Contacts of the helix formed by residues 152 - 160 (chain D) in PDB entry 6A5T
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 ASP 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D CYS* 4.8 0.7 - - - +
151D GLU* 1.3 85.9 + - + +
153D VAL* 1.3 65.9 + - - +
154D ASP* 3.9 15.3 - - + +
155D GLU* 2.9 20.7 + - - +
156D ALA* 3.5 4.7 + - - +
172D GLN* 2.9 22.5 + - - +
175D LEU* 4.7 7.3 - - - +
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Residues in contact with VAL 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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152D ASP* 1.3 73.0 - - - +
154D ASP* 1.3 54.8 + - - +
155D GLU 2.9 0.2 - - - -
156D ALA* 2.3 41.6 + - + -
157D ILE* 2.9 34.4 + - + +
163D LEU* 5.5 3.8 - - + +
169D VAL* 3.7 19.5 - - + -
171D LEU* 3.5 36.9 - - + +
172D GLN* 4.6 5.4 - - + +
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Residues in contact with ASP 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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152D ASP* 2.9 12.0 - - + +
153D VAL* 1.3 77.4 - - - +
155D GLU* 1.3 56.3 + - - +
157D ILE* 4.5 13.8 - - - +
158D THR* 2.8 19.8 + - - -
167G PHE* 3.7 14.4 - - - -
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Residues in contact with GLU 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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150D CYS* 3.1 41.0 - - + +
151D GLU* 4.6 2.8 + - - +
152D ASP* 2.9 12.4 + - - +
153D VAL 2.9 1.7 - - - -
154D ASP* 1.3 78.9 - - - +
156D ALA* 1.3 58.1 - - - +
157D ILE 3.4 0.7 - - - -
158D THR* 2.9 16.2 + - - -
159D LEU* 2.9 37.5 + - + +
144G ARG* 4.3 8.7 + - - -
167G PHE* 3.5 46.2 - - + +
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Residues in contact with ALA 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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145D LEU* 6.5 0.9 - - + -
150D CYS* 6.1 1.1 - - + +
152D ASP 3.5 2.1 + - - +
153D VAL* 2.3 43.2 + - + +
155D GLU* 1.3 71.1 - - - +
157D ILE* 1.3 51.7 + - + +
158D THR 3.1 0.2 - - - -
159D LEU* 5.3 2.2 - - - -
160D ILE* 2.6 40.9 + - - +
163D LEU* 5.5 8.9 - - + +
171D LEU* 4.1 17.9 - - + -
175D LEU* 5.6 2.2 - - + -
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Residues in contact with ILE 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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153D VAL* 2.9 34.3 + - + +
154D ASP* 4.5 11.2 - - - +
156D ALA* 1.3 74.9 - - - +
158D THR* 1.3 67.6 + - - +
160D ILE 3.6 6.1 - - - -
161D PRO* 3.3 22.5 - - - +
163D LEU* 3.5 14.8 - - + +
164D ALA* 3.5 36.2 - - + +
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Residues in contact with THR 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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26D THR* 5.4 2.9 - - - +
154D ASP 2.8 21.7 + - - -
155D GLU 2.9 10.4 + - - -
157D ILE* 1.3 85.6 - - - +
159D LEU* 1.3 68.5 + - + +
161D PRO* 3.8 7.1 - - - +
165G GLU* 6.0 2.2 - - - +
166G ASP* 3.3 43.5 + - + +
167G PHE* 3.6 11.3 - - + -
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Residues in contact with LEU 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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25D ALA* 5.1 5.4 - - - +
26D THR* 5.0 5.0 - - - +
148D LEU* 4.2 15.7 - - + -
150D CYS* 4.8 5.2 - - - -
155D GLU* 2.9 48.9 + - + +
156D ALA* 4.7 1.8 - - - +
158D THR* 1.3 77.7 - - + +
160D ILE* 1.3 68.6 + - + +
161D PRO* 3.4 6.4 - - - +
86G VAL* 3.5 40.2 - - + +
144G ARG* 5.1 3.4 - - - +
166G ASP 4.1 19.5 - - - +
167G PHE* 5.0 2.5 - - + -
168G LEU* 4.4 11.7 - - + -
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Residues in contact with ILE 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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25D ALA 5.2 4.5 - - - +
141D GLU* 4.9 14.1 - - + +
144D GLN* 3.2 53.8 - - + +
145D LEU* 5.5 6.5 - - + -
148D LEU* 4.7 5.6 - - + -
156D ALA 2.6 25.0 + - - +
157D ILE* 3.6 2.9 - - - -
159D LEU* 1.3 85.0 - - + +
161D PRO* 1.3 59.9 - - + +
162D SER* 3.0 31.9 + - - +
163D LEU* 3.8 13.2 + - + +
86G VAL* 6.1 0.4 - - + -
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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