Contacts of the helix formed by residues 1618 - 1628 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1617A PRO* 1.4 75.1 - - - +
1619A MET* 1.4 56.2 + - - +
1620A ARG 3.5 3.1 - - - +
1621A LYS* 3.4 39.1 + - + +
1622A ILE* 3.2 31.7 + - + +
1804A PX4 3.3 36.2 - - + +
1635B SER* 3.7 18.7 + - - +
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Residues in contact with MET1619 (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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1613A VAL* 3.4 15.0 - - + +
1616A VAL* 3.4 29.4 - - + +
1617A PRO 3.0 6.0 + - - +
1618A GLN* 1.4 75.3 - - - +
1620A ARG* 1.4 58.1 + - - +
1621A LYS 3.3 0.4 - - - -
1622A ILE* 3.3 14.4 - - - +
1623A VAL* 3.1 31.7 + - - +
1804A PX4 4.0 35.4 - - + -
1635B SER* 5.8 0.2 - - - -
1638B ALA* 3.7 36.6 - - + +
1639B LEU* 3.9 25.2 - - - +
1642B LEU* 3.9 20.6 - - + -
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Residues in contact with ARG1620 (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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1565A ASP* 5.3 0.6 + - - -
1567A TRP* 3.4 67.5 + - + +
1613A VAL 3.2 13.5 + - - +
1614A THR* 2.8 39.5 + - - +
1615A ALA* 4.3 9.2 + - - +
1616A VAL 3.5 7.2 + - - +
1617A PRO* 4.7 7.4 - - + +
1618A GLN 3.5 0.4 - - - +
1619A MET* 1.4 74.1 - - - +
1621A LYS* 1.4 57.1 + - - +
1623A VAL* 3.8 8.3 - - + +
1624A SER* 2.7 38.8 + - - +
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Residues in contact with LYS1621 (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 GLN* 3.4 43.5 + - + +
1620A ARG* 1.4 77.1 - - - +
1622A ILE* 1.4 61.7 + - + +
1624A SER* 3.3 7.3 + - - -
1625A ALA* 2.9 28.0 + - + +
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Residues in contact with ILE1622 (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 GLN* 3.3 18.6 - - + +
1619A MET* 3.3 23.6 - - - +
1621A LYS* 1.4 81.3 - - + +
1623A VAL* 1.4 55.0 + - - +
1625A ALA* 3.0 10.9 + - + +
1626A LEU* 2.8 46.2 + - + +
1635B SER* 3.2 49.1 - - - +
1636B VAL* 4.3 10.1 - - + +
1639B LEU* 3.6 22.2 - - + -
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Residues in contact with VAL1623 (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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1567A TRP* 6.4 0.4 - - - +
1613A VAL* 4.1 23.8 - - + +
1614A THR* 6.0 2.9 - - - -
1619A MET 3.1 22.4 + - - +
1620A ARG* 3.8 12.3 - - + +
1621A LYS 3.4 0.2 - - - -
1622A ILE* 1.4 75.5 - - - +
1624A SER* 1.4 60.4 + - - +
1626A LEU* 3.5 8.3 + - + +
1627A ILE* 3.0 48.3 + - + +
1639B LEU* 3.6 22.0 - - + -
1643B PHE* 4.4 11.0 - - + -
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Residues in contact with SER1624 (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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1567A TRP* 4.4 15.8 + - - -
1620A ARG* 2.7 30.0 + - - +
1621A LYS* 3.6 5.8 - - - -
1623A VAL* 1.4 75.9 - - - +
1625A ALA* 1.3 60.4 + - - +
1627A ILE* 3.7 13.8 - - - +
1628A SER* 3.0 28.2 + - - -
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Residues in contact with ALA1625 (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 LYS* 2.9 15.7 + - + +
1622A ILE* 3.0 15.0 + - + +
1624A SER* 1.3 75.2 - - - +
1626A LEU* 1.3 60.9 + - + +
1628A SER* 2.7 20.2 + - - -
1629A VAL* 3.3 15.3 - - - +
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Residues in contact with LEU1626 (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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1622A ILE* 2.8 28.8 + - + +
1623A VAL* 3.8 6.3 - - + +
1625A ALA* 1.3 71.1 - - + +
1627A ILE* 1.3 61.1 + - - +
1628A SER 3.1 1.8 - - - -
1629A VAL* 2.9 28.9 + - - +
1630A ILE* 3.7 2.1 + - - +
1636B VAL* 5.6 6.1 - - + -
1639B LEU* 3.5 31.4 - - + -
1643B PHE* 6.0 1.1 - - + -
1710B PHE* 3.3 32.2 - - + -
1711B VAL* 4.3 14.8 - - + -
1714B ASN* 3.4 39.5 - - + +
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Residues in contact with ILE1627 (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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1623A VAL* 3.0 38.1 + - + +
1624A SER* 3.7 13.5 - - - +
1625A ALA 3.4 0.2 - - - -
1626A LEU* 1.3 75.3 - - - +
1628A SER* 1.3 58.3 + - - +
1629A VAL 3.3 0.2 - - - -
1630A ILE* 3.2 34.9 - - + +
1631A PRO* 3.5 9.5 - - - +
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Residues in contact with SER1628 (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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1624A SER 3.0 14.1 + - - -
1625A ALA* 2.7 25.5 + - - -
1627A ILE* 1.3 75.6 - - - +
1629A VAL* 1.4 60.1 + - - +
1631A PRO* 3.4 17.5 - - - +
1632A GLY 5.3 0.5 + - - -
1722A ASP* 4.5 5.9 - - - +
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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