Contacts of the helix formed by residues 1666 - 1676 (chain A) in PDB entry 4C6J
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 SER1666 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1646A SER* 4.2 1.8 - - - -
1647A HIS* 3.6 27.8 - - - -
1665A GLY* 1.3 76.3 - - - +
1667A ARG* 1.3 65.0 + - - +
1668A GLN* 3.2 27.8 + - - +
1669A ASP* 3.0 38.8 + - - -
1670A VAL* 3.1 13.3 + - - +
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Residues in contact with ARG1667 (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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1646A SER* 4.3 10.6 + - - +
1647A HIS* 5.4 1.2 - - - +
1648A ASP* 2.6 45.0 + - - +
1666A SER* 1.3 73.8 - - - +
1668A GLN* 1.3 76.4 + - + +
1670A VAL* 3.4 6.6 + - - +
1671A GLU* 2.9 47.1 + - - +
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Residues in contact with GLN1668 (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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1618A LYS* 4.4 14.5 - - + +
1666A SER* 3.1 22.2 + - - +
1667A ARG* 1.3 96.6 + - + +
1669A ASP* 1.3 64.4 + - - +
1671A GLU* 3.9 11.1 - - - +
1672A ALA* 3.0 24.6 + - - +
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Residues in contact with ASP1669 (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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1616A ALA 3.8 14.1 - - - +
1617A ARG* 3.5 15.1 - - - +
1618A LYS* 2.9 35.5 + - - +
1619A GLU 4.6 0.3 + - - -
1642A HIS 5.4 0.2 - - - -
1647A HIS* 5.3 0.7 - - - -
1665A GLY* 3.5 9.3 - - - -
1666A SER* 3.0 38.9 + - - +
1668A GLN* 1.3 76.2 - - - +
1670A VAL* 1.3 63.7 + - + +
1672A ALA* 3.2 4.0 + - - +
1673A LEU* 3.1 27.3 + - - +
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Residues in contact with VAL1670 (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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1642A HIS* 3.6 17.0 - - - +
1643A LEU 3.5 26.9 - - - +
1644A PHE* 5.5 0.4 - - - -
1645A LEU 3.4 25.8 - - - +
1646A SER* 4.0 9.6 - - - -
1665A GLY* 4.7 4.7 - - - +
1666A SER 3.1 13.4 + - - +
1667A ARG* 3.7 8.1 - - - +
1669A ASP* 1.3 75.2 - - + +
1671A GLU* 1.3 66.8 + - + +
1673A LEU* 3.2 12.8 + - - +
1674A TRP* 3.2 28.1 + - + -
1722A ARG* 5.4 1.3 - - - +
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Residues in contact with GLU1671 (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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1667A ARG* 2.9 32.5 + - - +
1668A GLN* 3.9 10.7 - - - +
1670A VAL* 1.3 79.6 - - + +
1672A ALA* 1.3 58.4 + - - +
1674A TRP* 3.4 7.8 + - - +
1675A GLU* 2.9 30.6 + - - +
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Residues in contact with ALA1672 (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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1618A LYS* 3.6 38.6 - - + -
1621A ILE* 4.1 3.0 - - + +
1668A GLN 3.0 18.6 + - - +
1669A ASP 3.2 4.9 + - - +
1671A GLU* 1.3 73.9 - - - +
1673A LEU* 1.3 65.5 + - - +
1675A GLU* 4.3 4.0 - - - -
1676A ASN* 2.9 38.4 + - - +
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Residues in contact with LEU1673 (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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1615A VAL* 3.8 32.5 - - + +
1616A ALA 4.0 15.0 - - - +
1617A ARG 4.2 7.2 - - - +
1621A ILE* 3.8 33.4 - - + -
1638A VAL* 4.1 11.2 - - + -
1642A HIS* 3.5 29.6 - - + +
1643A LEU* 3.8 11.4 - - + -
1669A ASP 3.1 16.5 + - - +
1670A VAL* 3.2 6.0 + - - +
1672A ALA* 1.3 76.0 - - - +
1674A TRP* 1.3 62.8 + - - +
1676A ASN* 3.2 5.1 + - - -
1677A MET* 3.2 17.7 + - - -
1680A ILE* 3.6 14.7 - - + +
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Residues in contact with TRP1674 (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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1643A LEU* 3.0 41.7 + - + +
1644A PHE* 3.7 25.8 - + - -
1670A VAL* 3.2 33.0 + - + +
1671A GLU* 3.8 8.5 - - - +
1673A LEU* 1.3 77.1 - - - +
1675A GLU* 1.3 61.1 + - - +
1676A ASN 3.2 0.9 + - - -
1677A MET* 3.2 44.5 + - + +
1714A LEU* 5.0 3.4 - - + -
1717A ALA* 3.8 22.4 - - + -
1722A ARG* 3.2 64.6 - - + +
1723A LEU* 4.1 10.8 - - + -
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Residues in contact with GLU1675 (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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1671A GLU 2.9 18.5 + - - +
1672A ALA* 3.8 7.0 - - - +
1674A TRP* 1.3 76.6 - - - +
1676A ASN* 1.3 68.7 + - - +
1677A MET 3.4 2.2 + - - -
1678A ALA* 5.1 0.5 + - - +
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Residues in contact with ASN1676 (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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1621A ILE* 3.9 21.1 - - + +
1622A LEU* 3.9 22.5 - - - +
1625A LYS* 3.5 29.5 + - - +
1672A ALA* 2.9 31.7 + - - +
1673A LEU 3.3 5.1 - - - +
1674A TRP 3.1 0.4 - - - -
1675A GLU* 1.3 91.3 - - - +
1677A MET* 1.3 63.8 - - - +
1678A ALA* 3.1 4.3 - - - +
1679A VAL* 2.9 23.6 + - + +
1680A ILE* 3.7 6.2 + - - +
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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