Contacts of the helix formed by residues 129 - 141 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B PHE* 5.3 1.4 - - - -
127B VAL* 3.8 9.6 + - + +
128B THR* 1.3 78.8 - - - +
130B LYS* 1.3 58.9 + - - +
131B LYS 3.4 1.8 - - - -
132B LEU* 3.3 23.8 + - + +
133B VAL* 3.0 33.1 + - + +
158B CYS 2.8 27.3 + - - -
159B GLY* 4.0 10.3 + - - -
162B VAL* 6.3 0.4 - - - -
163B LEU* 4.0 26.7 - - + +
282B VAL* 3.8 6.1 - - - +
283B GLU* 2.7 39.8 + - - -
286B LEU* 3.9 31.6 - - + +
290B LYS* 5.1 3.4 - - + +
321B PRO* 5.1 0.8 - - - +
901B ADP 3.9 21.5 + - - +
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B THR* 3.7 10.6 - - - +
129B ARG* 1.3 75.7 - - - +
131B LYS* 1.3 57.5 + - - +
133B VAL* 4.6 4.3 - - - +
134B ASN* 2.8 55.0 + - - +
290B LYS* 6.0 0.2 - - - +
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG 3.4 0.6 - - - -
130B LYS* 1.3 79.8 - - - +
132B LEU* 1.3 59.1 + - + +
134B ASN* 4.0 4.1 - - - +
135B ALA* 3.1 28.2 + - + +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 3.3 49.7 + - + +
131B LYS* 1.3 81.5 - - + +
133B VAL* 1.3 64.8 + - - +
135B ALA* 3.3 5.8 + - + +
136B ILE* 3.1 30.2 + - + +
163B LEU* 3.9 13.7 - - + -
280B VAL* 4.3 12.4 - - + +
281B PRO 3.5 24.5 - - - +
282B VAL* 4.1 15.5 - - + -
283B GLU* 3.6 18.6 - - + +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 3.0 26.2 + - + +
130B LYS* 4.0 4.7 - - - +
132B LEU* 1.3 75.5 - - - +
134B ASN* 1.3 65.8 + - - +
136B ILE* 3.3 8.6 + - - +
137B GLN* 3.0 49.6 + - - +
163B LEU* 3.6 22.4 - - + +
166B GLU* 3.9 26.2 - - + +
167B ALA* 3.9 14.8 - - - +
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Residues in contact with ASN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS* 2.8 43.9 + - - +
131B LYS* 4.0 5.1 - - - +
133B VAL* 1.3 74.4 - - - +
135B ALA* 1.3 57.8 + - - +
137B GLN* 3.3 19.8 + - - +
138B GLN* 2.8 37.5 + - + +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS 3.1 19.6 + - - +
132B LEU* 3.3 6.5 + - + +
134B ASN* 1.3 76.0 - - - +
136B ILE* 1.3 61.7 + - - +
138B GLN* 3.6 7.7 + - - +
139B LYS* 3.2 32.1 + - - +
280B VAL* 4.2 18.6 - - + -
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU 3.1 20.3 + - - +
133B VAL* 3.6 7.2 - - - +
134B ASN 3.3 0.2 - - - -
135B ALA* 1.3 76.2 - - - +
137B GLN* 1.3 57.6 + - - +
139B LYS* 3.3 4.8 + - - +
140B LEU* 2.9 37.1 + - + +
150B VAL* 4.5 1.7 - - + +
152B ILE* 3.6 32.8 - - + -
163B LEU* 3.9 32.1 - - + +
167B ALA* 3.5 19.7 - - + -
261B LEU* 4.1 21.1 - - + -
280B VAL* 4.0 20.0 - - + -
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Residues in contact with GLN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 3.0 30.2 + - - +
134B ASN* 3.5 25.3 + - - +
136B ILE* 1.3 72.7 - - - +
138B GLN* 1.3 63.2 + - + +
140B LEU* 3.4 9.2 + - - +
141B SER* 3.0 29.3 + - - -
166B GLU 4.1 2.0 + - - -
167B ALA* 3.0 37.0 + - + +
170B ASP* 3.6 26.5 - - - +
173B LEU* 3.9 14.5 - - + +
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Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ASN* 2.8 25.4 + - + +
135B ALA* 3.8 8.7 - - - +
137B GLN* 1.3 74.8 - - - +
139B LYS* 1.3 66.3 + - + +
141B SER* 2.6 30.1 + - - -
142B LYS* 3.4 18.2 + - - +
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ALA* 3.2 19.7 + - - +
136B ILE 3.5 5.6 - - - +
138B GLN* 1.3 75.8 - - + +
140B LEU* 1.3 67.1 + - - +
142B LYS* 2.9 42.4 + - + +
143B LEU* 3.7 4.2 + - - +
150B VAL* 3.7 23.8 - - + +
278B TYR* 3.9 33.3 - - + +
279B VAL 3.8 19.6 + - - +
280B VAL* 3.8 16.2 - - + -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ILE* 2.9 39.1 + - + +
137B GLN* 3.7 5.2 - - - +
139B LYS* 1.3 77.9 - - - +
141B SER* 1.3 61.1 + - - +
143B LEU* 3.3 24.1 + - + +
144B LYS 4.5 1.0 + - - -
150B VAL* 4.1 17.5 - - + -
167B ALA* 4.4 8.7 - - + -
168B VAL* 4.4 11.9 - - + -
173B LEU* 4.3 22.7 - - + -
177B CYS* 4.8 3.2 - - - +
178B PHE* 4.0 22.7 - - + -
239B LEU* 3.7 31.2 - - + -
259B GLN* 5.1 0.2 - - - +
261B LEU* 4.2 13.7 - - + -
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLN 3.0 14.8 + - - -
138B GLN* 2.6 32.9 + - - -
140B LEU* 1.3 76.0 - - - +
142B LYS* 1.3 61.8 + - - +
143B LEU 3.3 0.2 - - - -
144B LYS* 3.4 29.8 + - - +
173B LEU* 4.6 2.4 - - - +
177B CYS* 4.1 20.8 - - - -
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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