Contacts of the helix formed by residues 129 - 134 (chain A) in PDB entry 1PE0
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 ALA 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS 4.2 10.3 - - - +
107A ALA* 4.3 11.2 - - + -
110A THR* 4.2 16.1 - - + +
125A THR* 3.6 14.4 - - - +
126A HIS* 2.8 12.8 + - + +
128A LEU* 1.3 76.7 - - - +
130A ARG* 1.3 64.6 + - - +
131A ASP 3.4 2.2 - - - -
132A LYS* 3.3 11.4 + - + +
133A MET* 3.0 24.3 + - - +
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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
----------------------------------------------------------
125A THR* 3.6 8.1 - - - -
126A HIS 3.3 2.6 + - - -
127A PRO* 3.2 42.7 + - - +
129A ALA* 1.3 77.5 - - - +
131A ASP* 1.3 82.1 + - - +
133A MET* 3.3 2.3 + - - +
134A MET* 2.9 33.7 + - + +
141A TYR* 3.5 48.6 - - + +
143A GLU* 5.9 3.2 + - - -
156A ARG* 5.4 1.6 - - - +
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PRO 4.8 0.8 + - - -
128A LEU 5.1 3.0 + - - +
129A ALA 3.4 0.6 - - - -
130A ARG* 1.3 97.8 + - - +
132A LYS* 1.3 62.0 + - - +
134A MET* 3.4 4.6 + - - +
135A ASN* 3.1 23.4 + - - +
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Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN* 6.6 0.4 - - - +
83A SER* 5.0 6.5 + - - -
110A THR* 3.6 37.2 + - + +
113A LEU* 3.1 23.4 - - + +
114A ALA* 6.0 1.8 - - - +
128A LEU 5.5 0.8 + - - +
129A ALA* 3.3 14.7 + - + +
130A ARG 3.3 0.4 - - - -
131A ASP* 1.3 77.7 - - - +
133A MET* 1.3 62.9 + - - +
135A ASN* 3.3 15.3 + - - +
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Residues in contact with MET 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 3.2 48.5 - - + +
110A THR* 3.8 10.0 - - + +
112A LEU* 4.5 4.0 - - + -
113A LEU* 3.6 16.2 - - - +
123A VAL* 3.7 31.4 - - + -
125A THR* 3.7 18.4 - - + -
129A ALA 3.0 17.7 + - - +
130A ARG* 3.6 4.7 - - - +
132A LYS* 1.3 78.8 - - - +
134A MET* 1.3 63.7 + - + +
135A ASN 3.3 2.1 + - - +
138A HIS 5.3 0.7 + - - -
139A TYR* 3.6 45.8 - - + -
141A TYR* 4.9 1.1 - - + -
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Residues in contact with MET 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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123A VAL* 5.0 0.4 - - - -
130A ARG* 2.9 25.7 + - + +
131A ASP* 3.7 4.7 - - - +
132A LYS 3.3 0.2 - - - -
133A MET* 1.3 82.8 - - - +
135A ASN* 1.3 60.5 + - - +
136A GLY 3.0 1.0 + - - -
137A GLY* 2.9 27.7 + - - +
138A HIS 5.5 0.2 - - - +
139A TYR* 3.1 39.5 - - - +
140A THR* 4.1 0.4 - - - -
141A TYR* 3.6 49.4 - - + +
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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