Contacts of the helix formed by residues 133 - 145 (chain A) in PDB entry 3O9Z
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 HIS 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLN 3.3 5.7 + - - +
130A LEU* 3.1 24.4 + - + +
132A VAL* 1.3 77.1 - - - +
134A PRO* 1.3 74.8 - - + +
135A SER* 3.1 35.4 + - - -
136A LEU* 3.0 13.9 + - + +
137A LEU* 2.9 21.9 + - - +
255A GLU 5.5 0.4 - - - -
256A PHE* 3.1 33.2 + - + -
258A GLU 3.0 25.7 + - - -
259A GLY 4.8 0.2 - - - -
260A PHE* 4.6 4.3 - - - -
263A LEU* 4.0 19.7 - - + -
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Residues in contact with PRO 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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132A VAL 3.2 9.4 - - - +
133A HIS* 1.3 93.0 - - + +
135A SER* 1.3 55.5 + - - +
137A LEU* 3.9 9.8 - - + +
138A ALA* 3.0 28.6 + - - +
263A LEU* 4.4 11.0 - - + -
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Residues in contact with SER 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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133A HIS* 3.1 23.7 + - - -
134A PRO* 1.3 78.8 - - - +
136A LEU* 1.3 60.0 + - - +
138A ALA* 3.5 6.6 + - - +
139A LEU* 3.0 26.0 + - - +
142A ARG* 4.8 2.4 + - - -
254A VAL* 4.1 22.2 - - - +
255A GLU 5.2 3.6 + - - -
256A PHE* 5.0 0.9 - - - -
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Residues in contact with LEU 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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130A LEU* 3.8 49.8 - - + +
133A HIS* 3.0 13.3 + - + +
135A SER* 1.3 76.9 - - - +
137A LEU* 1.3 63.7 + - - +
138A ALA 3.2 0.2 - - - -
139A LEU* 3.4 11.1 + - + +
140A LYS* 3.0 24.1 + - - +
189A LEU* 3.9 19.3 - - + -
192A TRP* 4.1 12.8 - - + -
193A LEU* 4.5 1.7 - - - +
247A ILE* 4.1 13.5 - - + -
254A VAL* 4.0 16.4 - - + -
256A PHE* 3.9 33.9 - - + -
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Residues in contact with LEU 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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131A ARG 3.5 20.9 - - - +
132A VAL* 3.9 28.3 - - + +
133A HIS 2.9 13.1 + - - +
134A PRO* 3.9 8.5 - - + +
136A LEU* 1.3 77.4 - - - +
138A ALA* 1.3 61.2 + - - +
140A LYS* 3.3 4.7 + - + +
141A GLU* 3.1 27.4 + - + +
192A TRP* 3.9 18.1 - - + -
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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 PRO 3.0 18.5 + - - +
135A SER* 3.6 8.5 - - - +
136A LEU 3.2 0.2 - - - -
137A LEU* 1.3 74.1 - - - +
139A LEU* 1.3 64.7 + - - +
141A GLU* 3.2 9.0 + - - +
142A ARG* 3.1 40.8 + - - +
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Residues in contact with LEU 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 SER 3.0 17.2 + - - +
136A LEU* 3.6 16.2 - - + +
137A LEU 3.3 0.2 - - - -
138A ALA* 1.3 75.9 - - - +
140A LYS* 1.3 61.8 + - - +
142A ARG* 3.2 30.8 + - + +
143A LEU* 3.0 44.8 + - + +
193A LEU* 4.4 14.8 - - + -
247A ILE* 3.7 33.0 - - + -
249A VAL* 4.4 17.5 - - + -
252A GLU* 6.0 1.6 - - - +
254A VAL* 4.4 10.3 - - + -
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Residues in contact with LYS 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 LEU 3.0 14.4 + - - +
137A LEU* 3.7 6.7 - - + +
139A LEU* 1.3 75.8 - - - +
141A GLU* 1.3 75.3 + - - +
143A LEU* 3.3 5.8 + - + +
144A GLY* 3.2 18.2 + - - -
192A TRP* 3.6 62.8 - - + +
193A LEU* 3.4 25.1 - - + +
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Residues in contact with GLU 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 LEU* 3.1 15.8 + - + +
138A ALA* 3.2 10.3 + - - +
140A LYS* 1.3 92.6 + - - +
142A ARG* 1.3 63.0 + - + +
144A GLY* 3.3 11.7 + - - -
145A GLN* 3.7 17.6 + - - +
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Residues in contact with ARG 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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135A SER 4.8 1.6 + - - -
138A ALA* 3.1 34.1 + - - +
139A LEU* 3.2 42.4 + - + +
141A GLU* 1.3 77.2 - - + +
143A LEU* 1.3 62.4 + - + +
145A GLN* 3.2 25.7 + - - +
146A GLU* 3.4 15.5 - - - +
252A GLU* 4.8 13.3 + - - -
254A VAL* 3.9 17.6 - - - +
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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 LEU* 3.0 43.3 + - + +
140A LYS* 3.7 4.7 - - + +
141A GLU 3.2 0.2 - - - -
142A ARG* 1.3 73.9 - - + +
144A GLY* 1.3 60.9 + - - +
145A GLN 3.0 5.2 - - - -
146A GLU* 2.9 44.8 + - - +
150A LYS* 4.0 10.3 - - + -
193A LEU* 4.2 18.8 - - + +
194A PHE* 3.9 28.9 - - + -
249A VAL* 3.9 22.9 - - + -
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Residues in contact with GLY 144 (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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140A LYS 3.2 13.2 + - - -
141A GLU* 3.3 6.4 + - - -
143A LEU* 1.3 75.8 - - - +
145A GLN* 1.3 65.8 + - - +
146A GLU 3.2 4.8 + - - +
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Residues in contact with GLN 145 (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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141A GLU* 3.7 17.4 + - - +
142A ARG* 3.2 16.6 + - - +
143A LEU 3.0 1.0 - - - -
144A GLY* 1.3 79.9 - - - +
146A GLU* 1.3 62.7 + - + +
147A LYS* 4.1 6.6 + - - +
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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