Contacts of the helix formed by residues 127 - 137 (chain A) in PDB entry 2PU1
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 PRO 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ALA* 4.2 0.2 - - - -
125A GLY 5.0 0.2 - - - +
126A VAL* 1.3 90.7 - - + +
128A LEU* 1.3 67.3 + - - +
129A TYR* 3.3 39.9 - - + +
130A ARG* 3.0 24.4 + - + +
131A TYR 3.0 9.7 + - - -
383A ASP* 5.0 0.2 - - - +
416A GLU* 3.7 9.9 - - - +
700A EDO 3.8 10.8 - - - +
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Residues in contact with LEU 128 (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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117A SER* 3.9 31.9 - - - +
118A LYS* 3.9 25.8 - - + +
121A ALA* 3.9 11.2 - - + +
126A VAL 3.6 1.6 + - - -
127A PRO* 1.3 71.4 - - - +
129A TYR* 1.4 58.6 + - - +
131A TYR* 3.0 3.8 + - + +
132A LEU* 2.8 56.5 + - + +
380A TYR* 3.8 31.2 - - + -
383A ASP* 3.3 27.9 + - + +
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Residues in contact with TYR 129 (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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127A PRO* 3.5 17.0 - - + +
128A LEU* 1.4 72.2 - - - +
130A ARG* 1.3 84.0 + - + +
132A LEU* 4.7 0.2 - - - -
133A ALA* 3.0 27.4 + - - +
141A LEU* 3.7 17.0 - - + +
383A ASP* 3.1 56.4 + - - +
386A VAL* 4.2 8.7 - - + -
387A ALA* 3.3 15.2 - - - +
413A ILE* 3.7 26.7 - - + -
416A GLU* 2.7 40.8 + - - +
417A LEU* 3.7 27.9 - - + +
700A EDO 3.5 10.5 - - - -
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Residues in contact with ARG 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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126A VAL* 3.9 17.5 - - + -
127A PRO* 3.0 24.0 + - + +
129A TYR* 1.3 97.8 + - + +
131A TYR* 1.3 64.4 + - - +
133A ALA* 3.3 6.2 + - - +
134A SER* 3.1 25.1 + - - -
141A LEU* 3.4 26.0 - - - +
417A LEU* 3.5 20.6 - - - +
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Residues in contact with TYR 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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82A GLU 4.4 0.5 + - - -
83A LEU* 3.1 29.3 + - + +
85A GLN* 4.7 3.2 - - - +
117A SER* 3.5 22.7 - - - -
120A ALA* 3.3 27.9 - - + +
121A ALA* 3.5 27.1 - - + -
124A LYS* 4.0 32.3 - - + -
126A VAL* 3.7 9.8 - - + +
127A PRO 3.0 4.2 + - - -
128A LEU 3.0 4.3 + - - +
130A ARG* 1.3 76.9 - - - +
132A LEU* 1.3 69.2 + - + +
134A SER* 3.1 13.3 + - - -
135A LEU* 3.1 54.5 + - + +
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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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117A SER* 4.1 12.6 - - - -
128A LEU* 2.8 33.4 + - + +
131A TYR* 1.3 76.1 - - + +
133A ALA* 1.3 59.2 + - - +
135A LEU* 3.2 24.8 + - + +
136A ALA* 2.9 30.7 + - - +
350A ILE* 4.3 8.1 - - + -
354A ILE* 4.6 4.8 - - + +
380A TYR* 3.4 42.8 - - + +
383A ASP 4.6 0.4 - - - -
384A LEU* 4.1 27.8 - - + +
387A ALA* 3.4 16.8 - - + -
388A LEU* 5.5 0.2 - - - +
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Residues in contact with ALA 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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129A TYR 3.0 18.2 + - - +
130A ARG* 3.6 8.5 - - - +
131A TYR 3.3 0.2 - - - -
132A LEU* 1.3 75.8 - - - +
134A SER* 1.3 57.2 + - - +
136A ALA 3.2 0.7 + - - -
137A GLY* 2.9 25.6 + - - -
138A THR* 3.0 20.7 + - - +
141A LEU* 3.5 27.1 - - + -
387A ALA* 3.5 16.7 - - - +
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Residues in contact with SER 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 ARG 3.1 12.9 + - - -
131A TYR* 3.1 15.1 + - - -
133A ALA* 1.3 77.9 - - - +
135A LEU* 1.3 61.8 + - - +
137A GLY* 3.3 11.5 + - - -
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Residues in contact with LEU 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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83A LEU 5.0 2.7 - - - +
85A GLN* 3.8 36.3 - - + +
131A TYR* 3.1 52.7 + - + +
132A LEU* 3.2 25.1 + - + +
134A SER* 1.3 77.6 - - - +
136A ALA* 1.3 58.9 + - - +
137A GLY 3.7 0.3 + - - -
350A ILE* 4.9 0.4 - - + -
354A ILE* 3.9 22.8 - - + +
358A LYS* 5.0 2.9 - - - +
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Residues in contact with ALA 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 2.9 16.9 + - - +
133A ALA* 4.6 0.2 - - - -
135A LEU* 1.3 75.4 - - - +
137A GLY* 1.3 62.7 + - - +
138A THR* 3.4 18.5 + - - +
354A ILE* 3.8 19.3 - - + -
358A LYS* 2.9 30.3 + - + +
388A LEU* 3.8 24.2 - - + -
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Residues in contact with GLY 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 ALA 2.9 7.0 + - - -
134A SER* 3.3 10.8 + - - -
135A LEU 3.4 1.0 + - - -
136A ALA* 1.3 77.5 - - - +
138A THR* 1.3 62.7 + - - +
139A LYS* 3.4 17.0 + - - +
358A LYS* 4.5 5.7 + - - -
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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