Contacts of the helix formed by residues 1605 - 1616 (chain D) in PDB entry 5EK0
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 ARG1605 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1649A ILE* 3.8 16.2 + - - +
1653A GLN* 2.8 45.0 + - - +
1521D MET* 3.1 69.9 + - + +
1524D GLU* 3.1 17.1 + - - -
1540D ASN* 5.2 1.0 - - - +
1602D ARG* 3.2 45.1 + - - +
1604D ALA* 1.4 78.8 - - - +
1606D ILE* 1.4 67.3 + - + +
1607D GLY 3.3 0.9 + - - -
1608D ARG* 3.3 30.5 + - - +
1609D ILE 3.9 0.2 + - - -
1806D 5P2 3.5 35.6 + - - +
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Residues in contact with ILE1606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1646A ILE* 3.8 20.6 - - + -
1649A ILE* 3.6 21.1 - - + -
1650A MET* 3.6 38.4 - - + -
1653A GLN* 3.5 24.7 - - - +
1521D MET* 4.2 0.2 - - - -
1603D LEU* 3.3 24.7 + - + +
1604D ALA 3.2 0.2 - - - -
1605D ARG* 1.4 80.5 - - + +
1607D GLY* 1.3 53.2 + - - +
1608D ARG 3.3 0.2 - - - -
1609D ILE* 2.9 10.3 + - + +
1610D LEU* 2.7 43.8 + - + +
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Residues in contact with GLY1607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1574D VAL* 3.4 31.1 - - - +
1577D ILE* 5.0 8.7 - - - -
1603D LEU 4.5 0.6 + - - -
1604D ALA* 3.2 12.9 + - - +
1605D ARG 3.2 1.8 - - - -
1606D ILE* 1.3 78.0 - - - +
1608D ARG* 1.3 59.9 + - - +
1609D ILE 3.3 0.7 + - - -
1610D LEU* 3.4 17.3 + - - +
1611D ARG 3.5 6.6 + - - -
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Residues in contact with ARG1608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514D ILE* 3.2 22.3 - - - +
1517D ASN* 2.8 26.1 + - - +
1521D MET* 3.5 18.4 - - - -
1540D ASN* 2.8 33.1 + - - -
1544D ILE* 3.5 22.8 - - - +
1547D PHE* 4.0 25.7 - - + -
1574D VAL* 3.8 14.6 - - + +
1575D VAL* 6.0 0.9 - - + -
1578D SER* 3.3 30.8 + - - +
1604D ALA 4.5 0.4 + - - -
1605D ARG* 3.3 16.3 + - - +
1606D ILE 3.3 0.4 - - - -
1607D GLY* 1.3 75.7 - - - +
1609D ILE* 1.3 60.3 + - + +
1611D ARG* 3.7 10.8 - - - +
1806D 5P2 2.9 34.8 + - - -
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Residues in contact with ILE1609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1646A ILE* 3.8 33.4 - - + +
1649A ILE* 4.4 8.1 - - + -
1514D ILE* 3.5 21.1 - - + +
1517D ASN* 3.7 12.3 - - + +
1518D MET* 3.4 53.8 - - + +
1521D MET* 3.8 21.5 - - + -
1605D ARG 3.9 0.2 + - - -
1606D ILE* 2.9 20.4 + - - +
1608D ARG* 1.3 78.4 - - - +
1610D LEU* 1.3 61.6 + - - +
1611D ARG 3.1 2.2 - - - -
1612D LEU* 3.2 27.4 + - + +
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Residues in contact with LEU1610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1643A PHE* 6.0 7.4 - - + -
1646A ILE* 4.8 19.0 - - + +
1570D PHE* 4.1 23.6 - - + -
1606D ILE* 2.7 29.5 + - + +
1607D GLY* 3.4 11.9 + - - +
1609D ILE* 1.3 68.0 - - - +
1611D ARG* 1.3 58.0 + - - +
1612D LEU* 3.0 11.8 + - - +
1613D VAL* 3.3 38.6 + - + +
1614D THR* 4.3 0.6 + - + -
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Residues in contact with ARG1611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1510D ILE* 3.8 19.2 - - - +
1514D ILE* 3.9 23.2 - - + +
1547D PHE* 3.7 23.0 - - - +
1550D GLU* 2.8 44.0 + - - -
1554D ARG* 4.3 0.6 - - - +
1570D PHE* 3.6 22.6 - - + -
1571D ASP* 3.0 37.7 + - - +
1574D VAL* 3.7 27.3 - - + +
1575D VAL* 6.3 0.4 - - - +
1607D GLY 3.5 4.3 + - - +
1608D ARG* 3.7 15.4 + - - +
1609D ILE 3.1 0.2 - - - -
1610D LEU* 1.3 76.1 - - - +
1612D LEU* 1.4 50.9 + - - +
1613D VAL 3.3 0.4 - - - -
1614D THR* 3.6 7.0 - - - +
1615D ALA* 2.7 44.0 + - - +
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Residues in contact with LEU1612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1642A LEU* 3.8 30.3 - - + -
1803A PX4 4.7 10.3 - - + -
1511D ILE* 5.3 1.8 - - + +
1514D ILE* 3.8 28.2 - - + +
1515D VAL* 4.4 21.3 - - + +
1518D MET* 3.7 34.8 - - + -
1609D ILE* 3.2 23.9 + - + +
1610D LEU 3.0 2.4 + - - +
1611D ARG* 1.4 76.6 - - - +
1613D VAL* 1.3 60.9 + - - +
1615D ALA* 4.8 2.0 - - - -
1616D VAL* 3.2 45.4 + - + +
1619D MET* 4.1 2.1 - - - +
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Residues in contact with VAL1613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1639A LEU* 3.8 26.2 - - + -
1642A LEU* 3.7 22.6 - - + +
1643A PHE* 4.2 14.6 - - + -
1646A ILE* 5.6 2.7 - - + -
1610D LEU* 3.3 30.5 + - + +
1612D LEU* 1.3 77.6 - - - +
1614D THR* 1.3 69.0 + - + +
1616D VAL 3.5 1.7 - - - +
1619D MET* 3.2 12.1 - - + +
1620D ARG* 3.1 28.2 + - - -
1623D VAL* 3.9 21.8 - - + -
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Residues in contact with THR1614 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1567D TRP* 3.8 35.2 - - + +
1570D PHE* 3.3 41.4 - - + -
1571D ASP* 3.7 7.8 + - - -
1610D LEU 4.8 0.2 - - - +
1611D ARG* 3.3 9.2 + - - +
1613D VAL* 1.3 88.3 - - + +
1615D ALA* 1.3 59.3 + - - +
1620D ARG* 2.9 31.1 + - - +
1623D VAL* 6.1 2.9 - - + -
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Residues in contact with ALA1615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1507D THR* 4.9 1.6 + - - -
1510D ILE* 5.7 2.0 - - + -
1511D ILE* 3.4 17.1 - - + +
1514D ILE* 3.9 24.5 - - + -
1571D ASP* 5.0 4.9 - - - +
1611D ARG* 2.7 34.5 + - - +
1612D LEU* 4.6 0.9 - - - +
1614D THR* 1.3 73.5 + - - +
1616D VAL* 1.3 62.3 + - - +
1617D PRO* 3.3 5.9 - - - +
1620D ARG* 3.3 16.3 + - - +
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Residues in contact with VAL1616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1803A PX4 5.2 10.5 - - + -
1511D ILE* 4.0 28.0 - - + -
1514D ILE* 6.3 0.4 - - + -
1612D LEU* 3.2 36.3 + - + +
1613D VAL 3.5 2.4 - - - +
1615D ALA* 1.3 74.2 - - - +
1617D PRO* 1.4 65.9 - - + +
1618D GLN* 2.9 36.3 + - + +
1619D MET* 3.2 16.6 + - + -
1620D ARG* 3.1 20.8 + - - +
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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