Contacts of the helix formed by residues 129 - 141 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D PHE* 5.2 1.8 - - + -
127D VAL* 3.7 8.9 + - + +
128D THR* 1.3 80.7 - - - +
130D LYS* 1.3 59.0 + - - +
131D LYS 3.4 2.2 - - - -
132D LEU* 3.3 24.4 + - + +
133D VAL* 2.9 34.5 + - + +
158D CYS 3.0 26.5 + - - -
159D GLY* 4.1 8.7 - - - -
162D VAL* 6.2 0.4 - - - -
163D LEU* 3.9 29.6 - - + +
282D VAL* 4.1 4.8 - - - +
283D GLU* 3.2 36.0 + - - +
286D LEU* 3.8 34.5 - - + +
290D LYS* 5.3 2.5 - - + +
321D PRO* 5.1 0.8 - - - +
903D ADP 3.7 22.8 + - - +
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Residues in contact with LYS 130 (chain D).
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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128D THR* 3.7 10.2 + - - +
129D ARG* 1.3 75.1 - - - +
131D LYS* 1.3 58.6 + - - +
133D VAL* 4.6 4.3 - - - +
134D ASN* 2.8 58.0 + - - +
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Residues in contact with LYS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ARG 3.4 0.4 - - - -
130D LYS* 1.3 79.3 - - - +
132D LEU* 1.3 61.1 + - + +
134D ASN* 4.0 4.8 - - - +
135D ALA* 3.1 28.4 + - + +
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ARG* 3.3 43.3 + - + +
130D LYS 3.3 0.2 - - - -
131D LYS* 1.3 78.7 - - + +
133D VAL* 1.3 64.3 + - - +
135D ALA* 3.2 5.0 + - + +
136D ILE* 3.0 29.6 + - + +
163D LEU* 3.8 22.7 - - + -
280D VAL* 4.1 15.3 - - + -
281D PRO 3.6 24.2 - - - +
282D VAL* 4.3 13.0 - - + -
283D GLU* 3.8 22.0 - - - +
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 6.0 1.3 - - + -
129D ARG* 2.9 27.6 + - + +
130D LYS* 4.0 4.3 - - - +
132D LEU* 1.3 73.7 - - - +
134D ASN* 1.3 65.1 + - - +
136D ILE* 3.2 9.6 + - - +
137D GLN* 3.0 36.1 + - - +
163D LEU* 3.7 21.5 - - + +
166D GLU* 3.9 23.8 - - + +
167D ALA* 3.9 24.7 - - - +
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Residues in contact with ASN 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D LYS* 2.8 48.7 + - - +
131D LYS* 4.1 4.6 - - - +
133D VAL* 1.3 76.0 - - - +
135D ALA* 1.3 56.4 + - - +
137D GLN* 3.2 21.4 + - - +
138D GLN* 2.9 31.2 + - - +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LYS* 3.1 21.3 + - + +
132D LEU* 3.2 6.3 + - + +
134D ASN* 1.3 74.8 - - - +
136D ILE* 1.3 62.7 + - - +
138D GLN* 3.6 11.6 + - - +
139D LYS* 3.2 32.5 + - - +
280D VAL* 4.2 17.7 - - + -
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU 3.0 20.4 + - - +
133D VAL* 3.6 7.6 - - - +
135D ALA* 1.3 74.4 - - - +
137D GLN* 1.3 57.4 + - - +
139D LYS* 3.2 5.2 + - - +
140D LEU* 2.9 33.1 + - + +
150D VAL* 4.7 1.7 - - + +
152D ILE* 3.9 32.1 - - + -
163D LEU* 3.8 39.0 - - + +
167D ALA* 3.4 20.9 - - + -
261D LEU* 4.1 15.9 - - + -
280D VAL* 4.1 23.1 - - + -
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Residues in contact with GLN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D VAL* 3.0 24.9 + - - +
134D ASN* 3.2 28.7 + - - +
136D ILE* 1.3 74.9 - - - +
138D GLN* 1.3 57.3 + - - +
140D LEU* 3.3 9.4 + - - +
141D SER* 2.9 30.5 + - - -
166D GLU 4.1 2.4 + - - -
167D ALA* 2.9 39.5 + - + +
170D ASP* 3.7 26.0 - - - +
173D LEU* 3.8 17.2 - - + +
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Residues in contact with GLN 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ASN 2.9 17.9 + - - +
135D ALA* 3.7 10.4 - - - +
137D GLN* 1.3 78.0 - - - +
139D LYS* 1.3 78.7 + - - +
141D SER* 2.8 24.0 + - - +
142D LYS* 2.6 46.6 + - - +
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Residues in contact with LYS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ALA* 3.2 19.7 + - - +
136D ILE 3.2 6.1 + - - +
138D GLN* 1.3 95.6 + - - +
140D LEU* 1.3 66.5 + - - +
141D SER 3.1 0.2 - - - -
142D LYS* 2.9 29.0 + - + +
143D LEU* 3.7 4.2 + - - +
150D VAL* 3.7 23.1 - - + +
278D TYR* 3.7 32.8 - - + +
279D VAL 4.0 17.2 + - - +
280D VAL* 3.8 16.6 - - + -
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ILE* 2.9 32.4 + - + +
137D GLN* 3.6 7.9 - - - +
139D LYS* 1.3 76.2 - - - +
141D SER* 1.3 56.6 + - - +
143D LEU* 3.2 27.5 + - + +
144D LYS 4.5 1.2 + - - -
150D VAL* 4.1 19.1 - - + -
167D ALA* 4.3 9.4 - - + -
168D VAL* 4.4 13.0 - - + -
173D LEU* 3.8 24.5 - - + -
177D CYS* 4.7 2.2 - - - +
178D PHE* 3.9 23.1 - - + -
239D LEU* 3.9 31.4 - - + -
261D LEU* 4.2 14.4 - - + -
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Residues in contact with SER 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLN 2.9 14.9 + - - -
138D GLN* 2.8 19.6 + - - +
139D LYS 3.1 0.2 - - - -
140D LEU* 1.3 75.3 - - - +
142D LYS* 1.3 62.2 + - - +
143D LEU 3.3 0.6 + - - -
144D LYS* 3.9 22.3 + - - +
173D LEU* 4.4 4.0 - - - -
177D CYS* 3.9 23.7 - - - -
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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