Contacts of the helix formed by residues 117 - 131 (chain D) in PDB entry 5BXD
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 LEU 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D TYR* 4.1 15.5 - - + -
53D GLU* 5.7 0.4 - - - +
54D SER* 3.8 21.3 - - - +
56D ILE* 4.4 2.0 - - + -
87D ILE* 3.8 31.6 - - + -
90D PHE* 4.1 21.3 - - + -
91D LEU* 3.8 24.7 - - + -
112D ALA 2.9 11.7 + - - +
115D PHE* 3.9 15.7 - - + +
116D GLN* 1.3 74.2 - - - +
118D GLN* 1.3 64.9 + - - +
119D PRO* 3.3 5.8 - - - -
120D MET* 3.0 30.9 + - + +
121D LEU* 3.3 13.7 + - - +
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Residues in contact with GLN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D TYR* 5.9 0.2 + - - -
116D GLN 3.6 5.0 + - - +
117D LEU* 1.3 73.7 - - - +
119D PRO* 1.4 71.5 - - + +
121D LEU* 3.1 39.2 + - - +
122D LEU* 3.2 33.0 + - + +
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Residues in contact with PRO 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D TYR* 4.4 22.4 - - + +
53D GLU* 5.2 5.4 - - - +
90D PHE* 3.8 16.4 - - + -
117D LEU* 3.5 5.8 - - - -
118D GLN* 1.4 94.3 - - + +
120D MET* 1.3 59.7 + - - +
122D LEU* 3.4 13.6 + - + +
123D GLU* 3.2 27.4 + - + +
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Residues in contact with MET 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D TYR* 3.7 20.4 - - + +
87D ILE* 3.9 19.7 - - + -
90D PHE* 3.5 48.6 - - + -
96D LEU* 3.9 28.9 - - + -
108D LEU* 3.9 30.1 - - + -
112D ALA* 3.9 11.9 - - + -
117D LEU* 3.0 16.8 + - + +
119D PRO* 1.3 76.8 - - - +
121D LEU* 1.3 60.4 + - - +
123D GLU* 3.3 4.7 + - - +
124D MET* 2.9 36.1 + - + +
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D TYR* 3.5 66.0 + - + +
112D ALA* 3.6 16.2 - - + -
113D LYS* 3.8 23.8 - - + +
116D GLN* 6.2 0.4 - - - -
117D LEU 3.8 9.9 - - - +
118D GLN* 3.1 40.9 + - - +
120D MET* 1.3 79.0 - - - +
122D LEU* 1.3 58.3 + - + +
124D MET* 3.3 4.7 + - - +
125D GLU* 2.9 27.9 + - - +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D GLN* 3.2 31.0 + - + +
119D PRO* 3.7 12.8 - - + +
120D MET 3.3 0.2 - - - -
121D LEU* 1.3 77.6 - - + +
123D GLU* 1.3 63.9 + - + +
125D GLU* 3.3 11.2 + - + +
126D ARG* 3.2 28.8 + - + +
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D PHE* 5.0 4.5 - - + -
94D SER 5.3 4.8 - - - +
95D LYS* 5.9 1.1 - - - -
96D LEU* 3.7 31.7 - - + +
119D PRO* 3.2 16.4 + - + +
120D MET* 3.6 9.0 - - - +
122D LEU* 1.3 78.9 - - + +
124D MET* 1.3 57.2 + - - +
126D ARG* 3.2 19.8 + - - +
127D TRP* 2.9 28.2 + - - +
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Residues in contact with MET 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D LEU* 3.7 25.4 - - + -
98D ILE* 5.4 2.2 - - + -
102D PHE* 5.4 0.7 - - + -
105D TYR* 3.3 61.7 + - + +
108D LEU* 3.7 29.2 - - + +
109D TYR* 3.5 29.6 - - + +
112D ALA* 4.5 10.8 - - - -
120D MET* 2.9 24.8 + - - +
121D LEU* 3.6 5.8 - - - +
122D LEU 3.3 0.2 - - - -
123D GLU* 1.3 73.9 - - - +
125D GLU* 1.3 64.5 + - - +
127D TRP* 3.2 1.8 + - - +
128D LYS 3.0 20.6 + - - -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D TYR* 3.5 11.7 + - - -
109D TYR* 4.3 14.7 + - - -
121D LEU 2.9 13.3 + - - +
122D LEU* 3.4 16.4 - - + +
124D MET* 1.3 76.0 - - - +
126D ARG* 1.3 61.2 + - + +
128D LYS* 3.1 31.0 + - - +
129D GLN* 3.2 37.5 + - - +
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Residues in contact with ARG 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D LEU* 3.2 15.3 + - - +
123D GLU* 3.5 22.3 + - - +
124D MET 3.2 0.4 - - - -
125D GLU* 1.3 76.4 - - + +
127D TRP* 1.3 65.6 + - - +
129D GLN* 3.3 24.0 + - - +
130D ASP* 3.6 16.2 + - - +
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Residues in contact with TRP 127 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C ASP* 6.2 0.4 - - - -
96D LEU* 3.7 13.5 - - + -
98D ILE* 3.4 35.8 + - + +
99D PRO 3.5 21.2 + - - -
100D ASP* 4.0 2.2 + - - -
102D PHE* 3.6 29.6 - + + -
105D TYR* 3.9 28.7 - + + -
123D GLU 2.9 14.1 + - - +
124D MET 3.5 6.7 - - - +
126D ARG* 1.3 76.5 - - - +
128D LYS* 1.3 82.5 + - + +
130D ASP* 3.2 12.7 + - - +
131D ARG* 3.0 76.5 + - + +
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D TYR* 3.7 36.5 + - + -
124D MET 3.0 14.9 + - - +
125D GLU* 3.1 35.6 + - - +
126D ARG 3.3 0.2 - - - -
127D TRP* 1.3 89.8 - - + +
129D GLN* 1.3 61.8 + - - +
131D ARG* 3.1 6.8 + - - +
132D GLU* 2.8 30.4 + - - -
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Residues in contact with GLN 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D GLU* 3.2 34.3 + - - +
126D ARG* 3.3 14.3 + - - +
127D TRP 3.2 0.8 - - - -
128D LYS* 1.3 80.5 - - - +
130D ASP* 1.3 64.1 + - - +
131D ARG 3.1 1.8 - - - -
132D GLU* 3.0 37.5 + - - +
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ARG* 3.6 13.7 + - - +
127D TRP* 3.2 12.8 + - - +
129D GLN* 1.3 78.4 - - - +
131D ARG* 1.3 74.8 + - - +
132D GLU* 3.4 5.7 - - - +
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Residues in contact with ARG 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ASP* 3.0 45.3 + - - +
127D TRP* 3.0 77.7 + - + +
128D LYS 3.1 7.1 + - - +
129D GLN 3.1 0.2 - - - -
130D ASP* 1.3 95.4 + - - +
132D GLU* 1.3 75.7 + - - +
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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