Contacts of the helix formed by residues 197 - 210 (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 VAL 197 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1959 LEU* 2.9 6.8 - - - +
1969 HIS* 1.0 96.6 - - + +
1989 ASP* 1.4 64.0 + - + +
1999 GLU* 3.0 27.1 - - + +
2009 ALA* 2.9 26.8 + - + +
2019 MET* 2.9 10.6 + - - +
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Residues in contact with ASP 198 (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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1089 LEU* 3.9 23.0 - - + +
1969 HIS 5.3 0.7 - - - +
1979 VAL* 1.4 73.4 - - - +
1999 GLU* 1.0 77.5 + - + +
2009 ALA 2.7 1.3 - - - -
2019 MET* 3.0 20.3 + - + +
2029 MET* 3.1 13.5 + - - +
2319 ASN* 5.2 5.4 + - - +
2329 THR* 3.3 30.9 + - + +
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Residues in contact with GLU 199 (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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1979 VAL* 3.0 15.0 - - + +
1989 ASP* 1.0 90.3 - - + +
2009 ALA* 1.4 54.5 + - - +
2029 MET* 3.8 16.2 - - + +
2039 ASP* 2.5 38.6 + - - +
2359 ALA* 5.7 9.2 - - + -
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Residues in contact with ALA 200 (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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1959 LEU* 2.6 55.3 - - + +
1969 HIS 4.8 0.2 - - - +
1979 VAL* 2.9 19.7 + - + +
1989 ASP 2.7 0.2 - - - -
1999 GLU* 1.4 79.7 - - - +
2019 MET* 1.3 69.6 + - - +
2039 ASP* 2.8 8.0 - - - +
2049 GLU* 2.7 15.8 + - - +
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Residues in contact with MET 201 (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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1069 ALA* 4.7 16.4 - - - -
1079 GLY 4.2 19.5 - - - +
1089 LEU* 3.7 35.7 - - + +
1929 ALA* 5.5 1.8 - - - -
1939 GLY 5.3 6.5 - - - +
1959 LEU* 4.1 2.9 - - - +
1979 VAL 2.9 7.5 + - - +
1989 ASP* 3.3 20.4 - - + +
2009 ALA* 1.3 74.3 - - - +
2029 MET* 1.3 80.3 + - + +
2049 GLU* 2.5 49.6 + - - +
2059 ILE* 3.0 5.2 + - - -
2199 PHE* 4.4 23.6 - - + -
2329 THR* 5.0 7.2 - - + +
2369 PHE* 6.0 0.9 - - + -
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Residues in contact with MET 202 (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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1989 ASP 3.1 8.2 + - - +
1999 GLU* 3.8 19.5 - - + +
2019 MET* 1.3 91.4 - - + +
2039 ASP* 1.3 58.2 + - - +
2059 ILE* 2.5 41.7 + - + +
2069 LYS* 2.6 19.5 + - + -
2199 PHE* 5.3 1.6 - - + -
2359 ALA* 4.6 9.4 - - + +
2369 PHE* 4.2 16.6 - - + -
2399 ALA* 3.2 35.2 - - + -
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Residues in contact with ASP 203 (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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1959 LEU* 4.0 11.4 - - - +
1999 GLU 2.5 24.0 + - - +
2009 ALA* 2.8 16.2 - - - +
2029 MET* 1.3 75.6 - - - +
2049 GLU* 1.3 56.3 + - - +
2069 LYS* 2.8 40.2 + - - +
2079 GLN* 4.2 1.0 + - - +
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Residues in contact with GLU 204 (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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1409 TYR* 3.0 15.0 + - - +
1929 ALA 4.2 6.6 - - - +
1939 GLY* 2.8 44.2 + - - -
1949 ARG* 3.4 3.3 + - - +
1959 LEU* 3.2 24.5 - - + +
2009 ALA 2.7 10.8 + - - +
2019 MET* 2.5 38.3 + - - +
2039 ASP* 1.3 69.6 - - - +
2059 ILE* 1.3 52.9 + - - +
2069 LYS 2.5 15.9 + - - -
2079 GLN* 3.1 16.1 + - - +
2089 VAL* 3.2 17.3 + - + +
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Residues in contact with ILE 205 (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* 3.1 39.5 - - + -
1069 ALA* 3.6 28.0 - - + -
1919 THR* 4.3 4.9 - - + -
2019 MET* 3.0 4.7 + - - +
2029 MET* 2.5 59.3 + - + +
2049 GLU* 1.3 74.9 - - - +
2069 LYS* 1.3 69.5 + - - +
2089 VAL* 3.3 22.6 - - + +
2099 HIS* 2.4 25.3 + - + +
2179 THR* 5.2 1.1 - - + -
2199 PHE* 4.3 12.8 - - + -
2399 ALA* 5.9 0.9 - - + -
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Residues in contact with LYS 206 (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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2029 MET* 2.6 12.1 + - + +
2039 ASP* 2.8 36.0 + - - +
2049 GLU 2.5 3.2 + - - -
2059 ILE* 1.3 82.0 - - - +
2079 GLN* 1.3 68.5 + - - +
2099 HIS* 2.7 6.2 + - - +
2109 ALA* 2.8 18.8 + - + +
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Residues in contact with GLN 207 (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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1699 VAL* 3.5 30.7 - - + +
2039 ASP 5.4 0.7 - - - +
2049 GLU 3.1 5.9 + - - +
2069 LYS* 1.3 82.0 - - - +
2089 VAL* 1.3 72.6 + - + +
2099 HIS 2.6 0.7 + - - -
2109 ALA* 2.8 26.4 + - - +
2119 SER* 3.1 16.4 + - - -
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Residues in contact with VAL 208 (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* 3.2 30.3 - - + -
1689 PRO* 5.3 16.6 - - + -
1699 VAL* 5.5 7.4 - - + +
1729 VAL* 6.1 3.6 - - + -
1919 THR* 4.4 19.1 - - + +
1929 ALA 5.9 0.7 - - - +
2049 GLU* 3.2 20.6 - - + +
2059 ILE* 3.1 25.8 - - + +
2079 GLN* 1.3 83.6 - - + +
2099 HIS* 1.3 63.1 + - - +
2119 SER* 4.1 2.2 - - - -
2129 ILE* 3.0 32.4 - - + +
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Residues in contact with HIS 209 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049 LEU* 3.8 15.3 - - + -
2059 ILE* 2.4 33.5 + - + +
2069 LYS* 3.3 3.1 - - - +
2079 GLN 2.6 4.3 + - - -
2089 VAL* 1.3 65.2 - - - +
2109 ALA* 1.3 68.4 + - + +
2119 SER 2.6 15.9 + - - -
2129 ILE 2.8 13.2 + - - -
2139 ASN* 3.0 15.9 + - - -
2149 PRO* 3.0 43.0 + - + +
2179 THR* 3.7 13.4 + - + -
2409 LEU* 4.0 26.0 - - + +
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Residues in contact with ALA 210 (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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2069 LYS* 2.8 12.4 + - + +
2079 GLN* 2.8 18.7 + - - +
2099 HIS* 1.3 81.2 - - + +
2119 SER* 1.3 58.9 + - - +
2139 ASN* 4.7 7.2 - - - -
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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