Contacts of the helix formed by residues 1618 - 1628 (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 GLN1618 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1508D LYS* 6.0 0.2 + - - -
1616D VAL* 2.9 22.0 + - + +
1617D PRO* 1.3 86.0 - - - +
1619D MET* 1.4 69.1 + - + +
1620D ARG* 3.2 4.3 - - - +
1621D LYS* 3.3 18.4 + - - +
1622D ILE* 3.2 32.3 + - + +
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Residues in contact with MET1619 (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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1638A ALA* 4.1 10.1 - - + +
1639A LEU* 3.7 41.1 - - + +
1642A LEU* 3.8 38.6 - - + -
1803A PX4 5.5 6.3 - - + -
1612D LEU 4.4 2.0 - - - +
1613D VAL* 3.2 21.9 - - + +
1616D VAL* 3.2 28.4 + - + +
1618D GLN* 1.4 77.4 - - + +
1620D ARG* 1.3 62.8 + - - +
1621D LYS 3.3 0.2 - - - -
1622D ILE* 3.9 20.2 - - - -
1623D VAL* 3.3 30.1 + - - +
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Residues in contact with ARG1620 (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* 5.4 2.4 + - - -
1567D TRP* 3.6 42.1 - - + +
1613D VAL 3.1 9.4 + - - +
1614D THR 2.9 22.1 + - - +
1615D ALA* 3.3 23.6 + - - +
1616D VAL 3.1 7.8 + - - +
1617D PRO* 3.5 28.6 - - + +
1618D GLN 4.2 4.7 - - - +
1619D MET* 1.3 77.0 - - - +
1621D LYS* 1.4 59.7 + - - +
1623D VAL* 3.6 5.0 + - - +
1624D SER* 3.4 25.3 + - - -
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Residues in contact with LYS1621 (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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1618D GLN* 3.3 18.7 + - - +
1620D ARG* 1.4 76.4 - - - +
1622D ILE* 1.4 61.7 + - + +
1623D VAL 3.3 0.2 + - - -
1624D SER* 3.3 6.2 + - - -
1625D ALA* 3.0 32.9 + - + +
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Residues in contact with ILE1622 (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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1635A SER* 3.4 50.0 - - - +
1636A VAL* 4.3 21.5 - - + -
1638A ALA* 5.7 0.2 - - + -
1639A LEU* 4.5 15.7 - - + -
1618D GLN* 3.2 22.6 + - + +
1619D MET* 3.8 25.5 + - - +
1620D ARG 3.6 0.2 - - - -
1621D LYS* 1.4 75.7 - - + +
1623D VAL* 1.4 58.7 + - - +
1625D ALA* 3.6 9.0 + - + +
1626D LEU* 3.1 36.7 + - + +
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Residues in contact with VAL1623 (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* 3.7 23.3 - - + -
1643A PHE* 4.7 7.6 - - + -
1567D TRP* 5.5 7.2 - - + -
1613D VAL* 3.9 23.3 - - + -
1614D THR* 6.1 2.5 - - + -
1619D MET 3.3 20.1 + - - +
1620D ARG* 3.7 6.7 - - - +
1621D LYS 3.2 1.2 - - - -
1622D ILE* 1.4 74.4 - - - +
1624D SER* 1.4 61.8 + - - +
1626D LEU* 3.1 11.0 + - - +
1627D ILE* 3.0 42.4 + - + +
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Residues in contact with SER1624 (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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1567D TRP* 4.0 20.1 - - - -
1620D ARG 3.4 13.6 + - - -
1621D LYS* 3.3 6.0 + - - -
1623D VAL* 1.4 75.6 - - - +
1625D ALA* 1.4 59.6 + - - +
1626D LEU 3.2 0.7 - - - -
1627D ILE* 3.6 12.9 - - - +
1628D SER* 3.1 30.3 + - - -
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Residues in contact with ALA1625 (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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1621D LYS* 3.0 19.4 + - + +
1622D ILE* 3.7 12.6 - - + +
1623D VAL 3.3 0.2 - - - -
1624D SER* 1.4 75.7 - - - +
1626D LEU* 1.4 62.4 + - + +
1628D SER* 3.2 16.6 + - - -
1629D VAL* 3.4 13.3 - - - +
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Residues in contact with LEU1626 (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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1636A VAL* 5.6 6.1 - - + -
1639A LEU* 3.8 27.6 - - + -
1710A PHE* 3.1 41.0 - - + -
1711A VAL* 4.2 24.7 - - + -
1714A ASN* 3.6 33.7 - - + +
1622D ILE* 3.1 23.1 - - + +
1623D VAL* 3.1 9.5 + - + +
1625D ALA* 1.4 80.4 - - + +
1627D ILE* 1.3 65.3 + - + +
1628D SER 3.5 0.4 - - - -
1629D VAL* 3.4 12.0 - - - +
1630D ILE* 3.9 0.2 - - - +
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Residues in contact with ILE1627 (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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1710A PHE* 6.0 1.1 - - + -
1623D VAL* 3.0 32.3 + - + +
1624D SER* 3.3 14.6 + - - +
1626D LEU* 1.3 74.5 - - + +
1628D SER* 1.4 58.4 + - - +
1629D VAL 3.0 10.7 + - - -
1630D ILE* 3.2 36.5 + - + +
1631D PRO* 3.4 8.5 - - + +
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Residues in contact with SER1628 (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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1624D SER 3.1 13.2 + - - -
1625D ALA* 3.2 21.0 + - - -
1627D ILE* 1.4 74.5 - - - +
1629D VAL* 1.3 60.4 + - - +
1631D PRO* 3.3 17.4 - - - +
1632D GLY 5.0 0.3 + - - -
1722D ASP* 5.0 3.6 - - - +
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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