Contacts of the helix formed by residues 128 - 137 (chain A) in PDB entry 4CAA
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 ASP 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LEU 3.5 3.6 + - - -
127A LEU* 1.3 69.7 - - - +
129A ARG* 1.3 71.7 + - + +
131A THR* 3.1 8.5 + - - -
132A GLU* 2.8 47.9 + - - +
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Residues in contact with ARG 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 LEU* 3.2 10.5 - - + +
128A ASP* 1.3 84.1 - - + +
130A PHE* 1.3 57.7 + - - +
132A GLU* 3.1 25.4 + - - +
133A ASP* 2.8 50.0 + - - +
320A GLY 5.9 0.4 - - - +
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Residues in contact with PHE 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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63A PHE* 4.3 16.2 - + - -
64A LEU* 5.4 1.1 - - - -
66A LEU* 3.6 45.1 - - + -
67A GLY* 4.1 9.4 - - - -
118A MET* 3.6 31.2 - - + -
126A LEU* 4.0 17.3 - - + -
127A LEU* 3.1 10.5 + - - +
129A ARG* 1.3 77.1 - - - +
131A THR* 1.3 65.8 + - - +
133A ASP* 4.1 3.5 - - - -
134A ALA* 3.0 28.2 + - - +
182A MET* 4.6 2.9 - - + -
184A LEU* 4.6 9.9 - - + -
320A GLY 3.4 22.2 + - - +
321A ILE* 4.0 31.9 - - + +
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Residues in contact with THR 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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118A MET* 4.8 5.6 - - + -
126A LEU* 3.7 27.7 + - + +
127A LEU 3.2 10.0 + - - -
128A ASP* 3.1 9.4 + - - -
130A PHE* 1.3 79.3 - - - +
132A GLU* 1.3 62.3 + - - +
134A ALA* 4.1 6.1 - - + +
135A LYS* 3.7 17.5 + - - +
142A ALA* 4.6 20.0 - - + -
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Residues in contact with GLU 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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128A ASP* 2.8 39.9 + - - +
129A ARG* 3.5 29.3 + - - +
131A THR* 1.3 75.8 - - - +
133A ASP* 1.3 65.5 + - - +
134A ALA 3.1 1.1 - - - -
135A LYS* 2.9 7.1 + - - +
136A ARG* 2.8 30.9 + - - +
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Residues in contact with ASP 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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66A LEU* 3.8 24.4 - - + +
129A ARG* 2.8 39.9 + - - +
130A PHE* 4.2 1.6 - - - +
132A GLU* 1.3 75.8 - - - +
134A ALA* 1.3 55.8 + - - +
136A ARG* 3.2 28.3 + - - +
137A LEU* 2.7 47.3 + - + +
138A TYR 3.7 0.3 + - - -
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Residues in contact with ALA 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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63A PHE* 3.9 23.8 - - + -
66A LEU* 3.9 9.8 - - + +
118A MET* 4.6 9.9 - - + -
130A PHE* 3.0 21.6 + - + +
131A THR* 4.2 7.0 - - - +
132A GLU 3.1 0.2 - - - -
133A ASP* 1.3 76.2 - - - +
135A LYS* 1.3 57.5 + - - +
138A TYR* 3.1 9.0 + - - +
139A GLY 2.9 22.0 + - - -
140A SER* 3.1 19.0 + - - -
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A THR 3.7 11.3 + - - +
132A GLU* 2.9 8.3 + - - +
134A ALA* 1.3 76.5 - - - +
136A ARG* 1.3 69.4 + - - +
139A GLY* 3.3 18.6 - - - -
140A SER 3.4 27.8 + - - +
141A GLU* 4.9 10.3 + - - +
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLN* 3.2 30.1 + - - +
97A GLN* 3.2 25.2 + - - +
132A GLU 2.8 16.7 + - - +
133A ASP* 3.2 30.6 + - - +
135A LYS* 1.3 82.4 - - - +
137A LEU* 1.3 81.4 + - - +
139A GLY 4.4 1.2 + - - -
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Residues in contact with LEU 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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66A LEU* 4.6 4.5 - - + -
93A HIS* 3.8 31.4 - - + +
94A GLN* 4.0 9.0 - - - +
97A GLN* 3.2 61.5 + - + +
100A LEU* 3.7 2.6 - - - +
133A ASP* 2.7 34.3 + - + +
136A ARG* 1.3 111.8 - - - +
138A TYR* 1.3 70.0 + - + +
139A GLY 3.7 0.2 - - - -
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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