Contacts of the helix formed by residues 115 - 127 (chain D) in PDB entry 1M6X
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 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B LYS* 3.7 30.3 + - - +
114D SER* 1.3 79.1 - - - +
116D ILE* 1.3 65.6 + - - +
117D THR* 2.5 33.9 + - - +
118D ASP* 3.0 27.8 + - - +
119D ILE* 2.9 23.0 + - - +
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Residues in contact with ILE 116 (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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41B LEU* 4.8 10.3 - - + -
45B ILE* 3.8 22.7 - - + -
92B SER* 2.9 52.3 - - - +
93B LEU* 4.0 2.2 - - + +
95B LYS* 5.2 4.7 - - + +
96B LEU* 4.3 36.6 - - + +
114D SER 4.2 1.0 + - - +
115D ASP* 1.3 72.4 + - - +
117D THR* 1.3 58.1 + - + +
119D ILE* 2.7 13.4 + - + +
120D VAL* 2.6 53.8 + - + +
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Residues in contact with THR 117 (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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16B VAL* 6.2 0.9 - - + -
96B LEU* 4.4 19.5 - - + -
115D ASP* 2.5 23.7 + - - +
116D ILE* 1.3 78.5 - - + +
118D ASP* 1.3 62.9 + - - +
120D VAL* 3.8 8.8 - - - +
121D SER* 2.9 27.9 + - - -
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Residues in contact with ASP 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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114D SER* 5.9 1.1 - - - -
115D ASP* 3.2 29.9 + - + +
116D ILE 2.9 0.4 - - - -
117D THR* 1.3 86.1 + - - +
119D ILE* 1.3 67.7 + - + +
121D SER* 2.7 23.0 + - - -
122D SER* 2.8 12.7 + - - -
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Residues in contact with ILE 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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44B MET* 4.0 22.0 - - + +
45B ILE* 4.3 16.8 - - + +
48B ASN* 4.0 17.3 - - - +
49B GLY* 3.6 30.1 - - - +
114D SER* 4.0 18.6 - - - +
115D ASP 3.1 23.1 - - - +
116D ILE* 2.7 15.5 + - + +
118D ASP* 1.3 73.3 - - + +
120D VAL* 1.3 65.7 + - + +
122D SER* 3.1 8.3 - - - -
123D LEU* 2.9 33.6 + - + +
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Residues in contact with VAL 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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12B PRO* 4.0 4.0 - - + -
13B LYS* 3.9 25.8 - - + +
16B VAL* 3.4 36.1 - - + -
40B TYR* 6.4 1.8 - - + -
41B LEU* 5.4 1.8 - - + -
116D ILE* 2.6 45.7 + - + +
117D THR* 3.8 8.1 - - - +
119D ILE* 1.3 72.5 - - + +
121D SER* 1.3 52.8 + - - +
123D LEU* 2.6 35.6 + - + +
124D GLN 2.6 16.6 + - - -
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Residues in contact with SER 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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117D THR 2.9 12.7 + - - -
118D ASP* 2.7 24.1 + - - -
120D VAL* 1.3 78.4 - - - +
122D SER* 1.3 52.7 + - - +
124D GLN* 3.1 11.6 + - - +
125D LEU* 2.7 36.7 + - - +
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Residues in contact with SER 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 ASP 2.8 13.6 + - - -
119D ILE* 3.1 14.1 - - - -
121D SER* 1.3 78.7 + - - +
123D LEU* 1.3 57.8 + - - +
125D LEU* 3.1 13.3 - - - +
126D GLN* 3.0 43.2 + - - +
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Residues in contact with LEU 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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12B PRO* 3.6 15.0 - - + +
40B TYR* 3.3 24.7 - - + +
44B MET* 3.8 26.0 - - + -
49B GLY* 3.4 31.4 - - - +
119D ILE* 2.9 25.8 + - + +
120D VAL* 2.6 18.3 + - + +
122D SER* 1.3 68.0 - - - +
124D GLN* 1.3 53.2 + - - +
125D LEU 2.9 4.8 + - - -
126D GLN* 3.0 25.2 + - - +
127D PHE* 2.7 35.5 + - - +
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Residues in contact with GLN 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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11B PRO* 3.5 14.7 - - - +
12B PRO* 3.5 14.5 - - + +
13B LYS* 2.8 62.6 + - + +
120D VAL 2.6 15.0 + - - +
121D SER* 3.4 15.0 - - - +
123D LEU* 1.3 72.1 - - - +
125D LEU* 1.3 58.2 + - - +
127D PHE* 3.7 11.2 - - - +
128D GLU* 3.0 37.2 + - - +
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Residues in contact with LEU 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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121D SER 2.7 11.9 + - - +
122D SER* 3.1 16.2 - - - +
124D GLN* 1.3 76.7 - - - +
126D GLN* 1.3 66.4 + - + +
127D PHE 3.1 1.1 - - - -
128D GLU* 3.1 32.3 + - - +
129D SER* 3.6 4.0 + - - -
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Residues in contact with GLN 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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49B GLY* 5.0 5.0 + - - +
264B ASN* 4.2 7.7 + - - +
122D SER* 3.0 30.3 + - - +
123D LEU* 3.0 33.2 + - - +
125D LEU* 1.3 76.9 - - + +
127D PHE* 1.3 62.7 + - - +
128D GLU 2.9 1.7 + - - -
129D SER* 3.0 25.9 + - - +
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Residues in contact with PHE 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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8B CYS 4.1 11.0 - - - -
9B LYS 3.9 10.1 - - - -
10B THR 3.8 13.9 - - - -
11B PRO* 3.5 37.2 - - + -
12B PRO* 3.6 21.5 - - + -
264B ASN* 2.8 50.3 + - - +
123D LEU 2.7 20.4 + - - +
124D GLN* 3.7 13.9 - - - +
125D LEU 3.1 0.2 - - - -
126D GLN* 1.3 72.7 - - - +
128D GLU* 1.3 62.1 + - + +
129D SER 3.6 0.7 - - - +
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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