7 - - - +
131R THR* 2.5 30.8 + - + +
137R ARG* 4.7 16.2 + - + +
140R ILE* 6.4 0.9 - - + -
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Residues in contact with ASP 129 (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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125R ARG 4.0 8.3 - - - +
126R LYS* 3.4 23.3 + - - +
128R TYR* 1.3 77.4 - - - +
130R LYS* 1.3 59.1 + - - +
132R VAL* 5.2 0.9 - - - +
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Residues in contact with LYS 130 (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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97R GLU* 5.7 9.6 - - + +
101R ARG* 4.0 18.2 - - + -
126R LYS 3.5 6.0 + - - +
127R THR* 3.2 10.5 + - - +
128R TYR 2.9 5.3 - - - +
129R ASP* 1.3 76.9 - - - +
131R THR* 1.3 61.5 + - - +
132R VAL* 2.3 40.1 + - + +
137R ARG* 5.3 0.3 + - - -
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Residues in contact with THR 131 (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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206J HIS* 5.1 1.7 - - - -
98R SER* 5.7 3.6 + - - -
101R ARG* 4.5 8.9 - - + +
127R THR* 2.4 52.6 + - - +
128R TYR* 2.5 31.7 + - + +
130R LYS* 1.3 68.3 - - - +
132R VAL* 1.3 65.6 + - - +
133R ALA* 2.7 23.3 + - - +
136R HIS* 3.9 33.1 - - + +
137R ARG* 3.6 27.0 + - - +
140R ILE* 5.4 1.6 - - + -
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Residues in contact with VAL 132 (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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147J THR* 5.8 0.2 - - - -
205J HIS* 4.3 29.3 + - + +
206J HIS* 4.4 15.0 - - + +
97R GLU* 6.0 6.3 - - + -
128R TYR 4.3 0.2 + - - -
129R ASP 5.2 0.7 - - - +
130R LYS* 2.3 40.0 + - + +
131R THR* 1.3 79.0 + - - +
133R ALA* 1.3 66.0 + - - +
137R ARG* 3.5 24.6 + - - +
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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