Contacts of the helix formed by residues 126 - 138 (chain D) in PDB entry 4K81
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 126 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D ARG* 3.5 29.5 + - - +
124D THR 4.1 2.7 - - - +
125D VAL* 1.3 79.8 + - - +
127D SER* 1.3 65.0 + - - +
128D ARG* 4.1 10.3 - - + +
129D GLN* 3.1 35.0 + - + +
130D ALA* 3.2 8.8 + - - +
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Residues in contact with SER 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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123D ARG* 3.1 12.3 - - - +
126D GLU* 1.3 74.3 + - - +
128D ARG* 1.3 55.5 + - - +
130D ALA* 3.2 8.2 + - - +
131D GLN* 2.7 52.1 + - - +
141D TYR* 3.9 5.8 - - - -
143D GLU* 3.2 28.3 - - - -
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Residues in contact with ARG 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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126D GLU* 3.0 8.1 - - + +
127D SER* 1.3 80.0 + - - +
129D GLN* 1.3 64.2 + - + +
131D GLN* 3.5 18.3 + - - +
132D ASP* 3.1 31.9 + - - +
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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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90D PHE* 3.5 24.8 - - + -
124D THR 4.2 4.5 - - - +
125D VAL* 3.7 13.4 - - + +
126D GLU* 3.1 35.4 + - + +
128D ARG* 1.3 76.4 - - + +
130D ALA* 1.3 61.3 + - - +
132D ASP* 3.5 9.0 + - - +
133D LEU* 3.3 16.8 + - - +
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Residues in contact with ALA 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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82D PHE* 3.8 16.8 - - + -
90D PHE* 3.7 12.3 - - + -
113D LEU* 3.5 11.9 - - - +
125D VAL* 4.6 1.8 - - + -
126D GLU 3.2 8.2 + - - +
127D SER* 3.2 5.4 + - - +
129D GLN* 1.3 80.9 - - - +
131D GLN* 1.3 61.0 + - - +
133D LEU* 3.3 2.4 + - - +
134D ALA* 3.1 19.1 + - - +
141D TYR* 3.3 39.5 - - + +
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Residues in contact with GLN 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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127D SER* 2.7 40.3 + - - +
128D ARG* 3.8 19.8 - - - +
130D ALA* 1.3 73.0 - - - +
132D ASP* 1.3 59.0 + - - +
134D ALA* 3.6 1.6 + - - +
135D ARG* 2.9 30.4 + - - +
141D TYR* 3.6 27.6 - - + -
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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 ARG* 3.1 24.2 + - - +
129D GLN* 3.7 8.1 - - - +
130D ALA 3.3 0.2 - - - -
131D GLN* 1.3 75.7 - - - +
133D LEU* 1.3 55.9 + - - +
135D ARG* 3.3 13.8 + - - +
136D SER* 2.8 36.1 + - - -
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Residues in contact with LEU 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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90D PHE* 3.7 24.5 - - + -
93D ILE* 3.6 35.7 - - + -
94D HIS* 3.6 24.5 - - + +
113D LEU* 4.1 7.0 - - + -
129D GLN 3.3 11.1 + - - +
130D ALA 3.3 7.8 + - - +
132D ASP* 1.3 75.8 - - - +
134D ALA* 1.3 62.3 + - - +
136D SER* 2.5 26.6 + - - +
137D TYR* 3.1 39.8 + - + +
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Residues in contact with ALA 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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113D LEU* 4.1 9.4 - - + +
130D ALA 3.1 15.7 + - - +
131D GLN 3.9 3.6 - - - +
133D LEU* 1.3 75.9 - - - +
135D ARG* 1.3 52.5 + - - +
137D TYR* 3.1 4.6 + - - +
138D GLY 2.8 30.1 + - - -
139D ILE* 3.0 43.3 + - + +
140D PRO 4.2 0.9 - - - +
141D TYR* 3.8 22.0 - - + -
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Residues in contact with ARG 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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131D GLN 2.9 19.3 + - - +
132D ASP* 3.3 14.1 + - - +
134D ALA* 1.3 77.1 - - - +
136D SER* 1.3 61.6 + - - +
138D GLY* 3.2 13.4 + - - +
139D ILE 5.2 0.7 - - - +
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Residues in contact with SER 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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97D ARG* 5.5 1.6 + - - -
132D ASP 2.8 17.4 + - - -
133D LEU* 2.5 28.6 + - - +
135D ARG* 1.3 72.9 - - - +
137D TYR* 1.3 70.9 + - - +
138D GLY 3.8 0.2 + - - -
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Residues in contact with TYR 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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93D ILE* 3.5 31.7 - - + +
94D HIS* 3.8 20.8 - - - +
97D ARG* 3.2 60.6 + - - +
98D GLU* 4.9 0.9 + - - -
107D ASP 5.1 6.1 - - - +
111D MET* 4.1 1.8 - - + -
113D LEU* 5.5 0.9 - - + -
133D LEU* 3.1 45.1 + - + +
134D ALA* 3.1 5.6 + - - +
136D SER* 1.3 84.5 - - - +
138D GLY* 1.3 63.5 + - - +
139D ILE* 3.8 34.5 - - + +
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Residues in contact with GLY 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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134D ALA 2.8 7.8 + - - -
135D ARG* 3.2 12.8 + - - -
136D SER 3.4 0.2 - - - -
137D TYR* 1.3 80.0 - - - +
139D ILE* 1.3 60.8 + - - +
162D GLU* 4.7 5.0 - - - +
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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