Contacts of the helix formed by residues 129 - 134 (chain A) in PDB entry 2PQG
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 ARG 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A TYR* 4.8 1.6 - - - -
127A GLY* 5.7 0.6 - - - -
128A GLY* 1.4 82.3 - - - +
130A TYR* 1.3 55.2 + - - +
131A GLN* 2.5 38.8 + - - +
132A ASP* 2.8 26.6 + - - +
133A LEU* 3.0 17.2 + - - +
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Residues in contact with TYR 130 (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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94A TYR* 4.1 12.1 + + - -
128A GLY 3.6 1.7 + - - -
129A ARG* 1.3 68.1 - - - +
131A GLN* 1.3 79.3 + - + +
133A LEU* 3.5 9.2 - - + -
134A ILE* 2.6 39.9 + - + +
139A LEU* 3.6 36.0 - - + +
199A VAL* 3.8 22.7 - - + -
202A VAL* 3.9 12.7 - - + +
203A VAL* 3.4 26.1 - - + +
207A GLU* 2.7 48.1 - - - +
238A VAL* 4.3 2.9 - - + -
239A GLN* 4.2 19.7 - - + +
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Residues in contact with GLN 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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129A ARG* 2.5 32.9 + - - +
130A TYR* 1.3 109.9 - - + +
132A ASP* 1.3 58.8 + - - +
133A LEU 3.5 0.9 - - - +
135A GLY* 3.2 31.7 - - - +
239A GLN* 4.1 16.7 - - - +
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Residues in contact with ASP 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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126A PHE* 4.8 5.6 - - + +
127A GLY* 3.2 40.8 + - - +
129A ARG* 2.8 42.9 + - - +
131A GLN* 1.3 77.5 - - - +
133A LEU* 1.3 59.8 + - - +
134A ILE 3.9 0.2 - - - -
135A GLY 4.7 1.2 + - - -
195A LYS* 3.7 21.1 + - - +
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Residues in contact with LEU 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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94A TYR* 5.0 0.9 - - - +
108A PHE* 4.4 9.9 - - + -
126A PHE* 4.0 26.7 - - + -
127A GLY 4.1 10.3 - - - +
128A GLY 3.8 17.0 - - - +
129A ARG 3.0 14.2 + - - +
130A TYR* 3.7 9.6 - - + +
131A GLN 3.1 0.6 - - - -
132A ASP* 1.3 78.4 - - - +
134A ILE* 1.3 66.8 + - + +
135A GLY 3.6 1.1 + - - -
195A LYS* 3.7 42.8 - - + +
198A LEU* 4.8 2.7 - - + -
199A VAL* 3.7 37.5 - - + +
202A VAL* 4.5 12.1 - - + -
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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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130A TYR* 2.6 31.5 + - + +
133A LEU* 1.3 77.8 - - - +
135A GLY* 1.3 63.2 + - - +
136A ASN 3.4 0.2 + - - -
137A LYS* 2.7 51.0 + - + +
138A GLY 3.7 15.9 - - - +
139A LEU* 4.4 12.6 - - + +
141A THR* 4.5 4.9 - - - +
142A VAL* 4.5 13.2 - - + -
195A LYS 5.4 0.7 - - - +
196A SER* 6.0 0.7 - - - -
199A VAL* 3.7 31.4 - - + -
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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