Contacts of the helix formed by residues 1712 - 1725 (chain A) in PDB entry 5ZCS
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 ASP1712 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1685A LEU* 3.7 24.3 - - - +
1704A MET* 3.7 13.1 - - + +
1709A ARG 4.6 1.4 + - - -
1711A ILE* 1.3 81.6 - - + +
1713A ALA* 1.3 59.7 + - - +
1714A PHE 3.2 0.2 - - - -
1715A GLN* 2.9 30.4 + - - +
1716A HIS* 2.9 36.6 + - - -
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Residues in contact with ALA1713 (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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1701A MET 5.9 0.4 - - - +
1704A MET* 3.5 27.9 - - + +
1705A TRP* 4.1 18.8 - - + -
1709A ARG 3.3 21.0 + - - +
1710A LYS* 5.0 0.2 - - - -
1711A ILE 3.4 1.0 - - - -
1712A ASP* 1.3 78.9 - - - +
1714A PHE* 1.3 55.5 + - - +
1716A HIS* 3.7 6.6 - - + +
1717A MET* 2.9 30.3 + - - +
1757A TRP* 4.5 8.9 - - + -
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Residues in contact with PHE1714 (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 TRP* 5.0 5.4 - + + -
1710A LYS 4.4 9.2 + - - +
1711A ILE 3.7 11.7 + - - +
1712A ASP 3.2 0.4 - - - -
1713A ALA* 1.3 78.5 - - - +
1715A GLN* 1.3 73.9 + - - +
1717A MET* 3.9 26.8 + - + +
1718A GLN* 3.4 48.4 + - - +
1754A LEU 5.6 2.9 - - - -
1757A TRP* 5.2 16.6 - + + -
1758A GLN* 4.9 16.2 - - - -
1761A LEU* 3.6 35.7 - - + -
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Residues in contact with GLN1715 (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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1711A ILE 4.4 9.2 + - - +
1712A ASP* 2.9 20.7 + - - +
1714A PHE* 1.3 97.2 - - - +
1716A HIS* 1.3 59.8 + - - +
1717A MET 3.2 0.4 - - - -
1718A GLN* 3.2 22.8 + - - +
1719A HIS* 2.9 46.5 + - + +
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Residues in contact with HIS1716 (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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1681A PRO 5.7 3.1 - - - -
1685A LEU* 4.4 24.0 - - + +
1687A HIS 5.4 5.8 - - - -
1688A PRO* 5.8 1.9 - - + +
1689A LEU* 4.3 36.1 + - + +
1700A TYR* 5.2 8.1 + + + -
1701A MET* 5.3 7.0 - - + -
1704A MET* 3.6 25.7 - - + +
1712A ASP* 2.9 51.8 + - - -
1713A ALA* 3.3 8.0 + - + +
1715A GLN* 1.3 72.6 - - + +
1717A MET* 1.3 60.2 + - - +
1719A HIS* 3.4 15.6 + + - +
1720A PHE* 2.9 29.8 + - - +
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Residues in contact with MET1717 (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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1701A MET* 5.0 9.8 - - - +
1713A ALA 2.9 18.0 + - - +
1714A PHE* 3.9 35.2 - - + +
1715A GLN 3.2 0.2 - - - -
1716A HIS* 1.3 76.2 - - - +
1718A GLN* 1.3 59.5 + - + +
1720A PHE* 3.3 6.7 + - + +
1721A VAL* 2.9 38.6 + - + +
1750A CYS 5.5 3.4 - - - +
1753A LYS* 3.3 31.0 - - - +
1754A LEU* 3.7 37.0 - - + +
1757A TRP* 3.5 23.3 - - + -
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Residues in contact with GLN1718 (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 PHE* 3.4 45.6 + - + +
1715A GLN* 3.2 28.6 + - - +
1717A MET* 1.3 79.7 - - + +
1719A HIS* 1.3 60.8 + - + +
1721A VAL* 3.4 4.7 + - - +
1722A GLN* 2.9 46.5 + - + +
1754A LEU* 6.3 1.3 - - + -
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Residues in contact with HIS1719 (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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1685A LEU 5.7 3.5 + - - -
1686A ASP 5.6 5.4 + - - -
1688A PRO* 4.3 31.2 - - + +
1689A LEU* 5.3 4.5 - - + +
1715A GLN* 2.9 42.5 + - + +
1716A HIS* 3.8 18.2 - + - +
1717A MET 3.4 0.2 - - - -
1718A GLN* 1.3 75.5 - - + +
1720A PHE* 1.3 55.7 + - - +
1722A GLN* 3.5 9.7 + - - +
1723A THR* 2.7 38.1 + - - +
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Residues in contact with PHE1720 (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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1689A LEU* 5.3 8.7 - - + +
1690A PRO 5.7 2.2 - - - -
1694A PRO* 4.9 13.7 - - + -
1697A THR* 3.6 35.0 - - + -
1698A TYR* 5.9 0.2 - - + -
1701A MET* 3.7 26.9 - - + -
1716A HIS 2.9 18.1 + - - +
1717A MET* 3.7 5.4 - - + +
1718A GLN 3.3 0.2 - - - -
1719A HIS* 1.3 76.4 - - - +
1721A VAL* 1.3 64.5 + - + +
1723A THR* 3.4 3.8 + - - -
1724A MET* 2.9 65.6 + - + +
1746A LEU* 5.3 2.7 - - + -
1747A MET* 5.8 3.6 - - + -
1750A CYS* 3.6 36.8 - - + -
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Residues in contact with VAL1721 (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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1717A MET* 2.9 23.9 + - + +
1718A GLN* 4.0 4.7 - - - +
1720A PHE* 1.3 84.9 - - + +
1722A GLN* 1.3 60.2 + - + +
1724A MET* 4.3 2.9 - - - +
1725A GLN* 2.9 39.2 + - + +
1750A CYS* 5.7 4.0 - - + +
1751A PHE* 3.7 33.6 - - + -
1754A LEU* 4.0 26.5 - - + -
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Residues in contact with GLN1722 (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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1718A GLN* 2.9 33.1 + - - +
1719A HIS* 4.1 9.6 + - - +
1721A VAL* 1.3 77.7 - - + +
1723A THR* 1.3 61.2 + - - +
1725A GLN* 3.4 34.2 + - - +
1726A GLN* 4.4 11.1 + - - +
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Residues in contact with THR1723 (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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1688A PRO* 5.0 8.0 - - - +
1689A LEU 4.8 13.0 + - - +
1691A THR* 3.6 26.5 - - + +
1719A HIS* 2.7 25.5 + - - +
1720A PHE* 3.8 5.8 - - - -
1722A GLN* 1.3 79.4 - - - +
1724A MET* 1.3 77.1 + - + +
1725A GLN 3.3 0.9 + - - -
1726A GLN* 3.6 17.4 + - - +
1727A GLN* 4.4 2.6 + - - +
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Residues in contact with MET1724 (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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1690A PRO 4.8 2.9 - - - +
1691A THR* 3.8 37.5 - - + +
1694A PRO* 4.9 10.1 - - + -
1720A PHE* 2.9 55.8 + - + +
1721A VAL* 4.3 2.9 - - - +
1723A THR* 1.3 95.5 - - + +
1725A GLN* 1.3 63.2 + - - +
1726A GLN 3.2 3.0 + - - -
1727A GLN* 3.4 36.8 + - + +
1728A ALA* 4.0 3.1 + - - +
1743A LEU* 5.3 5.2 - - - -
1747A MET* 3.9 29.6 - - + +
1751A PHE* 6.0 1.1 - - + -
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Residues in contact with GLN1725 (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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1721A VAL* 2.9 24.3 + - + +
1722A GLN* 3.4 41.7 + - - +
1724A MET* 1.3 77.9 - - - +
1726A GLN* 1.3 68.3 + - + +
1727A GLN 3.4 0.2 - - - -
1728A ALA* 4.1 10.6 + - - +
1729A GLN* 4.0 15.5 + - - +
1747A MET* 5.4 3.6 - - - -
1751A PHE* 5.9 4.9 - - + -
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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