Contacts of the helix formed by residues 134 - 142 (chain w) in PDB entry 6AH0
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 134 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132w ASP 4.0 0.2 - - - -
133w GLU* 1.3 77.9 - - - +
135w GLY* 1.3 63.6 + - - +
136w TYR 4.1 0.2 - - - +
138w ARG* 3.6 14.2 + - - -
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Residues in contact with GLY 135 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134w GLU* 1.3 73.4 - - - +
136w TYR* 1.3 59.1 + - - +
137w GLY 3.4 0.2 - - - -
138w ARG* 3.9 1.3 - - - -
139w TYR* 2.9 27.1 + - - -
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Residues in contact with TYR 136 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132w ASP 5.1 7.8 - - - -
133w GLU* 4.4 1.9 - - - +
134w GLU 3.3 2.8 - - - +
135w GLY* 1.3 76.4 - - - +
137w GLY* 1.3 58.8 + - - +
138w ARG 3.2 0.4 - - - -
140w LEU* 2.9 26.2 + - - +
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Residues in contact with GLY 137 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133w GLU* 3.8 22.8 + - - +
134w GLU 4.5 0.2 - - - -
135w GLY 3.4 0.2 - - - -
136w TYR* 1.3 76.1 - - - +
138w ARG* 1.3 57.7 + - - +
140w LEU* 3.9 0.4 - - - -
141w ASP* 2.9 21.2 + - - -
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Residues in contact with ARG 138 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134w GLU 3.6 11.7 + - - -
135w GLY* 3.6 4.4 + - - -
136w TYR 3.2 0.2 - - - -
137w GLY* 1.3 75.6 - - - +
139w TYR* 1.3 59.0 + - - +
140w LEU 3.0 0.9 - - - -
141w ASP* 2.7 20.8 + - - +
142w LEU* 3.0 11.4 + - - -
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Residues in contact with TYR 139 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17w ARG* 6.4 2.0 - - - +
135w GLY 2.9 20.3 + - - -
136w TYR* 4.2 0.7 - - - +
138w ARG* 1.3 71.5 - - - +
140w LEU* 1.3 60.8 + - - +
142w LEU* 3.4 8.3 + - - -
143w HIS* 3.4 12.8 + - - -
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Residues in contact with LEU 140 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136w TYR 2.9 19.9 + - - -
137w GLY* 3.9 0.7 - - - -
139w TYR* 1.3 72.8 - - - +
141w ASP* 1.3 61.3 + - - +
142w LEU 3.0 6.5 + - - -
143w HIS* 3.4 12.2 + - - +
159w ASP* 4.8 6.1 + - - -
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Residues in contact with ASP 141 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137w GLY 2.9 16.7 + - - -
138w ARG* 2.7 15.3 + - - +
140w LEU* 1.3 71.8 - - - +
142w LEU* 1.3 55.1 + - - -
158w LEU 4.8 0.2 - - - -
159w ASP* 4.2 5.0 + - - +
160w TYR* 3.2 32.8 + - - +
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Residues in contact with LEU 142 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21w VAL* 4.5 16.3 - - - -
138w ARG 3.0 10.0 + - - -
139w TYR 3.4 4.2 + - - -
140w LEU 3.0 0.2 - - - -
141w ASP* 1.3 80.3 - - - +
143w HIS* 1.3 59.8 + - - +
158w LEU* 5.2 3.6 - - - +
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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