Contacts of the helix formed by residues 131 - 139 (chain A) in PDB entry 4YON
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.6 30.1 - - + -
57A ILE* 4.2 32.8 - - + -
117A LEU* 3.9 21.5 - - + +
120A CYS* 3.7 20.4 - - + -
121A LEU* 3.9 24.7 - - + -
129A HIS 4.2 0.2 + - - -
130A GLU* 1.3 80.9 - - - +
132A GLY* 1.3 67.5 + - - +
133A ASN 3.3 2.9 - - - -
134A VAL* 3.0 22.5 + - - +
135A PHE* 3.5 17.6 - - + -
209A LEU* 4.6 8.1 - - + -
219A ASP* 3.0 8.5 + - - +
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Residues in contact with GLY 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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131A LEU* 1.3 78.5 - - - +
133A ASN* 1.3 60.9 + - - +
134A VAL 3.3 0.3 + - - -
135A PHE* 3.3 3.0 + - - -
136A LEU* 3.3 22.9 + - - +
206A LEU* 6.0 0.4 - - - -
219A ASP* 3.1 10.9 + - - -
222A ALA* 3.6 32.1 - - - -
223A VAL* 4.0 8.8 - - - +
226A ALA* 3.7 9.9 - - - +
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Residues in contact with ASN 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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130A GLU* 4.8 14.8 + - + +
131A LEU 3.3 1.2 - - - -
132A GLY* 1.3 73.5 - - - +
134A VAL* 1.3 61.2 + - + +
136A LEU* 3.3 16.4 + - - +
137A LYS* 2.9 30.2 + - - +
219A ASP* 4.7 0.4 + - - -
222A ALA* 3.7 19.1 - - - +
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Residues in contact with VAL 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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113A PHE* 3.8 22.2 - - + -
116A ALA* 3.7 32.3 - - + +
117A LEU* 3.9 15.5 - - + -
120A CYS* 3.4 32.1 - - - -
130A GLU 4.8 0.2 - - - +
131A LEU* 3.0 15.8 + - - +
133A ASN* 1.3 79.4 - - + +
135A PHE* 1.3 62.9 + - - +
137A LYS* 3.3 5.9 + - - +
138A PHE* 3.2 27.3 + - + +
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Residues in contact with PHE 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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57A ILE* 4.5 17.5 - - + -
113A PHE* 3.5 35.0 - + - -
117A LEU* 4.4 10.1 - - + -
131A LEU* 3.5 29.6 - - + -
132A GLY 3.3 1.8 + - - +
134A VAL* 1.3 78.8 - - + +
136A LEU* 1.3 63.2 + - - +
138A PHE* 3.2 2.7 + - - +
139A LYS* 3.0 23.9 + - - +
142A PHE* 5.4 0.4 - - - -
202A TYR* 3.8 26.5 - + - -
205A LEU* 6.3 1.3 - - + -
206A LEU* 3.8 33.9 - - + -
226A ALA* 3.7 20.9 - - + -
229A ALA* 5.2 1.2 - - - +
230A MET* 3.8 32.3 - - + +
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Residues in contact with LEU 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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132A GLY 3.3 12.5 + - - +
133A ASN* 3.6 26.5 - - - +
134A VAL 3.3 0.2 - - - -
135A PHE* 1.3 77.5 - - - +
137A LYS* 1.3 63.4 + - - +
138A PHE 3.4 0.3 + - - -
139A LYS* 3.5 19.0 + - + +
140A ASP* 5.2 0.3 - - - +
222A ALA* 4.1 9.4 - - - +
225A SER* 3.7 46.0 - - - +
226A ALA* 3.8 6.1 - - - +
229A ALA* 4.1 10.3 - - + -
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Residues in contact with LYS 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 ASN 2.9 17.7 + - - +
134A VAL* 3.6 7.4 - - - +
135A PHE 3.2 0.2 - - - -
136A LEU* 1.3 77.5 - - - +
138A PHE* 1.3 80.1 + - + +
140A ASP* 3.3 5.9 - - - +
141A LYS* 3.0 33.9 + - - +
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Residues in contact with PHE 138 (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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109A VAL* 3.8 11.2 - - + -
112A ASP* 3.6 22.0 - - + -
113A PHE* 3.6 46.2 - + + -
116A ALA* 3.9 20.9 - - + -
134A VAL* 3.2 26.2 + - + +
135A PHE 3.2 1.7 + - - +
137A LYS* 1.3 102.1 - - + +
139A LYS* 1.3 65.7 + - - +
140A ASP 3.2 3.1 - - - -
141A LYS* 2.9 39.4 + - + +
142A PHE* 3.1 30.2 + - + -
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Residues in contact with LYS 139 (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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135A PHE 3.0 11.5 + - - +
136A LEU* 3.6 16.2 - - + +
137A LYS 3.4 1.6 - - - -
138A PHE* 1.3 77.5 - - - +
140A ASP* 1.3 63.9 + - + +
141A LYS 3.4 0.2 + - - -
142A PHE* 3.4 22.4 + - - +
143A CYS 4.5 1.2 + - - -
229A ALA* 3.8 37.1 - - + +
230A MET* 5.1 1.3 - - - -
232A THR* 4.3 21.2 + - - +
233A VAL* 3.7 20.5 - - + +
236A ASN* 5.7 2.2 - - - +
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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