Contacts of the helix formed by residues 1776 - 1789 (chain X) in PDB entry 3HM6
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 THR1776 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1725X SER* 3.5 20.9 - - - +
1774X CYS 3.6 0.2 + - - -
1775X ASP* 1.3 78.6 - - - +
1777X ILE* 1.3 65.0 + - - +
1778X SER* 3.5 5.9 + - - -
1779X GLN* 2.9 30.3 + - - +
1780X ALA* 2.9 18.9 + - - +
1819X ASP* 3.7 12.6 - - - -
1833X LEU* 4.0 12.6 - - + -
1834X ASN 3.6 9.6 - - - -
1835X THR* 4.0 1.8 - - + +
1885X HIS* 3.4 34.3 - - + +
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Residues in contact with ILE1777 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X UNX 4.0 7.2 - - - -
1776X THR* 1.3 71.8 - - - +
1778X SER* 1.3 57.8 + - - +
1780X ALA* 3.4 2.7 + - + +
1781X LYS* 2.8 28.3 + - - +
1805X VAL* 3.7 24.0 - - + -
1817X LEU* 3.5 39.3 - - + +
1818X SER* 3.8 21.5 - - - +
1819X ASP* 3.0 12.4 + - - +
1834X ASN 3.2 11.7 + - - +
1835X THR 4.1 7.9 - - - +
1836X LEU* 3.6 30.7 - - + -
1839X TYR* 3.9 11.2 - - + -
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Residues in contact with SER1778 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1725X SER* 6.5 1.1 - - - -
1776X THR* 3.8 4.3 - - - -
1777X ILE* 1.3 76.0 - - - +
1779X GLN* 1.3 62.7 + - - +
1781X LYS* 3.2 16.5 + - - +
1782X GLU* 3.1 28.7 + - - +
1819X ASP* 2.5 32.7 + - - -
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Residues in contact with GLN1779 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1723X VAL* 2.7 44.8 + - - +
1725X SER* 3.7 19.5 - - - +
1775X ASP* 3.4 21.7 - - + +
1776X THR* 2.9 39.9 + - - +
1778X SER* 1.3 74.2 - - - +
1780X ALA* 1.3 62.0 + - - +
1782X GLU* 3.5 19.4 + - - +
1783X LYS* 3.3 29.0 + - - +
1885X HIS* 3.3 14.2 - - - -
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Residues in contact with ALA1780 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1751X LEU* 5.3 3.8 - - + -
1771X VAL* 4.4 8.2 - - + +
1775X ASP* 4.2 6.0 - - + +
1776X THR 2.9 17.5 + - - +
1777X ILE* 3.7 5.4 - - + +
1779X GLN* 1.3 74.8 - - - +
1781X LYS* 1.3 58.6 - - - +
1783X LYS* 3.3 8.4 + - - +
1784X MET* 2.9 36.2 + - - +
1805X VAL* 6.3 2.0 - - + -
1836X LEU* 3.8 34.5 - - + -
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Residues in contact with LYS1781 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X UNX 2.7 25.3 - - - -
1777X ILE 2.8 18.2 + - - +
1778X SER* 3.2 11.6 + - - +
1780X ALA* 1.3 75.9 - - - +
1782X GLU* 1.3 55.6 + - + +
1784X MET* 3.3 8.6 + - - +
1785X LEU* 2.9 42.0 + - + +
1800X PRO* 2.9 30.8 + - + +
1801X ARG* 4.7 2.6 - - - +
1803X LEU* 2.7 31.1 + - + +
1805X VAL* 3.8 21.9 - - + +
1849X LEU* 4.1 14.1 - - + +
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Residues in contact with GLU1782 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1778X SER* 3.1 15.9 + - - +
1779X GLN* 3.6 25.3 + - - +
1781X LYS* 1.3 72.7 - - + +
1783X LYS* 1.3 69.1 + - + +
1785X LEU* 3.1 12.7 + - + +
1786X ASP* 3.0 31.4 + - - +
1800X PRO* 6.0 6.7 - - + -
2000X GLN* 3.6 25.2 + - - +
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Residues in contact with LYS1783 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1719X ASP* 2.9 57.9 + - + +
1721X GLY 4.8 1.6 + - - -
1723X VAL* 6.2 1.0 - - - +
1769X VAL* 3.5 6.8 - - + +
1770X LYS 4.0 15.9 + - - +
1771X VAL* 4.0 14.7 - - + +
1772X LEU* 3.9 11.1 - - - +
1775X ASP* 2.7 37.4 + - - +
1779X GLN* 3.3 13.9 + - - +
1780X ALA 3.6 7.6 - - - +
1782X GLU* 1.3 80.6 - - + +
1784X MET* 1.3 61.0 - - - +
1786X ASP* 3.7 8.6 + - - +
1787X GLN* 2.9 30.0 + - - +
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Residues in contact with MET1784 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1751X LEU* 4.5 14.1 - - + -
1753X ALA* 3.9 15.7 - - + +
1754X LEU 4.4 1.8 - - - +
1769X VAL* 4.0 26.1 - - + +
1771X VAL* 4.9 0.2 - - + -
1780X ALA* 2.9 23.2 + - - +
1781X LYS* 3.5 9.6 - - - +
1783X LYS* 1.3 75.4 - - - +
1785X LEU* 1.3 58.8 + - - +
1787X GLN* 3.4 3.6 + - - +
1788X LEU* 2.9 30.6 + - - +
1805X VAL* 4.8 8.5 - - - -
1847X VAL* 3.1 45.3 - - + +
1848X ALA 4.3 1.1 - - - +
1849X LEU* 4.0 34.8 - - + -
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Residues in contact with LEU1785 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1781X LYS* 2.9 39.5 + - + +
1782X GLU* 3.6 8.3 - - + +
1784X MET* 1.3 72.8 - - - +
1786X ASP* 1.3 57.0 + - - +
1788X LEU* 4.2 3.4 - - - -
1789X TYR* 2.8 64.9 + - + +
1797X ARG* 4.0 13.0 + - - +
1798X PRO* 4.9 6.3 - - + +
1800X PRO* 4.2 31.4 - - + -
1803X LEU* 3.8 12.3 - - + -
1849X LEU* 3.7 19.7 - - + -
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Residues in contact with ASP1786 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1715X LYS* 2.7 34.1 + - - +
1719X ASP* 5.3 1.0 - - - +
1782X GLU* 3.0 20.4 + - - +
1783X LYS* 3.7 12.8 - - - +
1784X MET 3.3 0.2 - - - -
1785X LEU* 1.3 77.1 - - - +
1787X GLN* 1.3 66.1 + - - +
1789X TYR 3.3 5.2 - - - +
1790X LYS* 3.2 26.0 - - - +
1794X LEU* 5.4 0.7 - - - +
1797X ARG* 3.3 24.0 + - - +
2000X GLN* 5.8 3.5 + - - +
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Residues in contact with GLN1787 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1767X VAL* 4.9 11.2 - - + +
1768X PRO 3.9 23.8 - - - +
1769X VAL* 3.9 18.6 - - + +
1770X LYS 5.5 2.0 - - - -
1783X LYS* 2.9 26.5 - - - +
1784X MET 3.4 5.6 + - - +
1785X LEU 3.4 0.2 - - - -
1786X ASP* 1.3 84.4 - - - +
1788X LEU* 1.3 67.5 + - - +
1789X TYR 3.2 0.6 + - - -
1790X LYS* 3.5 24.0 + - + +
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Residues in contact with LEU1788 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1753X ALA* 5.9 6.2 - - + +
1754X LEU 5.7 3.1 - - - +
1755X LEU* 4.4 29.8 - - + +
1767X VAL* 5.3 7.8 - - - +
1769X VAL* 5.7 0.2 - - - +
1784X MET* 2.9 19.4 + - + +
1785X LEU* 3.9 4.9 - - - +
1787X GLN* 1.3 77.8 - - - +
1789X TYR* 1.3 72.7 + - + +
1790X LYS 3.8 1.4 + - - -
1849X LEU* 5.3 2.7 - - + -
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Residues in contact with TYR1789 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1755X LEU* 3.9 34.7 - - + +
1785X LEU* 2.8 49.3 + - + +
1786X ASP 3.3 3.1 - - - +
1788X LEU* 1.3 78.9 - - + +
1790X LYS* 1.3 61.4 + - - +
1791X GLY 3.3 3.6 + - - -
1792X VAL* 3.5 34.9 + - + -
1796X GLN 4.8 3.8 - - - -
1797X ARG* 2.9 42.6 + - + +
1798X PRO* 3.3 33.7 - - + +
1803X LEU* 5.0 0.9 - - - +
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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