Contacts of the helix formed by residues 123 - 138 (chain D) 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 GLU 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D PHE* 1.3 94.6 - - - +
124D ASP* 1.3 73.6 + - - +
125D GLU* 3.9 18.0 + - + +
126D GLU* 3.3 15.8 + - + +
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Residues in contact with ASP 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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108D ALA* 3.6 18.6 - - + +
109D GLU* 4.8 1.4 + - - +
112D LYS* 2.3 48.3 + - - +
118D LEU 5.3 0.7 - - - +
122D PHE* 4.0 6.8 - - - +
123D GLU* 1.3 79.5 - - - +
125D GLU* 1.3 52.9 + - - +
127D LEU* 3.3 9.8 + - - +
128D GLN* 2.8 36.1 + - - +
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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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123D GLU* 3.9 15.2 + - + +
124D ASP* 1.3 77.2 - - - +
126D GLU* 1.3 52.5 + - + +
128D GLN* 3.0 11.1 + - - +
129D GLN* 2.6 57.6 + - + +
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Residues in contact with GLU 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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90D LYS* 2.8 31.5 + - - -
122D PHE* 3.9 20.6 - - + +
123D GLU* 3.3 17.2 + - + +
125D GLU* 1.3 74.7 - - + +
127D LEU* 1.3 56.2 + - - +
129D GLN* 2.7 12.8 + - + +
130D ILE* 2.4 43.8 + - + +
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Residues in contact with LEU 127 (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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92D LEU* 5.6 3.8 - - + -
100D LEU* 3.9 18.6 - - + -
108D ALA* 4.0 17.0 - - + +
111D SER* 3.9 25.1 - - - -
112D LYS* 5.0 7.2 - - + -
118D LEU* 4.6 14.8 - - + +
122D PHE* 3.5 32.3 - - + -
123D GLU 4.6 0.2 - - - +
124D ASP* 3.3 12.5 + - - +
126D GLU* 1.3 77.2 - - - +
128D GLN* 1.3 57.8 + - - +
130D ILE* 4.0 13.9 - - + -
131D LEU* 2.7 51.6 + - + +
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Residues in contact with GLN 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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106D GLU 2.8 27.1 + - - -
107D THR* 3.2 7.6 - - - +
108D ALA* 2.6 33.8 + - + +
124D ASP 2.8 16.1 + - - +
125D GLU* 3.4 15.3 - - - +
127D LEU* 1.3 79.0 - - - +
129D GLN* 1.3 59.0 + - - +
131D LEU* 3.8 6.5 - - - +
132D ASP* 2.9 30.8 + - + +
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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* 2.6 46.3 + - + +
126D GLU* 2.7 18.2 + - + +
128D GLN* 1.3 71.7 - - - +
130D ILE* 1.3 61.7 + - - +
132D ASP* 3.4 16.6 + - - +
133D ASP* 3.1 21.8 + - - +
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Residues in contact with ILE 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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86D LEU* 5.4 12.0 - - + +
87D LEU* 3.6 28.5 - - + -
90D LYS* 3.6 39.7 - - + +
92D LEU* 5.3 3.6 - - + -
100D LEU* 5.1 2.2 - - + -
122D PHE* 4.7 8.3 - - + -
126D GLU* 2.4 32.2 + - + +
127D LEU* 3.5 24.5 - - + +
129D GLN* 1.3 66.0 - - + +
131D LEU* 1.3 64.8 - - + +
133D ASP* 3.3 8.5 + - - +
134D ILE* 2.9 37.0 + - + +
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Residues in contact with LEU 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 LEU* 4.2 13.5 - - + -
105D PRO* 3.3 33.7 - - + +
106D GLU* 3.5 2.7 - - - +
107D THR* 3.3 48.5 - - - +
108D ALA* 3.8 2.5 - - - +
111D SER* 3.6 6.3 - - - +
127D LEU* 2.7 47.1 + - + +
128D GLN* 3.8 12.6 - - - +
130D ILE* 1.3 72.5 - - + +
132D ASP* 1.3 55.5 + - - +
134D ILE* 3.1 8.4 + - + +
135D GLN* 2.8 40.4 + - - +
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Residues in contact with ASP 132 (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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128D GLN* 2.9 22.3 + - + +
129D GLN* 3.6 21.1 + - - +
130D ILE 3.3 0.2 - - - -
131D LEU* 1.3 75.3 - - - +
133D ASP* 1.3 54.9 + - - +
135D GLN* 3.6 7.3 + - - +
136D THR* 2.8 43.8 + - - -
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Residues in contact with ASP 133 (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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83D VAL* 5.3 5.0 - - - +
86D LEU* 3.4 29.0 - - + +
129D GLN 3.1 13.6 + - - +
130D ILE* 3.4 10.1 - - - +
131D LEU 3.2 0.2 - - - -
132D ASP* 1.3 75.6 + - - +
134D ILE* 1.3 66.4 + - - +
136D THR* 3.3 4.8 + - - -
137D LYS* 2.9 62.7 + - - +
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Residues in contact with ILE 134 (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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74D PHE* 4.8 11.0 - - + -
83D VAL* 5.0 17.0 - - + -
86D LEU* 6.2 2.2 - - + -
87D LEU* 5.0 8.5 - - + -
100D LEU* 3.6 34.5 - - + +
101D ALA* 5.7 2.9 - - - -
104D CYS* 4.4 28.0 - - + -
105D PRO* 5.3 2.9 - - + +
130D ILE* 2.9 29.8 + - + +
131D LEU* 3.1 14.8 + - + +
133D ASP* 1.3 75.7 + - - +
135D GLN* 1.3 58.0 + - - +
137D LYS* 3.0 7.3 + - - +
138D ARG* 2.6 39.7 + - + +
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Residues in contact with GLN 135 (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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104D CYS 3.6 4.6 + - - -
105D PRO 3.2 16.6 + - - +
106D GLU* 3.2 31.4 - - + +
131D LEU 2.8 25.5 + - - +
132D ASP* 3.8 7.9 - - - +
134D ILE* 1.3 76.2 - - - +
136D THR* 1.3 60.9 + - - +
138D ARG* 3.1 63.9 + - - +
140D PHE* 4.8 4.9 - - - -
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Residues in contact with THR 136 (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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132D ASP* 2.8 32.5 + - - -
133D ASP* 3.3 8.2 + - - -
135D GLN* 1.3 76.0 - - - +
137D LYS* 1.3 70.7 + - + +
138D ARG 4.4 2.6 - - - +
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Residues in contact with LYS 137 (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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74D PHE* 4.4 5.8 - - + -
79D THR* 4.0 33.8 - - + +
82D SER* 6.2 4.7 - - - -
83D VAL* 4.6 14.8 - - + -
133D ASP* 2.9 58.7 + - - +
134D ILE 3.6 3.8 - - - +
136D THR* 1.3 86.4 - - - +
138D ARG* 1.3 66.9 + - - +
139D SER* 3.4 10.2 + - - -
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Residues in contact with ARG 138 (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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73D ARG* 4.3 29.9 - - + +
74D PHE* 4.4 10.5 - - + -
104D CYS* 3.6 30.7 + - - +
106D GLU* 3.6 16.2 + - - +
134D ILE* 2.6 23.5 + - + +
135D GLN* 3.1 54.2 + - - +
136D THR 4.4 2.8 - - - +
137D LYS* 1.3 74.7 - - - +
139D SER* 1.3 65.6 + - - +
140D PHE* 3.3 35.6 - - + -
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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