Contacts of the helix formed by residues 132 - 142 (chain A) in PDB entry 3Q29
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 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A PRO* 3.5 30.2 - - + +
128A LYS* 3.5 7.8 + - - +
129A THR* 2.6 44.8 + - - +
131A GLU* 1.3 77.2 - - - +
133A ILE* 1.3 63.4 + - - +
134A PRO* 3.4 0.9 - - - -
135A ALA* 3.5 10.6 + - + +
136A LEU* 3.1 22.8 + - + +
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Residues in contact with ILE 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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116A LEU* 6.2 0.4 - - + -
127A PRO* 4.3 11.7 - - + -
129A THR 3.7 9.9 - - - +
130A TRP* 3.1 36.3 + - + +
132A GLU* 1.3 76.1 - - - +
134A PRO* 1.3 65.3 - - + +
136A LEU* 3.1 6.2 + - - +
137A ASP* 2.7 30.3 + - + +
147A ALA* 4.1 18.2 - - + -
148A LEU* 4.0 31.6 - - + -
199A LEU* 4.5 14.1 - - + -
204A HIS* 5.7 1.3 - - + -
225A MET* 4.1 12.3 - - + -
249A PRO* 4.5 12.6 - - + -
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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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130A TRP 3.6 5.2 - - - +
131A GLU 3.1 18.2 - - - +
133A ILE* 1.3 95.4 - - + +
135A ALA* 1.3 62.8 + - - +
137A ASP* 3.1 2.8 + - - +
138A LYS* 2.9 23.1 + - - +
195A PHE* 4.3 10.3 - - + -
199A LEU* 3.9 18.4 - - + -
204A HIS* 3.6 31.9 - - + +
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Residues in contact with ALA 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 GLU 5.0 0.2 + - - -
132A GLU* 3.5 11.3 + - + +
133A ILE 3.4 0.6 - - - -
134A PRO* 1.3 77.7 - - - +
136A LEU* 1.3 63.1 + - - +
138A LYS* 3.2 11.7 + - - +
139A GLU* 3.1 30.4 + - + +
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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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123A LEU* 3.9 35.0 - - + -
127A PRO* 4.3 12.8 - - + -
132A GLU* 3.1 16.2 + - + +
133A ILE* 3.1 9.4 + - - +
135A ALA* 1.3 77.4 - - - +
137A ASP* 1.3 61.7 + - - +
139A GLU* 3.2 22.1 + - + +
140A LEU* 2.9 38.7 + - + +
147A ALA* 4.1 5.4 - - + -
225A MET* 3.8 29.4 - - + -
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Residues in contact with ASP 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 ILE* 2.7 20.3 + - + +
134A PRO 3.6 4.3 - - - +
136A LEU* 1.3 72.9 - - - +
138A LYS* 1.3 58.6 + - - +
140A LEU* 3.2 1.1 + - - -
141A LYS* 2.8 63.4 + - - +
146A SER* 3.4 12.5 - - - -
147A ALA* 2.9 37.9 + - + +
148A LEU 5.5 0.2 - - - -
204A HIS* 2.7 39.7 + - + +
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Residues in contact with LYS 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 2.9 12.7 + - - +
135A ALA* 3.4 13.9 - - - +
136A LEU 3.2 0.2 - - - -
137A ASP* 1.3 79.8 + - - +
139A GLU* 1.3 62.8 + - + +
141A LYS* 3.5 12.9 + - - +
142A ALA* 3.6 10.6 + - - +
204A HIS* 4.7 7.4 + - + -
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Residues in contact with GLU 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 ALA* 3.1 22.3 + - - +
136A LEU* 3.5 20.8 - - + +
138A LYS* 1.3 74.8 - - + +
140A LEU* 1.3 65.3 + - + +
142A ALA* 3.2 20.4 + - - +
143A LYS* 3.8 22.6 + - - +
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Residues in contact with LEU 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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122A LEU* 4.5 21.1 - - + +
123A LEU* 5.3 2.0 - - + -
136A LEU* 2.9 38.8 + - + +
137A ASP 3.2 3.6 + - - +
139A GLU* 1.3 78.8 - - + +
141A LYS* 1.3 56.9 + - - +
143A LYS* 3.0 38.6 + - + +
145A LYS* 2.9 48.2 + - + +
146A SER 3.7 7.6 - - - +
147A ALA* 3.6 26.9 - - - -
224A ALA* 3.8 16.4 - - + -
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Residues in contact with LYS 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 ASP* 2.8 60.4 + - - +
138A LYS* 3.8 8.1 - - - +
139A GLU 3.2 0.2 - - - -
140A LEU* 1.3 77.5 - - - +
142A ALA* 1.3 57.1 + - - +
143A LYS 3.0 0.2 - - - -
144A GLY* 3.0 19.1 + - - -
145A LYS 3.1 11.7 - - - +
146A SER* 3.8 17.3 - - - -
203A LYS* 3.2 22.0 + - - +
204A HIS* 4.2 3.4 + - - +
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Residues in contact with ALA 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 LYS 3.6 7.6 + - - +
139A GLU* 3.2 14.2 + - - +
140A LEU 3.2 0.6 - - - -
141A LYS* 1.3 78.2 - - - +
143A LYS* 1.3 59.8 + - + +
144A GLY 3.3 1.3 + - - -
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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