Contacts of the helix formed by residues 130 - 142 (chain A) in PDB entry 1O4X
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 THR 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A LYS 4.7 4.7 - - - +
129A PRO* 1.3 75.1 - - - +
131A SER* 1.3 57.9 + - - +
132A GLU* 3.3 10.7 + - - +
133A GLU* 2.9 37.8 + - - +
134A ILE* 2.7 37.3 + - - +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A THR* 1.3 74.3 - - - +
132A GLU* 1.3 52.5 + - - +
134A ILE* 3.6 12.4 - - - +
135A THR* 2.4 39.9 + - - -
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A THR* 3.0 8.6 + - - +
131A SER* 1.3 77.7 - - - +
133A GLU* 1.3 68.7 + - + +
135A THR* 3.2 7.1 + - - -
136A MET* 3.0 29.8 + - + +
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASN* 3.1 29.5 + - - +
129A PRO* 3.3 14.0 - - + +
130A THR* 2.9 39.6 + - - +
132A GLU* 1.3 77.9 - - + +
134A ILE* 1.3 64.2 + - - +
136A MET* 3.2 9.5 + - - +
137A ILE* 3.0 31.4 + - + +
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Residues in contact with ILE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PRO* 3.4 36.3 - - + +
130A THR 2.7 22.5 + - - +
131A SER* 3.6 9.6 - - - +
133A GLU* 1.3 74.4 - - - +
135A THR* 1.3 65.1 + - - +
137A ILE* 3.1 10.9 + - - +
138A ALA* 2.9 21.7 + - - +
145A LYS* 4.3 12.1 - - + +
148A ILE* 3.9 22.2 - - + +
149A ARG* 3.9 37.5 - - + +
152A PHE* 5.0 4.7 - - + -
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A SER* 2.4 31.3 + - - -
132A GLU* 3.2 8.3 + - - -
134A ILE* 1.3 77.9 - - - +
136A MET* 1.3 64.5 + - - +
138A ALA* 3.3 7.7 + - + +
139A ASP* 3.2 20.8 + - + +
145A LYS* 5.3 12.3 - - + +
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Residues in contact with MET 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU* 3.0 18.1 + - + +
133A GLU* 3.2 10.1 - - - +
134A ILE 3.1 0.2 - - - -
135A THR* 1.3 79.2 - - - +
137A ILE* 1.3 55.9 + - + +
138A ALA 3.0 0.7 + - - -
139A ASP* 3.1 4.0 + - - +
140A GLN* 2.7 37.4 + - - +
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU* 4.6 8.3 - - + -
122A SER* 4.2 21.3 - - - +
129A PRO* 4.2 19.1 - - + -
133A GLU* 3.0 26.2 + - + +
134A ILE* 3.4 11.0 - - - +
136A MET* 1.3 75.6 - - + +
138A ALA* 1.3 57.0 + - - +
140A GLN* 3.1 13.6 - - + +
141A LEU* 3.0 45.6 + - + +
148A ILE* 4.6 12.3 - - + -
152A PHE* 4.4 6.7 - - + -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ILE 2.9 11.5 + - - +
135A THR* 3.4 12.3 - - + +
136A MET 3.0 0.2 + - - -
137A ILE* 1.3 73.6 - - - +
139A ASP* 1.3 54.5 + - - +
141A LEU* 2.9 3.6 + - - +
142A ASN 2.5 33.1 + - - -
143A MET* 3.0 27.3 + - - +
145A LYS* 4.1 21.8 - - + +
148A ILE* 4.1 15.2 - - + +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 3.2 7.7 + - + +
136A MET* 3.1 8.1 + - - +
138A ALA* 1.3 77.2 - - - +
140A GLN* 1.3 61.1 + - - +
142A ASN* 2.7 29.0 + - - +
143A MET 4.3 1.1 + - - +
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Residues in contact with GLN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A MET 2.7 22.0 + - - +
137A ILE* 3.1 19.3 - - + +
139A ASP* 1.3 77.8 + - - +
141A LEU* 1.3 83.6 + - + +
142A ASN* 5.2 0.2 - - - +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 3.9 32.9 - - + +
118A ALA* 4.5 20.2 - - + -
119A LEU* 3.9 24.7 - - + +
137A ILE* 3.3 24.7 - - + +
138A ALA 2.9 3.8 + - - +
140A GLN* 1.3 101.4 - - + +
142A ASN* 1.3 74.3 + - - +
143A MET* 3.5 17.2 - - + +
148A ILE* 4.8 3.4 - - + -
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ALA 2.5 12.4 + - - -
139A ASP* 2.7 15.8 + - - +
140A GLN 5.2 0.4 - - - +
141A LEU* 1.3 79.8 - - - +
143A MET* 1.3 65.7 + - - +
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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