Contacts of the helix formed by residues 1733 - 1741 (chain A) in PDB entry 4C6P
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 HIS1733 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1465A PRO* 3.4 35.7 - - + +
1466A GLY* 2.8 28.0 + - - -
1467A LEU* 4.2 10.8 - - + -
1468A ILE* 3.8 8.7 - - + +
1729A LEU* 3.0 12.4 + - + +
1731A ARG 3.6 1.2 - - - -
1732A LEU* 1.3 82.1 - - - +
1734A HIS* 1.3 92.0 + + - +
1735A ASN 3.5 1.1 - - - -
1736A PRO* 3.5 4.2 - - - +
1737A ARG* 3.1 70.0 + - + +
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Residues in contact with HIS1734 (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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1726A ASP* 5.4 0.2 - - - -
1729A LEU* 3.2 19.5 + - + +
1730A GLN* 3.5 37.0 + - - +
1733A HIS* 1.3 98.5 - + - +
1735A ASN* 1.3 65.7 + - - +
1737A ARG* 3.4 7.1 + - - +
1738A ARG* 3.1 26.0 + - - +
2824A ZN 2.1 36.9 - - - -
2827A FMT 2.8 32.9 + - - +
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Residues in contact with ASN1735 (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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1680A ILE 5.0 0.8 + - - -
1681A ASP* 2.8 41.9 + - - +
1682A CYS* 4.1 2.0 - - - -
1730A GLN* 2.8 42.1 + - - +
1731A ARG* 4.7 3.0 - - - +
1734A HIS* 1.3 70.0 - - - +
1736A PRO* 1.3 66.1 - - + +
1738A ARG* 2.9 32.5 + - - +
1739A ILE* 2.9 35.5 + - + +
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Residues in contact with PRO1736 (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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1468A ILE* 4.0 19.1 - - + +
1470A VAL* 3.7 24.2 - - + -
1682A CYS* 3.9 16.1 - - + -
1683A PHE 5.1 1.3 - - - +
1730A GLN 3.5 8.7 - - - +
1731A ARG 3.5 19.7 - - - +
1732A LEU* 3.9 4.7 - - - -
1733A HIS 3.5 18.6 - - - +
1735A ASN* 1.3 93.1 - - + +
1737A ARG* 1.3 61.9 + - - +
1740A PHE* 3.2 29.3 + - + +
1742A LEU* 3.9 4.8 - - - +
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Residues in contact with ARG1737 (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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1465A PRO* 5.7 0.2 - - - +
1468A ILE* 3.7 15.7 - - + +
1733A HIS* 3.1 54.9 + - - +
1734A HIS* 3.4 12.3 + - - +
1735A ASN 3.2 0.2 - - - -
1736A PRO* 1.3 76.4 - - - +
1738A ARG* 1.3 58.5 + - - +
1741A HIS* 2.8 26.3 + - - -
1742A LEU* 3.0 31.0 + - - +
1743A PRO 4.7 1.3 + - - +
1744A PRO* 3.8 38.8 - - - +
1745A GLN 4.7 3.0 + - - +
2827A FMT 3.0 35.8 + - - +
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Residues in contact with ARG1738 (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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1635A THR* 5.5 3.8 - - - +
1681A ASP* 4.6 13.1 + - - -
1734A HIS* 3.1 12.8 + - - +
1735A ASN* 2.9 34.9 + - - +
1737A ARG* 1.3 78.2 - - - +
1739A ILE* 1.3 78.3 + - + +
1741A HIS* 3.8 18.3 + - - +
2827A FMT 4.7 11.9 - - - +
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Residues in contact with ILE1739 (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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1586A PRO* 4.1 7.6 - - - +
1611A HIS* 4.1 6.3 - - + +
1635A THR* 3.8 44.9 - - + +
1681A ASP* 3.9 9.6 - - + +
1682A CYS* 3.7 22.9 - - - -
1735A ASN* 2.9 24.5 + - + +
1738A ARG* 1.3 88.6 - - + +
1740A PHE* 1.3 85.5 + - + +
1741A HIS* 3.5 16.1 + - - -
2826A FMT 4.9 9.9 - - - +
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Residues in contact with PHE1740 (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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1470A VAL* 3.7 30.5 - - + -
1501A CYS* 5.3 2.7 - - - -
1534A PHE* 4.0 13.0 - + - -
1553A ALA* 4.4 7.9 - - + +
1586A PRO* 3.8 24.2 - - + -
1588A VAL* 3.5 28.3 - - + -
1611A HIS* 3.8 21.3 - + + -
1682A CYS* 5.1 3.1 - - - -
1736A PRO* 3.2 20.5 + - + +
1739A ILE* 1.3 92.3 - - + +
1741A HIS* 1.3 69.3 + - - +
1742A LEU* 3.2 18.5 + - + +
1810A ARG* 2.8 31.9 + - - +
2828A FMT 3.5 16.2 - - - -
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Residues in contact with HIS1741 (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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1584A HIS 3.9 12.2 + - - -
1585A LEU 5.5 0.2 - - - -
1586A PRO* 4.0 13.5 - - + +
1737A ARG 2.8 11.8 + - - -
1738A ARG* 3.8 17.4 + - - +
1739A ILE 3.5 12.0 + - - -
1740A PHE* 1.3 81.9 - - - +
1742A LEU* 1.3 63.5 + - - +
1743A PRO* 3.9 1.0 - - - +
1810A ARG* 2.9 15.8 + - - -
1814A GLN 5.0 1.4 - - - +
1815A GLY* 4.0 7.3 - - - +
1816A ALA 5.1 1.1 - - - +
1817A VAL* 3.6 41.6 - - + +
1818A PRO* 5.0 7.8 - - + +
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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