Contacts of the helix formed by residues 126 - 138 (chain A) in PDB entry 4JYY
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 SER 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ILE* 3.6 9.5 + - - -
125A PRO* 1.3 76.1 - - - +
127A GLU* 1.3 80.1 + - - +
129A LEU* 3.4 6.9 + - - +
130A LYS* 3.2 21.6 + - - +
220A TRP 5.6 1.4 + - - -
221A ASN* 5.0 5.0 + - - -
224A LEU* 3.8 25.5 - - - +
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Residues in contact with GLU 127 (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 SER* 1.3 88.0 + - - +
128A SER* 1.3 67.9 + - - +
130A LYS* 3.6 4.8 - - - +
131A GLU* 3.2 31.9 + - - +
224A LEU* 3.6 20.5 - - + +
228A LYS* 2.8 33.2 + - - -
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Residues in contact with SER 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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127A GLU* 1.3 81.1 - - - +
129A LEU* 1.3 58.4 + - - +
131A GLU* 3.3 12.7 + - - +
132A ALA* 2.8 30.8 + - - +
224A LEU* 3.9 8.8 - - - +
227A TYR* 3.6 23.0 - - - -
228A LYS* 4.4 10.2 - - - +
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Residues in contact with LEU 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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125A PRO* 5.6 2.9 - - + -
126A SER 3.4 7.8 + - - +
127A GLU 3.3 1.0 - - - -
128A SER* 1.3 77.1 + - - +
130A LYS* 1.3 67.4 + - - +
132A ALA* 3.2 0.4 + - - -
133A ILE* 2.9 41.1 + - + +
162A LEU* 4.7 1.8 - - + -
170A LEU* 3.9 23.1 - - + -
189A ILE* 3.9 17.0 - - + -
220A TRP* 4.0 16.2 - - + +
223A ALA* 3.5 45.1 - - + +
224A LEU* 3.6 15.3 - - + +
227A TYR* 3.9 18.6 - - + -
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Residues in contact with LYS 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 PRO* 3.6 30.2 + - + +
126A SER* 3.2 33.3 + - - +
127A GLU 3.6 3.6 - - - +
129A LEU* 1.3 80.3 - - - +
131A GLU* 1.3 64.4 + - + +
133A ILE* 3.6 5.0 + - - +
134A ASP* 3.3 32.8 + - - +
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Residues in contact with GLU 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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127A GLU* 3.2 22.9 + - - +
128A SER* 3.7 11.0 - - - +
129A LEU 3.2 0.2 - - - -
130A LYS* 1.3 76.0 - - + +
132A ALA* 1.3 62.0 + - - +
134A ASP* 3.2 8.7 + - - +
135A ARG* 2.8 30.3 + - - +
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Residues in contact with ALA 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 SER 2.8 18.4 + - - +
129A LEU 3.2 2.2 + - - +
131A GLU* 1.3 76.1 - - - +
133A ILE* 1.3 56.5 + - - +
135A ARG* 3.2 22.5 + - - +
136A ASP* 2.8 35.2 + - - +
170A LEU* 3.7 17.9 - - + -
227A TYR* 3.4 27.1 - - + +
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Residues in contact with ILE 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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125A PRO* 4.7 7.2 - - + -
129A LEU* 2.9 32.2 + - + +
130A LYS* 3.8 4.7 - - - +
131A GLU 3.3 0.2 - - - -
132A ALA* 1.3 77.2 - - - +
134A ASP* 1.3 57.8 + - - +
137A PHE* 2.9 35.1 + - + +
139A SER 4.1 0.4 + - - +
140A PHE* 3.9 32.3 - - + +
143A PHE* 3.8 27.6 - - + -
162A LEU* 4.8 7.4 - - + -
170A LEU* 3.8 18.4 - - + -
220A TRP* 4.0 31.2 - - + -
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Residues in contact with ASP 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 LYS* 3.3 24.9 + - - +
131A GLU* 3.2 10.5 + - - +
133A ILE* 1.3 75.6 - - - +
135A ARG* 1.3 64.4 + - - +
138A GLY* 2.9 37.9 + - - +
139A SER* 3.4 19.9 - - - -
140A PHE* 3.4 10.4 + - - +
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Residues in contact with ARG 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 GLU* 2.8 14.2 + - - +
132A ALA* 3.5 18.4 - - - +
134A ASP* 1.3 79.8 - - - +
136A ASP* 1.3 92.5 + - - +
138A GLY* 4.3 1.7 + - - -
167A ASP 5.4 0.6 + - - -
168A GLY 3.0 24.5 + - - -
169A LYS* 4.0 9.3 + - - +
227A TYR* 3.9 7.3 + - - -
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Residues in contact with ASP 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 ALA 2.8 20.0 + - - +
135A ARG* 1.3 108.0 + - - +
137A PHE* 1.3 68.6 + - + +
169A LYS* 2.8 34.5 + - - +
170A LEU* 2.8 48.8 + - + +
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Residues in contact with PHE 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 ILE* 2.9 22.3 + - + +
136A ASP* 1.3 82.7 - - + +
138A GLY* 1.3 57.0 + - - +
139A SER 3.2 3.4 - - - +
142A LYS* 3.3 26.0 - - - +
143A PHE* 3.6 40.6 - + + +
146A GLU* 3.6 26.2 - - - -
162A LEU* 3.8 25.1 - - + -
170A LEU* 3.8 26.7 - - + -
171A SER* 3.8 21.3 - - - -
172A ILE* 3.8 18.8 - - + -
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Residues in contact with GLY 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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134A ASP* 2.9 27.1 + - - +
135A ARG 4.3 2.3 + - - -
136A ASP 3.7 0.8 - - - -
137A PHE* 1.3 76.7 - - - +
139A SER* 1.3 60.8 + - - +
142A LYS* 4.4 12.8 - - - -
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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