Contacts of the helix formed by residues 1700 - 1709 (chain E) in PDB entry 3COJ
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 THR1700 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1655E SER* 3.1 15.0 + - - +
1656E GLY* 5.0 9.2 - - - +
1689E MET* 3.4 9.0 - - + +
1698E GLU* 4.7 13.0 - - + -
1699E ARG* 1.3 76.1 - - - +
1701E LEU* 1.3 61.0 + - - +
1703E TYR* 3.0 34.6 + - - +
1704E PHE* 3.0 20.7 - - - -
1263M SEP 3.5 27.4 - - - +
1264M PRO* 3.4 19.5 - - - +
1265M THR* 5.0 1.8 - - - -
1266M PHE* 4.1 0.7 - - - -
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Residues in contact with LEU1701 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1679E LEU* 6.4 1.1 - - + -
1680E ILE* 5.0 2.9 - - + -
1700E THR* 1.3 73.6 - - - +
1702E LYS* 1.3 80.2 - - + +
1704E PHE* 3.6 11.6 + - - +
1705E LEU* 3.2 35.3 + - + +
1774E ASN 4.7 1.3 - - - +
1775E MET* 3.7 33.9 - - + -
1776E PRO* 4.1 9.2 - - + -
1779E GLN* 3.3 33.4 - - + +
1783E MET* 5.2 2.5 - - + -
1264M PRO* 4.1 21.7 - - + +
1266M PHE* 3.9 10.8 - - + -
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Residues in contact with LYS1702 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1653E VAL* 4.0 8.2 - - + +
1654E VAL 3.1 15.6 + - - -
1655E SER* 3.4 27.6 - - - +
1678E ASN 3.0 26.9 + - - -
1679E LEU* 3.9 19.6 - - - +
1680E ILE* 3.8 31.2 - - + +
1687E VAL* 3.6 20.3 - - + +
1700E THR 3.3 0.4 - - - -
1701E LEU* 1.3 85.9 - - + +
1703E TYR* 1.3 58.9 + - - +
1705E LEU* 3.8 1.1 - - - +
1706E GLY 2.9 22.2 + - - -
1263M SEP 2.8 30.2 + - - +
1264M PRO* 6.5 0.2 - - + -
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Residues in contact with TYR1703 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1687E VAL* 4.7 1.3 - - - -
1689E MET* 3.6 20.6 - - + -
1697E CYS* 3.4 28.5 - - - -
1698E GLU 4.2 7.9 - - - -
1699E ARG* 4.4 11.7 - - - -
1700E THR* 3.0 30.2 + - - +
1702E LYS* 1.3 77.0 - - - +
1704E PHE* 1.3 73.1 + + - +
1706E GLY* 3.1 10.6 + - - -
1707E ILE* 3.2 43.9 + - + +
1713E VAL* 4.2 6.5 - - + +
1736E VAL* 4.3 15.3 - - + -
1738E GLY* 4.1 10.6 + - - -
1739E ASP* 2.5 33.4 + - - -
1742E ASN* 4.5 0.5 + - - -
1749E PRO* 4.5 5.6 - - + +
1843E ALA* 4.4 11.5 + - + -
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Residues in contact with PHE1704 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1699E ARG* 3.2 46.0 - - - -
1700E THR 3.0 27.4 + - - -
1701E LEU* 3.9 7.4 - - - +
1703E TYR* 1.3 83.1 - + - +
1705E LEU* 1.3 52.2 + - - +
1707E ILE* 3.1 8.7 + - - +
1708E ALA* 2.8 34.9 + - - +
1775E MET* 4.3 8.1 - - + -
1783E MET* 3.5 24.7 - - + -
1839E LEU* 3.5 50.7 - - + -
1842E VAL* 3.7 11.0 - - + +
1843E ALA* 4.7 4.9 - - + -
1266M PHE* 3.6 25.4 - + - -
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Residues in contact with LEU1705 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1680E ILE* 4.0 32.7 - - + +
1701E LEU* 3.2 32.3 + - + +
1702E LYS 4.2 0.9 - - - +
1704E PHE* 1.3 79.6 - - - +
1706E GLY* 1.3 57.5 + - - +
1708E ALA* 3.7 4.0 - - + +
1709E GLY* 3.1 24.1 + - - -
1711E LYS* 4.6 2.3 + - - +
1779E GLN* 4.1 20.2 - - - +
1782E TRP* 3.6 38.1 - - + -
1783E MET* 3.8 37.2 - - + +
1786E LEU* 4.4 9.0 - - + +
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Residues in contact with GLY1706 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1680E ILE* 4.4 0.9 - - - -
1687E VAL* 3.9 22.0 - - - -
1702E LYS 2.9 16.0 + - - -
1703E TYR 3.1 5.3 + - - -
1705E LEU* 1.3 76.8 - - - +
1707E ILE* 1.3 60.4 + - - +
1710E GLY 3.5 1.2 + - - -
1711E LYS* 3.0 35.6 + - - +
1713E VAL* 3.7 11.2 - - - -
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Residues in contact with ILE1707 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1703E TYR* 3.2 49.9 + - + +
1704E PHE* 3.1 7.5 + - - +
1706E GLY* 1.3 73.0 - - - +
1708E ALA* 1.3 67.3 + - - +
1710E GLY* 3.1 9.5 + - - -
1713E VAL* 4.1 7.2 - - + -
1748E GLY 4.5 1.1 - - - +
1749E PRO* 3.9 24.7 - - + -
1752E ALA* 3.3 31.8 - - + +
1842E VAL* 3.1 27.1 - - + +
1843E ALA* 3.9 19.3 - - - +
1845E TYR* 3.7 14.1 - - + -
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Residues in contact with ALA1708 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704E PHE 2.8 19.9 + - - +
1705E LEU* 3.7 11.9 - - - +
1706E GLY 3.4 0.2 - - - -
1707E ILE* 1.3 74.3 - - - +
1709E GLY* 1.3 58.5 + - - +
1710E GLY* 3.1 5.0 + - - -
1756E GLN* 5.0 2.6 + - - +
1783E MET* 3.9 22.2 - - + +
1786E LEU* 3.5 38.2 - - + +
1787E CYS* 4.6 4.9 - - - -
1842E VAL* 3.9 10.9 - - + +
1845E TYR* 4.3 8.7 + - - -
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Residues in contact with GLY1709 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1705E LEU 3.1 9.2 + - - -
1707E ILE 3.4 0.2 - - - -
1708E ALA* 1.3 77.0 - - - +
1710E GLY* 1.3 61.2 + - - +
1711E LYS* 3.3 28.8 - - - +
1756E GLN* 4.4 6.3 + - - -
1786E LEU* 3.7 21.3 - - - +
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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