Contacts of the helix formed by residues 174 - 179 (chain C) in PDB entry 5T0H
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 LEU 174 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407B LEU* 4.5 13.7 - - + -
167C LEU* 4.0 21.1 - - + -
171C HIS* 3.0 52.2 + - + +
172C PRO 3.0 1.2 - - - -
173C GLU* 1.3 74.6 - - - +
175C PHE* 1.3 65.6 + - - +
176C GLU 3.3 0.9 - - - -
177C ALA* 3.3 17.4 - - + +
178C LEU* 3.2 19.6 + - - +
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Residues in contact with PHE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B LEU* 5.6 4.5 - - + -
163C GLU 5.6 0.7 - - - -
167C LEU* 3.5 28.0 - - + -
168C PRO* 3.5 41.3 - - + -
172C PRO* 2.7 42.8 + - + +
174C LEU* 1.3 73.0 - - - +
176C GLU* 1.3 49.4 + - - +
178C LEU* 3.2 8.0 + - + +
179C GLY 2.5 29.6 + - - -
180C ILE* 3.2 40.6 + - + +
181C ALA* 3.4 17.3 - - - -
182C GLN* 4.5 7.2 - - + -
183C PRO* 3.8 16.4 - - + -
287C LYS* 5.1 7.6 - - + -
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Residues in contact with GLU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ARG* 2.9 50.2 + - - +
172C PRO 3.9 2.8 + - - +
173C GLU 4.1 8.0 + - - +
175C PHE* 1.3 75.6 - - - +
177C ALA* 1.3 66.5 + - - +
178C LEU 3.6 0.2 - - - -
179C GLY* 3.0 18.3 + - - +
180C ILE 5.5 1.0 - - - +
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Residues in contact with ALA 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ARG 4.4 7.6 - - - +
373B THR* 5.8 1.6 + - - +
412B MET* 4.6 20.2 - - + +
173C GLU 4.0 2.9 + - - +
174C LEU* 3.3 28.0 + - + +
175C PHE 3.2 0.6 - - - -
176C GLU* 1.3 79.5 - - - +
178C LEU* 1.3 59.4 + - - +
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ARG 3.8 0.7 - - - -
372B MET* 3.1 63.4 + - + +
402B ALA 5.6 0.4 - - - +
403B GLY* 3.8 32.1 - - - +
406B ALA* 6.1 2.5 - - + -
407B LEU* 4.3 22.0 - - + -
411B ARG 4.9 9.2 - - - +
412B MET* 4.6 16.6 - - - +
413B LYS 6.1 0.7 - - - -
414B VAL* 5.2 2.9 - - + -
174C LEU 3.2 11.3 + - - +
175C PHE* 3.5 7.6 - - + +
176C GLU 3.6 0.2 - - - -
177C ALA* 1.3 77.1 - - - +
179C GLY* 1.3 56.7 + - - +
180C ILE* 3.7 27.1 - - + +
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Residues in contact with GLY 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B HIS 5.6 1.0 - - - +
371B ARG* 4.0 30.9 - - - +
372B MET* 5.0 4.4 - - - +
175C PHE 2.5 18.0 + - - -
176C GLU* 3.0 22.0 + - - +
178C LEU* 1.3 75.1 - - - +
180C ILE* 1.3 61.6 + - - +
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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