Contacts of the helix formed by residues 159 - 169 (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 GLY 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D ARG* 4.1 2.5 + - - -
157D GLY 3.2 3.8 + - - -
158D CYS* 1.3 78.9 - - - +
160D LYS* 1.3 62.1 + - - +
162D VAL* 3.5 2.8 + - - +
163D LEU* 3.0 30.3 + - - +
903D ADP 3.0 46.2 + - - -
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Residues in contact with LYS 160 (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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152D ILE* 3.8 27.8 - - + +
153D HIS 3.8 3.1 - - - -
154D GLY* 2.9 35.6 + - - +
155D MET 2.8 28.3 + - - -
156D ALA* 3.9 3.8 - - - +
158D CYS* 3.5 13.7 - - - -
159D GLY* 1.3 73.6 - - - +
161D SER* 1.3 58.2 + - - +
163D LEU* 3.2 7.2 + - - +
164D ALA* 2.9 28.9 + - - +
244D ASP* 5.4 4.2 + - - +
263D THR* 3.7 14.4 - - + +
264D THR* 3.7 22.4 - - - +
265D ARG* 4.2 6.2 - - - +
282D VAL* 4.2 3.8 - - + -
903D ADP 2.7 31.1 + - - +
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Residues in contact with SER 161 (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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120D PRO* 5.6 3.6 - - - +
160D LYS* 1.3 72.8 - - - +
162D VAL* 1.3 72.2 + - - +
164D ALA* 3.4 2.8 + - - +
165D ALA* 3.2 20.8 + - - +
184D TRP* 3.4 20.7 - - - -
243D ASP* 3.5 31.4 - - - -
263D THR* 4.4 0.4 - - - +
903D ADP 2.9 32.1 + - - -
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Residues in contact with VAL 162 (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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123D PRO* 4.1 24.0 - - + -
126D PHE* 3.9 23.1 - - + -
129D ARG* 6.2 0.2 - - - -
159D GLY 3.7 1.3 - - - +
161D SER* 1.3 86.5 + - - +
163D LEU* 1.3 62.6 + - + +
165D ALA* 3.9 5.0 - - - +
166D GLU* 3.1 23.7 + - + +
169D ARG* 5.0 0.2 + - - -
903D ADP 2.9 65.1 + - + +
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Residues in contact with LEU 163 (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* 3.9 28.0 - - + +
132D LEU* 3.8 24.2 - - + -
133D VAL* 3.7 25.9 - - + +
136D ILE* 3.8 16.4 - - + +
152D ILE* 4.8 1.1 - - + -
159D GLY 3.0 20.3 + - - +
160D LYS* 3.2 7.8 + - - +
162D VAL* 1.3 77.2 - - + +
164D ALA* 1.3 59.8 + - - +
166D GLU* 3.3 5.1 + - + +
167D ALA* 2.9 30.5 + - - +
282D VAL* 3.6 41.7 - - + -
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Residues in contact with ALA 164 (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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152D ILE* 3.9 20.8 - - + +
160D LYS 2.9 15.8 + - - +
161D SER 3.8 4.7 - - - +
162D VAL 3.4 0.2 - - - -
163D LEU* 1.3 77.0 - - - +
165D ALA* 1.3 62.6 + - - +
167D ALA* 3.6 10.4 + - - +
168D VAL* 3.6 12.8 + - - +
184D TRP* 4.1 15.5 - - + -
241D ILE* 4.2 4.1 - - + +
261D LEU* 3.9 21.1 - - + +
263D THR* 4.1 11.2 - - + -
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Residues in contact with ALA 165 (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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114D LEU* 4.3 0.5 - - - +
119D VAL* 3.6 29.6 - - + -
120D PRO* 4.1 8.3 - - + +
161D SER 3.2 15.1 + - - +
162D VAL* 3.9 4.7 - - - +
164D ALA* 1.3 76.9 - - - +
166D GLU* 1.3 64.1 + - - +
168D VAL* 3.2 9.3 + - - +
169D ARG* 3.2 38.6 + - - +
184D TRP* 3.9 7.5 - - + -
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Residues in contact with GLU 166 (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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122D ARG* 2.9 39.7 + - - +
126D PHE* 3.4 33.2 - - + -
133D VAL* 3.9 24.3 - - + +
137D GLN* 4.1 4.7 + - - -
162D VAL* 3.1 22.9 + - + +
163D LEU* 3.3 5.6 + - + +
165D ALA* 1.3 75.4 - - - +
167D ALA* 1.3 62.4 + - - +
169D ARG* 2.5 53.3 + - - +
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Residues in contact with ALA 167 (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* 3.9 6.5 - - + +
136D ILE* 3.4 37.5 - - + -
137D GLN* 2.9 32.7 + - + +
140D LEU* 4.3 6.1 - - + -
163D LEU 2.9 15.8 + - - +
164D ALA 3.7 6.7 - - - +
165D ALA 3.3 0.2 - - - -
166D GLU* 1.3 77.2 - - - +
168D VAL* 1.3 59.1 + - - +
170D ASP* 4.2 0.3 - - - +
173D LEU* 3.1 16.5 - - - +
261D LEU* 5.2 0.4 - - + -
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Residues in contact with VAL 168 (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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114D LEU* 3.6 20.4 - - + +
119D VAL* 4.5 3.8 - - + -
140D LEU* 4.4 10.3 - - + -
164D ALA 3.8 10.1 - - - +
165D ALA* 3.2 17.5 - - - +
167D ALA* 1.3 77.0 - - - +
169D ARG* 1.3 55.3 + - - +
170D ASP* 2.9 13.7 + - - +
173D LEU* 4.4 7.2 - - + -
174D LEU* 3.4 34.7 - - + +
178D PHE* 5.4 1.3 - - + -
182D VAL* 4.2 8.3 - - + -
239D LEU* 3.8 29.2 - - + -
241D ILE* 4.0 18.8 - - + -
261D LEU* 4.9 0.7 - - + -
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Residues in contact with ARG 169 (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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105D GLY 4.0 2.3 - - - +
106D ILE* 3.8 40.6 - - + +
110D VAL* 3.8 16.8 - - + -
114D LEU* 3.6 26.6 - - + +
119D VAL* 4.1 3.0 + - - +
120D PRO 2.7 30.9 + - - -
121D GLN* 3.9 6.7 - - - +
122D ARG* 3.7 21.6 - - - +
162D VAL 5.0 0.6 + - - -
165D ALA* 3.2 29.9 + - - +
166D GLU* 2.5 59.7 + - - +
168D VAL* 1.3 75.1 - - - +
170D ASP* 1.3 57.9 + - - +
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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