Contacts of the helix formed by residues 129 - 141 (chain A) in PDB entry 1Z6T
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 ARG 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A PHE* 5.2 1.6 - - - -
127A VAL* 3.7 9.4 + - + +
128A THR* 1.3 80.9 - - - +
130A LYS* 1.3 60.1 + - - +
131A LYS 3.4 2.0 - - - -
132A LEU* 3.3 28.9 + - + +
133A VAL* 2.9 33.4 + - + +
158A CYS 3.0 25.3 + - - -
159A GLY* 4.1 13.9 + - - -
163A LEU* 4.0 21.9 - - + +
282A VAL* 4.0 7.5 - - - +
283A GLU* 2.9 30.7 + - - -
286A LEU* 3.9 33.0 - - + +
290A LYS* 5.0 2.9 - - + +
321A PRO* 5.1 1.0 - - - +
900A ADP 3.7 23.4 + - - +
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Residues in contact with LYS 130 (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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128A THR* 3.7 10.4 + - - +
129A ARG* 1.3 75.9 - - - +
131A LYS* 1.3 58.1 + - - +
133A VAL* 4.5 4.5 - - - +
134A ASN* 2.8 56.4 + - - +
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Residues in contact with LYS 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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129A ARG 3.4 0.6 - - - -
130A LYS* 1.3 78.5 - - - +
132A LEU* 1.3 60.6 + - + +
134A ASN* 4.0 5.0 - - - +
135A ALA* 3.1 27.4 + - + +
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Residues in contact with LEU 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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129A ARG* 3.3 47.7 + - + +
131A LYS* 1.3 79.1 - - + +
133A VAL* 1.3 64.2 + - - +
135A ALA* 3.2 5.5 + - + +
136A ILE* 3.1 28.9 + - + +
163A LEU* 3.8 19.5 - - + -
280A VAL* 4.1 15.0 - - + -
281A PRO 3.6 24.2 - - - +
282A VAL* 4.2 11.2 - - + -
283A GLU* 3.7 20.9 - - + +
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Residues in contact with VAL 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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126A PHE* 6.0 0.9 - - + -
129A ARG* 2.9 27.1 + - + +
130A LYS* 4.0 4.7 - - - +
132A LEU* 1.3 74.7 - - - +
134A ASN* 1.3 61.5 + - - +
136A ILE* 3.2 8.7 + - - +
137A GLN* 3.0 50.0 + - - +
163A LEU* 3.8 21.3 - - + +
166A GLU* 3.8 26.9 - - + +
167A ALA* 3.9 12.6 - - - -
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Residues in contact with ASN 134 (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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130A LYS* 2.8 47.2 + - - +
131A LYS* 4.1 5.2 - - - +
133A VAL* 1.3 75.8 - - - +
135A ALA* 1.3 57.0 + - - +
137A GLN* 3.3 20.9 + - - +
138A GLN* 2.9 29.9 + - - +
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Residues in contact with ALA 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 LYS* 3.1 20.8 + - + +
132A LEU* 3.2 6.5 + - + +
134A ASN* 1.3 72.1 - - - +
136A ILE* 1.3 65.5 + - - +
138A GLN* 3.6 14.0 + - - +
139A LYS* 3.1 31.0 + - - +
280A VAL* 4.1 18.2 - - + -
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Residues in contact with ILE 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 LEU 3.1 20.8 + - - +
133A VAL* 3.6 7.4 - - - +
135A ALA* 1.3 75.2 - - - +
137A GLN* 1.3 57.3 + - - +
139A LYS* 3.2 4.2 + - - +
140A LEU* 2.9 38.4 + - + +
150A VAL* 4.9 1.3 - - + -
152A ILE* 3.6 26.0 - - + -
163A LEU* 4.0 32.8 - - + +
167A ALA* 3.5 19.5 - - + -
261A LEU* 4.1 21.5 - - + -
280A VAL* 4.0 25.1 - - + -
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Residues in contact with GLN 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 VAL* 3.0 28.7 + - - +
134A ASN* 3.3 27.9 + - - +
136A ILE* 1.3 76.6 - - - +
138A GLN* 1.3 57.4 + - - +
140A LEU* 3.4 8.8 + - - +
141A SER* 2.9 30.5 + - - -
166A GLU 4.1 2.0 + - - -
167A ALA* 2.9 36.2 + - - +
170A ASP* 3.7 25.4 + - - +
173A LEU* 3.7 17.1 - - + +
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Residues in contact with GLN 138 (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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134A ASN 2.9 18.4 + - - +
135A ALA* 3.7 12.2 + - - +
137A GLN* 1.3 77.3 - - - +
139A LYS* 1.3 83.0 + - - +
141A SER* 2.7 25.7 + - - +
142A LYS* 2.7 44.0 + - - +
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Residues in contact with LYS 139 (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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135A ALA* 3.1 17.1 + - - +
136A ILE 3.2 4.9 + - - +
138A GLN* 1.3 90.3 - - - +
140A LEU* 1.3 66.7 + - - +
142A LYS* 3.0 39.5 + - - +
143A LEU* 3.7 3.6 + - - +
150A VAL* 3.6 25.8 - - + +
278A TYR* 3.8 33.0 - - + -
279A VAL 3.9 17.3 - - - +
280A VAL* 3.7 17.3 - - + -
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Residues in contact with LEU 140 (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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136A ILE* 2.9 39.3 + - + +
137A GLN* 3.7 6.7 - - - +
139A LYS* 1.3 72.8 - - - +
141A SER* 1.3 61.0 + - - +
143A LEU* 3.2 28.1 + - + +
144A LYS 4.5 1.0 + - - -
150A VAL* 4.0 22.0 - - + -
167A ALA* 4.5 5.6 - - + -
168A VAL* 4.5 3.6 - - + -
173A LEU* 4.0 23.1 - - + -
177A CYS* 4.7 1.8 - - - -
178A PHE* 3.9 23.9 - - + -
239A LEU* 4.1 30.1 - - + -
261A LEU* 4.2 18.8 - - + -
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Residues in contact with SER 141 (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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137A GLN 2.9 15.4 + - - -
138A GLN* 2.7 20.7 + - - +
140A LEU* 1.3 75.3 - - - +
142A LYS* 1.3 62.1 + - - +
143A LEU 3.3 0.6 + - - -
144A LYS* 3.8 23.0 + - - +
173A LEU* 4.5 4.7 - - - +
177A CYS* 4.0 23.6 - - - -
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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