Contacts of the helix formed by residues 182 - 186 (chain 3) in PDB entry 3EPD
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 182 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2131 ALA* 5.1 0.7 - - - +
2331 MET 4.1 1.4 - - - +
2341 THR* 3.6 9.8 - - - -
2351 VAL* 2.9 41.3 + - - +
2361 ASP* 4.3 2.3 + - - +
1783 GLN* 3.3 29.3 + - - +
1803 THR 3.5 3.0 + - - +
1813 GLN* 1.3 84.0 + - - +
1833 SER* 1.3 65.9 + - - +
1843 PHE* 3.0 30.1 + - - +
1853 THR* 3.2 12.9 + - - +
1863 GLU* 3.1 20.8 + - - -
85R SER* 5.6 1.3 - - - -
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Residues in contact with SER 183 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2131 ALA* 3.5 18.6 - - - -
2141 LYS* 3.4 38.3 + - - +
2351 VAL* 5.6 1.4 - - - +
2222 LYS* 3.1 17.0 + - - -
1813 GLN* 5.4 0.4 - - - -
1823 ASP* 1.3 72.4 + - - +
1843 PHE* 1.3 66.5 + - - +
1863 GLU* 3.2 27.2 + - - +
85R SER* 4.4 10.8 + - - -
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Residues in contact with PHE 184 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011 LEU* 5.4 1.6 - - + -
2091 TYR* 3.4 37.7 - + - -
2121 PHE 4.5 0.2 - - - -
2131 ALA* 4.0 17.9 - - + +
2331 MET* 3.4 50.7 - - + +
2341 THR* 3.9 19.1 - - + +
2152 LEU* 6.1 2.7 - - + -
2182 ASP* 5.6 2.2 - - - -
2222 LYS* 4.2 9.9 + - + +
1733 ASN* 4.0 27.6 + - - +
1743 VAL* 3.9 21.3 - - + -
1823 ASP* 3.0 15.3 + - - +
1833 SER* 1.3 78.9 - - - +
1853 THR* 1.3 64.6 + - + +
1863 GLU* 3.5 0.6 + - - +
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Residues in contact with THR 185 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011 LEU* 3.9 27.8 - - + -
2341 THR* 4.2 8.5 - - + -
1733 ASN* 5.1 1.1 - - - -
1743 VAL* 3.9 15.3 - - + -
1773 ARG* 3.3 26.9 - - - +
1783 GLN* 3.5 29.6 + - + +
1803 THR 4.9 0.3 + - - -
1823 ASP* 3.2 19.5 + - - +
1833 SER 3.2 0.2 - - - -
1843 PHE* 1.3 90.7 - - + +
1863 GLU* 1.3 65.5 + - - +
1873 GLY 3.7 0.2 + - - -
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Residues in contact with GLU 186 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2131 ALA 4.8 0.5 - - - +
2141 LYS* 5.8 0.7 - - - -
1002 TYR* 4.3 3.3 + - - -
2222 LYS* 3.5 23.8 + - - +
883 SER* 5.8 0.2 - - - -
1373 PRO* 3.5 32.3 - - + +
1383 GLY* 4.3 7.2 + - - -
1773 ARG* 3.4 12.3 + - - -
1813 GLN* 4.5 12.1 - - - +
1823 ASP 3.1 10.8 + - - +
1833 SER* 3.2 25.8 + - - +
1843 PHE 3.5 0.6 - - - -
1853 THR* 1.3 80.4 - - - +
1873 GLY* 1.3 59.7 + - - +
1883 GLY 4.9 1.1 - - - +
1893 TYR* 4.2 12.8 + - - -
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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