Contacts of the helix formed by residues 168 - 173 (chain B) in PDB entry 5T0I
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 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ASP* 4.7 7.3 - - - +
167B THR* 1.3 106.1 + - - +
169B PRO* 1.3 73.9 - - + +
170B LEU* 3.1 14.8 - - + +
171B VAL* 3.8 3.6 + - - +
172B THR* 4.4 5.5 + - - -
265B LYS* 4.0 17.3 + - - +
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Residues in contact with PRO 169 (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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168B ASP* 1.3 88.9 - - + +
170B LEU* 1.3 60.3 + - + +
171B VAL 3.3 1.5 + - - -
172B THR* 3.4 17.7 + - - +
222C LYS 5.6 0.4 - - - +
223C PHE 3.8 22.7 - - - +
224C ILE* 4.5 5.4 - - + -
225C GLY* 4.2 18.6 - - - +
228C ALA* 5.3 1.3 - - + -
233C GLU* 2.8 31.0 - - - +
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Residues in contact with LEU 170 (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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168B ASP* 3.1 8.0 - - + -
169B PRO* 1.3 80.7 - - + +
171B VAL* 1.3 61.5 + - + +
173B VAL* 3.1 25.3 - - - +
265B LYS* 3.6 57.9 - - + +
268B ARG* 4.8 7.0 - - + -
269B GLU* 3.3 31.0 - - + +
272B ARG* 3.1 14.2 + - - +
227C GLY 4.2 0.9 - - - +
228C ALA* 3.7 26.0 - - + +
229C ARG* 4.2 6.7 - - - +
233C GLU* 3.2 9.0 - - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 4.5 11.7 - - - +
167B THR* 3.1 36.1 - - + +
168B ASP 3.8 2.2 + - - +
169B PRO 3.3 1.0 - - - -
170B LEU* 1.3 77.6 - - + +
172B THR* 1.3 63.4 + - - +
173B VAL* 3.2 5.4 + - - +
174B MET* 4.4 3.3 + - - +
175B LYS* 4.6 7.8 + - - +
272B ARG* 3.3 45.5 + - + +
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Residues in contact with THR 172 (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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166B ASP* 5.0 6.9 + - - -
168B ASP 4.4 5.0 + - - -
169B PRO* 3.4 16.5 + - - +
170B LEU 3.3 1.6 - - - -
171B VAL* 1.3 76.4 - - - +
173B VAL* 1.3 66.3 + - - +
174B MET 3.7 0.4 - - - -
175B LYS* 3.3 26.1 - - + +
233C GLU* 5.3 0.4 - - - -
236C VAL* 3.6 22.6 - - + +
239C ARG* 3.5 11.6 + - - +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU 3.1 19.5 - - - +
171B VAL 3.2 0.4 - - - +
172B THR* 1.3 81.6 - - - +
174B MET* 1.3 70.4 + - + +
175B LYS* 4.1 0.7 - - - +
272B ARG* 3.5 15.7 - - - +
229C ARG* 3.2 32.1 - - + +
232C ARG* 3.5 31.9 - - + +
233C GLU* 3.2 30.5 - - + +
235C PHE* 3.2 22.3 - - - -
236C VAL* 3.5 8.6 - - + +
239C ARG* 4.2 0.7 + - - -
279C GLN* 3.9 3.6 + - - -
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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