Contacts of the helix formed by residues 150 - 160 (chain D) in PDB entry 5TBY
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 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B THR* 5.9 2.5 - - - -
148D VAL 3.7 0.6 + - - -
149D MET* 1.3 72.1 - - - +
151D ALA* 1.3 57.4 + - - +
153D LEU* 3.1 8.1 + - - +
154D ARG* 2.9 31.7 + - - +
173D MET* 3.8 17.7 - - - +
181D GLY 3.0 15.9 + - - -
183D ILE* 5.5 4.5 - - - -
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Residues in contact with ALA 151 (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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166B LEU* 4.6 16.4 - - + +
167B THR* 6.1 0.9 - - + -
169B ARG* 5.6 4.0 - - - +
254B ALA 5.0 8.3 - - - +
255B THR* 5.6 4.6 - - + +
149D MET* 3.5 1.5 - - + +
150D GLY* 1.3 72.6 - - - +
152D GLU* 1.3 67.2 + - + +
154D ARG* 2.9 51.0 + - - +
155D HIS* 3.1 11.5 + - - +
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Residues in contact with GLU 152 (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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167B THR* 3.8 10.7 - - + +
169B ARG* 2.6 44.5 + - - +
714B LEU* 4.1 19.9 - - + +
717B ASP* 4.4 9.8 - - + +
140D PHE* 2.8 49.6 - - + -
148D VAL* 4.9 2.2 - - + -
149D MET* 3.3 22.9 + - + +
151D ALA* 1.3 77.3 - - + +
153D LEU* 1.3 59.3 + - - +
155D HIS* 4.0 5.3 + - - +
156D VAL* 3.5 26.7 + - - +
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Residues in contact with LEU 153 (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 LEU* 5.9 6.5 - - + -
148D VAL* 3.7 35.2 - - + +
149D MET 3.0 17.0 + - - +
150D GLY* 3.4 6.5 - - - +
151D ALA 3.1 0.2 - - - -
152D GLU* 1.3 77.5 - - - +
154D ARG* 1.3 60.6 + - - +
155D HIS 3.4 0.2 - - - -
156D VAL* 3.1 29.8 - - + +
157D LEU* 3.4 17.0 - - + +
173D MET* 4.6 13.7 - - + -
183D ILE* 4.1 24.0 - - + -
188D PHE* 4.7 29.2 - - + -
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Residues in contact with ARG 154 (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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166B LEU* 4.8 8.1 - - - +
254B ALA 4.5 0.4 + - - -
255B THR* 2.8 44.5 + - - +
256B GLY* 2.3 38.6 - - - +
150D GLY 2.9 11.6 + - - +
151D ALA* 2.9 41.6 + - - +
153D LEU* 1.3 72.8 - - - +
155D HIS* 1.3 68.5 + - + +
157D LEU* 3.1 22.1 + - - +
158D ALA* 3.3 9.7 + - - +
166D GLU* 5.8 4.0 + - - -
169D VAL* 3.4 34.3 - - + +
173D MET* 4.1 10.7 - - + +
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Residues in contact with HIS 155 (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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144B GLY* 5.7 7.2 - - - -
146B LYS* 5.4 1.0 + - - -
167B THR* 6.1 6.9 - - + +
713B ILE* 6.4 0.2 - - - +
717B ASP* 3.4 26.7 + - - +
721B ARG* 3.7 16.1 + - - -
151D ALA 3.1 16.3 + - - +
152D GLU* 4.2 6.3 - - - +
153D LEU 3.4 0.2 - - - -
154D ARG* 1.3 81.5 - - + +
156D VAL* 1.3 62.4 + - - +
158D ALA* 3.2 11.7 + - - +
159D THR* 3.0 48.5 - - + +
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Residues in contact with VAL 156 (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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717B ASP* 3.3 23.3 - - - +
720B GLN* 4.4 26.9 - - + -
721B ARG* 4.1 24.2 - - + +
723B ARG* 5.4 6.1 + - - +
785B ILE* 5.3 3.8 - - - +
788B ILE* 5.0 8.6 - - + +
789B GLN* 4.6 6.8 + - - -
137D LEU* 6.0 4.5 - - + -
140D PHE* 6.2 0.9 - - + -
152D GLU 3.5 13.2 + - - +
153D LEU* 3.1 33.9 - - + +
155D HIS* 1.3 76.4 - - - +
157D LEU* 1.3 65.6 + - + +
159D THR* 3.9 8.4 + - - -
160D LEU* 4.8 2.6 + - - +
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Residues in contact with LEU 157 (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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788B ILE* 4.2 24.2 - - + -
789B GLN* 3.6 16.4 + - + +
153D LEU* 3.4 26.0 - - + +
154D ARG* 3.1 13.6 + - - +
156D VAL* 1.3 82.4 - - + +
158D ALA* 1.3 59.8 + - - +
164D LEU* 3.4 38.7 + - + +
169D VAL* 4.4 11.4 - - + -
172D LEU* 3.5 30.7 - - + -
173D MET* 5.4 2.9 - - + -
188D PHE* 5.1 17.7 - - + -
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Residues in contact with ALA 158 (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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143B ARG* 6.4 0.4 - - - +
154D ARG 3.3 8.2 + - - +
155D HIS* 3.2 11.7 + - - +
157D LEU* 1.3 81.3 - - - +
159D THR* 1.3 62.8 + - + +
163D ARG* 3.1 29.8 + - - +
164D LEU 3.7 16.9 - - - +
165D THR 5.5 2.9 - - - -
166D GLU* 5.9 4.0 - - - +
169D VAL* 5.1 7.9 - - + -
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Residues in contact with THR 159 (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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144B GLY 5.9 2.7 - - - +
146B LYS* 4.3 15.1 - - - +
721B ARG* 2.8 29.7 - - - +
778B ASP* 4.0 1.2 - - - +
155D HIS* 3.0 50.5 + - + +
156D VAL 3.9 2.9 + - - -
157D LEU 3.5 2.2 - - - -
158D ALA* 1.3 80.9 - - + +
160D LEU* 1.3 76.1 + - - +
163D ARG* 3.1 24.1 + - - +
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Residues in contact with LEU 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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146B LYS* 3.3 22.2 - - + +
721B ARG* 3.6 34.1 - - + +
722B TYR* 4.7 2.0 - - + -
774B GLU 3.3 22.0 - - - +
777B ARG* 4.0 17.7 - - + +
778B ASP* 3.2 17.7 - - - +
781B LEU* 3.8 31.4 - - + -
785B ILE* 3.6 13.1 - - + +
789B GLN* 2.5 29.6 + - - -
156D VAL 4.8 2.4 + - - +
159D THR* 1.3 89.0 + - - +
161D GLY* 1.3 54.3 + - - +
163D ARG* 3.5 2.2 - - - -
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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