Contacts of the strand formed by residues 187 - 191 (chain 9) in PDB entry 2J28
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 187 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019 ALA 3.4 19.1 + - - +
1029 VAL* 4.1 5.1 - - + -
1039 VAL* 2.7 42.1 + - - +
1339 LEU* 2.8 55.0 - - + +
1349 VAL* 3.7 7.0 - - - -
1359 VAL* 4.1 6.1 - - + -
1729 VAL* 6.3 2.0 - - + -
1759 ALA* 5.4 0.2 - - + -
1769 LEU* 4.0 40.8 - - + +
1869 VAL* 1.3 76.5 - - - +
1889 LEU* 1.3 65.5 + - - +
1899 VAL* 3.3 22.7 - - + -
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Residues in contact with LEU 188 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039 VAL* 3.0 38.6 - - + -
1179 VAL* 3.7 22.1 - - + +
1209 LEU* 3.0 42.0 - - + -
1219 GLY* 2.9 38.1 - - - +
1249 LEU* 5.1 2.5 - - + -
1329 VAL* 5.7 2.2 - - + -
1339 LEU 3.0 4.8 + - - +
1349 VAL* 3.2 31.5 - - + +
1359 VAL 3.3 1.9 + - - -
1869 VAL* 4.7 9.4 - - + +
1879 LEU* 1.3 75.3 - - - +
1899 VAL* 1.3 66.6 + - - +
1909 ASP 4.3 0.2 - - - -
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Residues in contact with VAL 189 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029 VAL* 6.4 0.9 - - + -
1039 VAL* 3.0 17.4 + - - +
1049 LEU* 4.2 3.9 - - + +
1059 MET* 2.9 26.5 + - - +
1359 VAL* 2.9 41.1 - - + +
1379 ALA* 3.2 21.2 - - + +
1729 VAL* 5.2 13.2 - - + -
1759 ALA* 6.2 0.2 - - + -
1879 LEU* 3.3 31.9 - - + -
1889 LEU* 1.3 80.7 - - - +
1909 ASP* 1.3 63.3 + - - +
1919 THR* 3.6 2.3 + - - +
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Residues in contact with ASP 190 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059 MET* 3.1 23.4 - - + +
1079 GLY* 4.3 1.7 + - - -
1139 LYS* 3.0 59.1 - - - +
1149 THR* 3.2 8.0 + - - -
1179 VAL* 3.8 16.2 - - + +
1359 VAL 4.0 4.4 + - - +
1379 ALA* 2.5 30.0 + - - +
1389 ASP* 2.4 27.3 - - - +
1889 LEU 4.3 0.2 - - - -
1899 VAL* 1.3 72.6 - - - +
1919 THR* 1.3 66.9 + - - +
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Residues in contact with THR 191 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049 LEU* 4.4 11.0 - - + -
1059 MET 2.4 41.4 + - - +
1069 ALA* 3.6 7.9 - - - -
1079 GLY* 2.8 26.0 + - - +
1379 ALA* 2.7 26.6 + - - +
1389 ASP* 2.7 7.4 - - - -
1689 PRO* 5.3 6.4 - - - +
1899 VAL 4.4 0.7 - - - +
1909 ASP* 1.3 78.4 + - - +
1929 ALA* 1.3 72.1 + - - +
2059 ILE* 4.3 15.9 - - + -
2089 VAL* 4.4 16.0 - - + +
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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