Contacts of the helix formed by residues 1706 - 1720 (chain A) in PDB entry 4C6C
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 GLY1706 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1640A PRO* 6.1 2.2 - - - -
1641A HIS* 6.3 0.9 - - - -
1685A SER* 4.1 17.0 - - - -
1687A HIS* 3.0 9.4 + - - +
1704A PHE 3.7 2.1 + - - -
1705A PRO* 1.3 75.2 - - - +
1707A LEU* 1.3 66.6 + - - +
1708A GLU 3.3 2.9 - - - -
1709A THR* 3.3 11.7 + - - -
1710A MET* 3.0 28.6 + - - +
1774A PHE* 5.2 3.4 - - - -
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Residues in contact with LEU1707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469A ASP* 3.3 30.5 - - + +
1472A VAL* 3.9 14.1 - - + -
1474A LEU* 4.6 4.3 - - + -
1488A GLY 3.4 25.1 - - - +
1491A ALA* 3.9 17.3 - - + +
1492A ALA* 4.0 20.9 - - + +
1495A GLY* 3.5 17.5 - - - +
1497A ILE* 4.3 11.7 - - + +
1500A VAL* 4.5 2.0 - - + -
1685A SER* 4.7 1.6 - - - -
1687A HIS* 3.2 42.5 + - + +
1706A GLY* 1.3 77.3 - - - +
1708A GLU* 1.3 62.3 + - - +
1709A THR 3.5 0.2 + - - -
1710A MET* 3.9 9.5 + - + +
1711A LEU 4.9 0.3 + - - -
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Residues in contact with GLU1708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491A ALA* 3.4 23.9 - - + +
1494A ALA* 4.3 10.4 - - + +
1495A GLY* 4.3 7.8 - - - -
1687A HIS* 5.5 0.6 - - - -
1706A GLY* 3.3 0.6 - - - -
1707A LEU* 1.3 77.2 - - - +
1709A THR* 1.3 60.0 + - - +
1710A MET 3.7 0.2 - - - -
1712A PRO* 3.6 19.6 - - - +
1764A MET* 3.4 37.3 - - + +
1765A PRO* 3.4 12.5 - - - +
1766A PHE* 2.9 40.1 + - - -
1767A SER* 2.9 36.0 + - - -
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Residues in contact with THR1709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1705A PRO 4.5 0.9 + - - -
1706A GLY* 3.4 14.9 + - - -
1707A LEU 3.3 0.2 - - - -
1708A GLU* 1.3 82.2 - - + +
1710A MET* 1.3 63.8 + - - +
1711A LEU 3.4 1.3 - - - -
1712A PRO* 3.4 7.8 - - - +
1713A LEU* 3.0 29.8 + - - +
1758A TRP* 5.6 0.7 - - + -
1760A ILE* 3.9 22.9 - - + -
1764A MET* 3.9 27.1 - - + -
1772A THR* 4.1 14.7 + - - +
1774A PHE* 3.6 26.5 - - + -
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Residues in contact with MET1710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469A ASP* 3.4 29.2 - - - +
1497A ILE* 4.1 18.8 - - + -
1640A PRO* 3.5 31.9 - - + -
1683A PHE* 4.4 4.3 - - - -
1684A ALA* 3.9 10.3 - - - -
1685A SER* 3.7 20.2 - - - +
1706A GLY 3.0 17.1 + - - +
1707A LEU* 3.9 5.5 + - + +
1708A GLU 3.7 0.8 - - - -
1709A THR* 1.3 78.7 + - - +
1711A LEU* 1.3 64.8 + - - +
1713A LEU* 3.3 2.7 + - - +
1714A LEU* 3.0 36.0 + - + +
1732A LEU* 3.8 27.4 - - + -
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Residues in contact with LEU1711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1464A LEU* 4.5 3.4 - - + -
1467A LEU* 3.8 30.3 - - + -
1495A GLY 3.4 27.9 + - - +
1496A GLY* 4.2 3.8 - - - -
1497A ILE* 5.7 1.6 - - + -
1707A LEU 4.9 0.8 + - - -
1710A MET* 1.3 78.3 - - + +
1712A PRO* 1.3 66.3 - - + +
1714A LEU* 3.1 3.1 + - - -
1715A LEU* 2.8 52.8 + - + +
1728A LEU* 3.9 20.9 - - + -
1732A LEU* 4.3 9.0 - - + -
1750A VAL* 4.8 0.9 - - + -
1752A VAL* 4.1 16.4 - - + -
1783A VAL* 3.8 18.8 - - + -
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Residues in contact with PRO1712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495A GLY* 5.1 4.7 - - - +
1708A GLU 3.6 18.6 - - - +
1709A THR* 3.4 14.6 - - - +
1711A LEU* 1.3 94.7 - - + +
1713A LEU* 1.3 59.4 + - - +
1715A LEU* 3.8 6.3 - - + +
1716A THR* 2.8 29.2 + - - -
1758A TRP* 3.7 31.9 - - + -
1760A ILE* 5.8 1.1 - - + -
1779A VAL* 4.1 8.8 - - + +
1780A LYS 4.1 1.2 - - - +
1781A GLY 3.7 16.4 - - - +
1782A THR* 5.2 4.7 - - - +
1783A VAL* 5.4 5.8 - - + +
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Residues in contact with LEU1713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1640A PRO* 4.1 13.2 - - + -
1644A PHE* 3.5 34.5 - - + -
1709A THR* 3.0 27.4 + - - +
1710A MET 3.6 3.4 - - - +
1712A PRO* 1.3 76.4 - - - +
1714A LEU* 1.3 62.9 + - - +
1716A THR* 3.3 8.9 + - - -
1717A ALA 3.2 16.5 + - - -
1760A ILE* 4.2 9.2 - - + -
1774A PHE* 3.6 41.7 - - + -
1777A GLN* 3.3 26.7 - - - +
1779A VAL* 4.0 17.5 - - + -
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Residues in contact with LEU1714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1640A PRO* 5.3 4.0 - - + -
1643A LEU* 4.4 9.6 - - + -
1644A PHE* 3.9 24.0 - - + -
1674A TRP* 5.0 3.8 - - + -
1683A PHE* 3.7 46.4 - - + -
1710A MET* 3.0 40.0 + - + +
1711A LEU* 3.8 3.1 - - - +
1713A LEU* 1.3 74.3 - - - +
1715A LEU* 1.3 61.0 + - - +
1717A ALA* 3.1 4.7 + - - +
1718A VAL* 2.9 31.4 + - - +
1723A LEU* 4.1 7.5 - - + +
1728A LEU* 3.7 22.0 - - + -
1732A LEU* 4.0 7.0 - - + -
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Residues in contact with LEU1715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1464A LEU* 5.0 4.9 - - + -
1711A LEU* 2.8 44.9 + - + +
1712A PRO* 3.8 4.3 - - + +
1714A LEU* 1.3 68.7 - - - +
1716A THR* 1.3 65.6 + - - +
1718A VAL* 3.2 9.6 + - + +
1719A SER* 2.9 27.0 + - - -
1725A LEU* 5.0 7.4 - - + -
1728A LEU* 3.9 19.7 - - + -
1752A VAL* 4.1 28.5 - - + -
1754A LEU* 3.8 25.1 - - + +
1780A LYS 3.6 10.1 - - - +
1781A GLY* 4.2 18.6 - - - -
1782A THR* 4.3 2.5 - - - +
1783A VAL* 5.7 0.4 - - + -
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Residues in contact with THR1716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1644A PHE* 5.9 1.1 - - + -
1712A PRO 2.8 19.8 + - - -
1713A LEU* 3.4 10.3 - - - -
1715A LEU* 1.3 77.0 - - - +
1717A ALA* 1.3 61.4 + - - +
1719A SER* 3.1 7.1 + - - -
1720A GLU* 3.0 43.2 + - + +
1778A LYS 4.2 8.1 - - - +
1779A VAL* 3.2 15.8 - - - +
1780A LYS* 2.8 35.9 + - + +
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Residues in contact with ALA1717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1644A PHE* 4.0 8.9 - - + -
1674A TRP* 3.7 21.3 - - + -
1713A LEU 3.2 8.9 + - - +
1714A LEU* 3.1 9.9 + - - +
1716A THR* 1.3 80.0 - - - +
1718A VAL* 1.3 60.2 + - - +
1720A GLU* 3.2 4.4 + - - -
1721A GLY 3.2 3.8 + - - -
1722A ARG* 2.9 42.1 + - - +
1723A LEU* 3.6 17.7 - - + -
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Residues in contact with VAL1718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1714A LEU 2.9 19.0 + - - +
1715A LEU* 3.2 12.5 + - + +
1717A ALA* 1.3 75.0 - - - +
1719A SER* 1.3 62.2 + - - +
1721A GLY* 3.0 19.2 + - - -
1723A LEU* 3.4 30.4 - - + +
1724A SER* 3.9 12.8 - - - +
1725A LEU* 4.0 24.0 - - + +
1728A LEU* 4.1 19.5 - - + -
1754A LEU* 5.8 8.5 - - + -
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Residues in contact with SER1719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1715A LEU 2.9 17.7 + - - -
1716A THR* 3.1 7.6 + - - -
1718A VAL* 1.3 78.3 - - - +
1720A GLU* 1.3 61.1 + - - +
1721A GLY 3.3 1.2 + - - -
1754A LEU* 4.1 25.8 + - - +
1780A LYS* 4.4 24.0 + - - -
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Residues in contact with GLU1720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1716A THR* 3.0 35.9 + - + +
1717A ALA* 3.7 6.6 - - - +
1718A VAL 3.1 0.4 - - - -
1719A SER* 1.3 78.6 - - - +
1721A GLY* 1.3 62.0 + - - +
1722A ARG* 3.5 30.9 + - + +
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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