Contacts of the helix formed by residues 169 - 182 (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 169 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1679 LYS* 5.4 9.2 - - + -
1689 PRO* 1.3 87.9 - - + +
1709 ASP* 1.3 84.6 + - + +
1729 VAL* 2.5 22.9 + - - +
1739 ASN* 2.6 33.0 + - - +
2079 GLN* 3.5 37.2 - - + +
2089 VAL* 5.5 8.2 - - + +
2119 SER* 4.4 11.0 - - - +
2129 ILE* 6.0 2.7 - - - -
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Residues in contact with ASP 170 (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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1679 LYS* 4.8 20.0 + - + +
1689 PRO 2.6 6.5 + - - +
1699 VAL* 1.3 90.9 - - + +
1719 ILE* 1.3 54.0 + - - +
1739 ASN* 2.6 8.3 + - - +
1749 ALA* 2.4 41.9 + - - +
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Residues in contact with ILE 171 (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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1359 VAL* 4.5 5.6 - - + -
1369 SER 4.4 18.2 - - - +
1379 ALA* 5.8 0.9 - - - -
1399 VAL* 6.2 2.5 - - + -
1609 PHE* 4.0 14.1 - - + -
1619 PRO* 3.7 18.2 - - + -
1629 SER* 3.5 32.5 - - - +
1679 LYS 3.0 14.4 - - - +
1689 PRO* 3.0 29.4 - - + +
1709 ASP* 1.3 79.0 - - - +
1729 VAL* 1.3 81.5 + - + +
1749 ALA* 2.9 7.8 - - + +
1759 ALA* 2.6 22.7 + - - +
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Residues in contact with VAL 172 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049 LEU* 6.2 0.2 - - + -
1359 VAL* 5.0 3.8 - - - -
1379 ALA* 4.3 23.6 - - + -
1689 PRO* 4.1 6.5 - - + -
1699 VAL* 2.5 32.0 + - - +
1719 ILE* 1.3 88.3 - - + +
1739 ASN* 1.3 71.6 + - - +
1759 ALA* 2.7 14.0 + - - +
1769 LEU* 3.1 13.7 + - + +
1879 LEU* 6.3 1.6 - - + -
1899 VAL* 5.2 12.3 - - + -
1919 THR* 6.3 0.4 - - - -
2089 VAL* 6.1 3.1 - - + -
2129 ILE* 3.4 35.7 - - + -
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Residues in contact with ASN 173 (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* 2.6 37.4 + - - +
1709 ASP* 3.0 8.9 - - - +
1729 VAL* 1.3 75.5 - - - +
1749 ALA* 1.3 71.5 + - - +
1769 LEU* 3.0 28.4 - - + +
1779 LYS* 3.6 12.3 + - - +
2119 SER* 4.4 10.3 + - - +
2129 ILE* 3.9 26.5 - - - +
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Residues in contact with ALA 174 (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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1609 PHE* 4.9 9.2 - - + -
1709 ASP* 2.4 30.4 + - - +
1719 ILE* 2.9 18.4 - - + +
1739 ASN* 1.3 76.2 - - - +
1759 ALA* 1.3 73.9 - - - +
1779 LYS* 3.6 5.9 + - - +
1789 GLU* 3.6 5.6 + - - +
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Residues in contact with ALA 175 (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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1339 LEU* 5.6 1.6 - - - -
1359 VAL* 2.8 44.4 - - + -
1609 PHE* 4.3 8.7 - - + -
1719 ILE 2.6 14.5 + - - +
1729 VAL* 2.7 8.5 + - - +
1749 ALA* 1.3 81.3 - - - +
1769 LEU* 1.3 72.4 + - - +
1789 GLU* 2.4 30.8 + - - +
1879 LEU* 5.4 0.2 - - + -
1899 VAL* 5.8 0.2 - - + -
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Residues in contact with LEU 176 (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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1019 ALA 5.2 2.9 - - - +
1029 VAL* 4.6 20.9 - - + -
1339 LEU* 4.0 1.2 - - - +
1359 VAL* 4.6 0.2 - - - +
1729 VAL* 3.1 9.8 + - + +
1739 ASN* 3.0 22.7 - - + +
1759 ALA* 1.3 80.4 - - - +
1779 LYS* 1.3 81.1 + - + +
1789 GLU 2.3 16.1 + - - -
1799 ALA* 3.1 17.3 + - - +
1809 LYS* 3.4 16.7 + - + +
1879 LEU* 4.0 29.8 - - + +
2129 ILE* 4.7 21.5 - - + +
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Residues in contact with LYS 177 (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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1739 ASN* 3.6 10.3 + - + +
1749 ALA 4.1 5.4 - - - +
1759 ALA 2.8 1.0 + - - -
1769 LEU* 1.3 94.9 - - + +
1789 GLU* 1.3 51.8 + - - +
1809 LYS* 3.0 31.1 - - + +
1819 LEU* 2.3 39.3 + - + +
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Residues in contact with GLU 178 (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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1339 LEU* 5.2 9.6 - - + +
1359 VAL* 5.5 0.3 - - - +
1599 PHE 5.5 0.5 - - - +
1609 PHE* 3.6 44.8 - - - +
1749 ALA 3.6 3.5 + - - +
1759 ALA* 2.4 22.6 + - - +
1769 LEU 2.3 11.5 + - - +
1779 LYS* 1.3 67.0 - - - +
1799 ALA* 1.3 59.9 + - - +
1819 LEU* 2.3 37.3 + - - +
1829 LYS* 2.8 37.7 + - + +
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Residues in contact with ALA 179 (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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1339 LEU* 1.7 53.8 - - + -
1769 LEU 3.1 0.8 + - - -
1789 GLU* 1.3 80.6 - - - +
1809 LYS* 1.3 49.2 + - - +
1829 LYS* 2.6 6.5 + - - -
1839 PHE 2.3 32.6 + - - -
1849 TYR* 2.8 41.0 + - + -
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Residues in contact with LYS 180 (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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1009 PRO* 5.2 20.0 - - + -
1769 LEU* 3.4 14.6 + - + +
1779 LYS* 3.0 44.9 - - + +
1789 GLU 2.7 0.2 + - - -
1799 ALA* 1.3 79.5 - - - +
1819 LEU* 1.3 53.8 + - - +
1839 PHE* 2.3 41.0 + - + +
1849 TYR 4.4 2.7 - - - +
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Residues in contact with LEU 181 (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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1779 LYS 2.3 17.5 + - - +
1789 GLU* 2.3 26.9 + - - +
1809 LYS* 1.3 67.0 - - - +
1829 LYS* 1.3 57.5 + - + -
1839 PHE* 3.1 29.5 - - + -
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Residues in contact with LYS 182 (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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1589 ASP* 5.8 1.8 + - - -
1789 GLU* 2.8 33.5 + - + +
1799 ALA* 2.6 16.0 + - - +
1819 LEU* 1.3 75.5 - - + +
1839 PHE* 1.3 74.9 + - - +
1849 TYR* 3.2 41.7 + - + +
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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