Contacts of the helix formed by residues 1795 - 1806 (chain B) in PDB entry 5JCZ
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 SER1795 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1756B LYS 5.4 0.8 + - - -
1793B ARG 3.3 7.3 + - - -
1794B VAL* 1.3 78.7 - - - +
1796B VAL* 1.3 64.8 + - - +
1797B SER* 3.5 9.7 + - - -
1798B PHE* 3.1 25.5 + - - +
1799B ILE* 3.3 21.6 + - - +
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Residues in contact with VAL1796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1794B VAL 5.6 0.9 - - - +
1795B SER* 1.3 74.0 - - - +
1797B SER* 1.3 62.8 + - - +
1799B ILE* 3.5 10.9 + - + +
1800B ARG* 3.1 51.2 + - - +
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Residues in contact with SER1797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1795B SER* 3.2 9.8 - - - -
1796B VAL* 1.3 83.3 - - - +
1798B PHE* 1.3 62.8 + - - +
1800B ARG* 3.5 8.6 + - - +
1801B THR* 2.9 29.0 + - - -
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Residues in contact with PHE1798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1756B LYS* 3.6 29.2 - - + +
1757B LYS* 3.3 30.3 - - - +
1758B THR 3.3 24.2 - - - -
1761B ASP 4.1 0.7 - - - -
1762B ALA* 3.8 22.0 - - + -
1765B ILE* 3.8 28.0 - - + -
1781B LEU* 4.2 5.4 - - + -
1794B VAL* 3.7 20.9 - - + -
1795B SER* 3.1 22.2 + - - +
1796B VAL 3.3 0.2 - - - -
1797B SER* 1.3 75.2 - - - +
1799B ILE* 1.3 59.7 + - - +
1801B THR* 3.2 10.9 + - - -
1802B ILE* 3.0 42.7 + - + +
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Residues in contact with ILE1799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1778B VAL* 3.8 29.4 - - + -
1781B LEU* 4.4 14.8 - - + +
1782B ASN* 3.2 30.5 - - - +
1794B VAL* 3.8 25.6 - - + +
1795B SER 3.3 17.8 + - - +
1796B VAL* 3.8 12.6 - - + +
1797B SER 3.3 0.2 - - - -
1798B PHE* 1.3 72.9 - - - +
1800B ARG* 1.3 67.9 + - - +
1802B ILE* 3.2 9.5 + - + +
1803B GLN* 3.0 32.8 + - + +
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Residues in contact with ARG1800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1796B VAL* 3.1 40.8 + - - +
1797B SER* 3.7 8.0 - - - +
1798B PHE 3.3 0.2 - - - -
1799B ILE* 1.3 78.7 - - - +
1801B THR* 1.3 56.9 + - - +
1803B GLN* 3.3 17.9 + - - +
1804B MET* 2.9 29.8 + - - +
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Residues in contact with THR1801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1759B ASP* 3.6 26.4 + - - +
1762B ALA* 3.8 21.5 - - + -
1797B SER* 2.9 18.7 + - - -
1798B PHE* 3.2 14.2 + - + -
1800B ARG* 1.3 76.5 - - - +
1802B ILE* 1.3 60.9 + - - +
1804B MET* 3.3 7.0 + - - +
1805B ARG* 3.1 29.5 + - + +
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Residues in contact with ILE1802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1762B ALA* 3.7 39.9 - - + +
1765B ILE* 4.2 12.1 - - + -
1766B CYS* 4.2 7.9 - - - -
1777B ILE* 4.1 15.9 - - + -
1778B VAL* 4.6 8.1 - - + -
1781B LEU* 3.8 19.7 - - + -
1798B PHE* 3.0 25.6 + - + +
1799B ILE* 3.2 8.9 + - - +
1801B THR* 1.3 76.2 - - - +
1803B GLN* 1.3 57.5 + - - +
1805B ARG* 3.2 3.7 + - - +
1806B LEU* 2.9 51.2 + - + +
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Residues in contact with GLN1803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1774B THR* 5.0 7.7 - - + +
1778B VAL* 3.8 33.3 - - + +
1799B ILE* 3.0 29.4 + - - +
1800B ARG* 3.3 23.5 + - - +
1802B ILE* 1.3 77.3 - - - +
1804B MET* 1.3 61.2 + - - +
1806B LEU* 3.5 7.0 + - - +
1807B ARG* 3.3 21.8 + - - +
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Residues in contact with MET1804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1800B ARG 2.9 17.7 + - - +
1801B THR* 3.5 8.5 - - - +
1802B ILE 3.2 0.2 - - - -
1803B GLN* 1.3 77.5 - - - +
1805B ARG* 1.3 63.1 + - + +
1807B ARG* 3.3 29.5 - - + +
1808B ASP* 4.8 1.9 + - - -
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Residues in contact with ARG1805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1759B ASP* 4.6 8.9 + - - +
1762B ALA* 4.4 5.8 - - - +
1763B GLU* 3.4 65.9 + - - +
1766B CYS* 3.8 19.7 - - + +
1801B THR* 3.1 23.0 + - + +
1802B ILE 3.7 3.6 - - - +
1804B MET* 1.3 80.4 - - + +
1806B LEU* 1.3 61.9 + - - +
1807B ARG 3.1 4.0 + - - -
1808B ASP* 4.1 10.0 + - - +
1809B ARG* 4.7 4.5 - - - +
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Residues in contact with LEU1806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1766B CYS* 3.7 30.1 - - + -
1774B THR* 3.5 43.8 + - + +
1777B ILE* 3.7 27.1 - - + -
1802B ILE* 2.9 36.1 + - + +
1803B GLN 3.5 4.0 + - - +
1804B MET 3.3 0.2 - - - -
1805B ARG* 1.3 75.2 - - - +
1807B ARG* 1.3 62.3 - - - +
1808B ASP 3.4 1.1 - - - -
1809B ARG* 3.7 48.2 + - + +
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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