Contacts of the helix formed by residues 129 - 136 (chain A) in PDB entry 4C3I
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 LEU 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A LEU* 3.4 57.5 - - + +
125A LEU* 4.1 2.9 - - - +
127A TYR* 2.8 29.8 + - + -
128A GLY* 1.3 74.7 - - - +
130A ILE* 1.3 64.1 + - - +
131A ASP 3.6 0.4 - - - -
132A GLU* 3.4 35.7 - - + +
133A SER* 3.7 13.5 + - - -
192A ALA 4.0 14.6 - - - +
193A ILE* 4.6 5.4 - - + +
196A ALA* 3.8 25.4 - - + -
201A ARG* 5.2 4.9 - - + +
202A THR* 4.1 5.8 - - + -
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Residues in contact with ILE 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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125A LEU* 3.7 17.9 - - + -
128A GLY 4.0 3.0 + - - +
129A LEU* 1.3 68.8 - - - +
131A ASP* 1.4 65.8 + - - +
132A GLU 3.2 1.3 - - - -
133A SER* 2.7 28.0 + - - +
134A TYR* 3.2 25.6 + - + -
211A THR* 3.4 25.6 - - - +
212A VAL* 4.0 22.4 - - + -
215A GLU* 3.5 34.5 - - + -
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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
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130A ILE* 1.4 77.7 - - - +
132A GLU* 1.3 67.6 - - - +
134A TYR* 3.5 9.3 + - - +
135A LYS* 2.8 61.1 + - - +
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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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124A LEU* 3.8 8.9 - - + +
129A LEU* 3.4 40.2 - - + +
130A ILE 3.2 0.4 - - - -
131A ASP* 1.3 88.3 + - - +
133A SER* 1.4 60.1 + - - +
135A LYS* 3.2 3.5 + - + -
136A LEU* 3.1 24.9 + - - +
188A TYR* 3.4 34.5 - - + +
192A ALA* 4.0 16.2 - - + +
201A ARG* 2.9 37.3 + - - -
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Residues in contact with SER 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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121A LYS* 3.4 56.8 - - - +
124A LEU* 3.8 13.6 - - - +
125A LEU* 4.4 10.9 - - - +
129A LEU 3.7 9.9 + - - -
130A ILE* 2.7 24.0 + - - +
132A GLU* 1.4 76.1 - - - +
134A TYR* 1.3 70.7 + - - +
136A LEU* 3.5 8.8 - - - +
137A ASP 4.2 1.4 + - - -
215A GLU* 5.5 0.2 + - - -
219A LEU* 5.1 0.7 - - - +
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Residues in contact with TYR 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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121A LYS* 5.0 10.5 - - - -
130A ILE* 3.2 34.5 + - + -
131A ASP* 3.8 9.4 - - - +
133A SER* 1.3 81.1 + - - +
135A LYS* 1.4 56.5 + - - +
136A LEU 3.1 4.7 - - - -
137A ASP* 3.2 37.3 + - - +
138A GLU* 4.0 7.6 + - - +
215A GLU* 2.7 31.3 + - - -
218A LYS* 3.6 17.3 + - - -
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Residues in contact with LYS 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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131A ASP* 2.8 49.5 + - - +
132A GLU* 3.2 3.9 + - + +
134A TYR* 1.4 73.8 - - + +
136A LEU* 1.3 62.2 + - - +
137A ASP 3.3 0.2 - - - -
138A GLU* 3.3 39.8 + - - +
139A ILE* 3.7 11.8 - - - +
188A TYR* 3.4 28.5 - - + +
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Residues in contact with LEU 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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117A ARG* 3.7 40.4 - - + +
120A CYS* 3.8 13.5 - - + -
121A LYS* 3.8 11.2 - - + -
124A LEU* 4.3 2.9 - - + -
132A GLU 3.1 10.4 + - - +
133A SER* 3.5 13.5 - - - +
134A TYR 3.1 0.2 - - - -
135A LYS* 1.3 73.6 - - - +
137A ASP* 1.3 59.0 + - - +
138A GLU 3.1 0.4 - - - -
139A ILE* 3.0 32.6 + - + +
185A ARG* 3.9 29.7 + - + +
188A TYR* 4.1 13.9 - - + -
189A VAL* 3.7 30.3 - - + -
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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