Contacts of the helix formed by residues 131 - 143 (chain A) in PDB entry 4X86
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ARG 3.4 15.5 - - - +
130A LEU* 1.3 75.2 - - - +
132A LEU* 1.3 64.1 + - - +
133A ASP* 3.4 12.0 + - - +
134A ASP* 3.1 37.5 + - - +
135A ILE* 3.2 18.6 + - - +
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Residues in contact with LEU 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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131A THR* 1.3 74.6 - - - +
133A ASP* 1.3 62.2 + - - +
135A ILE* 3.3 12.7 + - + +
136A GLU* 3.0 24.7 + - - +
1111B LEU* 6.1 4.3 - - + -
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Residues in contact with ASP 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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131A THR* 3.4 10.7 + - - +
132A LEU* 1.3 81.4 - - - +
134A ASP* 1.3 68.0 + - - +
136A GLU* 3.4 6.1 + - - +
137A ARG* 3.1 23.5 + - - +
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Residues in contact with ASP 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 ARG 3.9 5.4 - - - +
130A LEU* 3.9 25.4 - - + +
131A THR* 3.1 33.5 + - - +
133A ASP* 1.3 80.4 - - - +
135A ILE* 1.3 61.0 + - - +
137A ARG* 3.3 7.0 + - - +
138A LEU* 3.0 31.5 + - - +
1058B GLU 5.5 4.5 - - - +
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Residues in contact with ILE 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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130A LEU* 4.5 15.5 - - + -
131A THR 3.2 14.5 + - - +
132A LEU* 3.3 12.5 + - + +
134A ASP* 1.3 76.9 - - - +
136A GLU* 1.3 63.1 + - - +
138A LEU* 3.2 18.8 + - + +
139A ALA* 3.2 12.8 + - - +
1107B ILE* 3.9 22.7 - - + +
1110B ARG* 5.8 1.1 - - + -
1111B LEU* 3.8 33.4 - - + +
1201B CPS 4.0 34.1 - - + +
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Residues in contact with GLU 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 LEU 3.0 16.4 + - - +
133A ASP* 3.6 7.4 - - - +
135A ILE* 1.3 77.6 - - - +
137A ARG* 1.3 62.1 + - - +
139A ALA* 3.3 16.3 + - - +
140A SER* 3.4 11.6 + - - -
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Residues in contact with ARG 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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133A ASP* 3.1 18.8 + - - +
134A ASP* 3.6 8.3 - - - +
135A ILE 3.3 0.2 - - - -
136A GLU* 1.3 75.6 - - - +
138A LEU* 1.3 62.5 + - - +
140A SER* 3.2 16.9 + - - -
141A ARG* 3.4 19.7 + - + +
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Residues in contact with LEU 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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130A LEU* 5.7 4.3 - - + -
134A ASP* 3.0 16.6 + - + +
135A ILE* 3.2 15.5 + - + +
137A ARG* 1.3 77.3 - - - +
139A ALA* 1.3 63.2 + - - +
141A ARG* 3.1 29.7 + - - +
142A PHE* 3.4 30.6 - - + -
1060B PRO* 5.3 8.7 - - + -
1062B LEU* 4.3 22.4 - - + -
1107B ILE* 4.2 16.4 - - + -
1201B CPS 4.0 39.2 - - + -
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Residues in contact with ALA 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 ILE 3.2 7.3 + - - +
136A GLU* 3.3 11.2 + - - +
138A LEU* 1.3 79.3 - - - +
140A SER* 1.3 61.4 + - - +
141A ARG 3.4 0.2 + - - -
142A PHE* 3.7 1.0 + - - +
143A LEU* 3.6 26.5 + - - +
1201B CPS 3.9 27.5 - - + +
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Residues in contact with SER 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 GLU 3.4 8.9 + - - -
137A ARG* 3.2 13.8 + - - -
138A LEU 3.2 0.8 - - - -
139A ALA* 1.3 79.7 - - - +
141A ARG* 1.3 63.1 + - - +
142A PHE 3.6 0.3 + - - -
143A LEU 3.9 11.2 - - - +
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Residues in contact with ARG 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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137A ARG* 3.4 17.2 + - + +
138A LEU* 3.1 21.7 + - - +
140A SER* 1.3 80.6 - - - +
142A PHE* 1.3 75.9 + - + +
1062B LEU* 3.6 30.3 - - - +
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Residues in contact with PHE 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 LEU* 3.4 21.8 - - + +
139A ALA* 3.7 2.5 + - - +
141A ARG* 1.3 100.8 - - + +
143A LEU* 1.3 77.6 + - + +
1062B LEU* 3.7 29.8 - - + -
1201B CPS 3.6 33.4 - - + +
1203B SO4 3.8 21.8 - - - -
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Residues in contact with LEU 143 (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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139A ALA 3.6 17.8 + - - +
140A SER* 3.9 11.4 - - - +
141A ARG 5.0 0.2 - - - -
142A PHE* 1.3 91.8 - - + +
1201B CPS 5.5 5.6 - - - +
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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