Contacts of the helix formed by residues 1621 - 1635 (chain A) in PDB entry 4C8D
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 ASP1621 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1617A TYR* 5.7 0.2 - - - -
1618A ALA* 2.9 27.3 + - - +
1620A LYS* 1.3 100.9 - - - +
1622A ALA* 1.3 63.4 + - - +
1623A GLU 3.4 1.3 - - - -
1624A LYS* 3.3 18.8 + - - +
1625A ILE* 3.1 26.0 + - + +
1668A VAL* 3.7 42.5 - - + +
1669A GLN 4.8 6.4 + - - +
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Residues in contact with ALA1622 (chain A).
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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1561A LEU* 4.9 2.5 - - + -
1618A ALA 3.7 1.4 + - - -
1619A ALA 3.2 17.9 + - - +
1620A LYS 3.2 0.8 - - - -
1621A ASP* 1.3 78.0 - - - +
1623A GLU* 1.3 57.1 + - - +
1625A ILE* 3.3 3.0 + - - +
1626A ARG* 2.8 52.4 + - - +
1647A ILE* 3.5 7.2 - - + +
1686A GLY 4.7 3.6 - - - +
1688A PRO* 3.8 26.9 - - + -
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Residues in contact with GLU1623 (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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1620A LYS 4.3 5.5 + - - +
1621A ASP 3.4 0.6 - - - -
1622A ALA* 1.3 74.3 - - - +
1624A LYS* 1.3 57.3 + - + +
1626A ARG* 2.9 33.5 + - - +
1627A GLU* 2.8 37.3 + - - +
1630A ARG* 3.7 20.7 + - - -
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Residues in contact with LYS1624 (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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1620A LYS 5.3 2.7 + - - +
1621A ASP* 3.3 21.9 + - - +
1623A GLU* 1.3 77.6 - - + +
1625A ILE* 1.3 60.4 + - - +
1627A GLU* 4.4 1.6 - - - -
1628A LEU* 3.3 19.1 + - - +
1662A LEU* 4.3 1.9 - - - +
1666A TYR* 3.5 43.7 - - + +
1668A VAL* 3.8 25.4 - - + -
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Residues in contact with ILE1625 (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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1559A LEU* 3.9 25.1 - - + -
1617A TYR* 3.6 44.9 - - + -
1621A ASP 3.1 17.2 + - - +
1622A ALA 3.5 6.3 - - - +
1623A GLU 3.1 0.6 - - - -
1624A LYS* 1.3 74.4 - - - +
1626A ARG* 1.3 63.8 + - - +
1628A LEU* 3.4 3.7 + - + +
1629A LEU* 3.2 32.6 + - + +
1647A ILE* 4.3 5.8 - - + -
1654A LEU* 4.5 8.5 - - + -
1662A LEU* 3.8 27.4 - - + -
1668A VAL* 4.4 4.5 - - + -
1688A PRO* 4.2 13.9 - - + -
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Residues in contact with ARG1626 (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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1561A LEU* 4.0 24.9 - - - +
1622A ALA* 2.8 26.5 + - - +
1623A GLU* 2.9 59.3 + - - +
1625A ILE* 1.3 73.6 - - - +
1627A GLU* 1.3 56.4 + - - +
1629A LEU* 3.2 2.2 + - - -
1630A ARG* 2.8 56.0 + - - +
1645A ASP* 3.0 41.3 + - - +
1646A PRO* 3.7 11.6 - - + +
1647A ILE* 3.7 16.5 - - + +
1716A LEU* 6.1 0.8 - - - +
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Residues in contact with GLU1627 (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 GLU* 2.8 19.9 + - - +
1624A LYS* 3.7 6.3 - - - +
1626A ARG* 1.3 72.7 - - - +
1628A LEU* 1.3 62.3 + - - +
1630A ARG* 3.5 13.4 + - - +
1631A LYS* 3.3 22.3 + - - +
1666A TYR* 3.2 25.9 + - + +
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Residues in contact with LEU1628 (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 LYS 3.3 10.8 + - - +
1625A ILE* 3.6 9.9 - - + +
1626A ARG 3.3 0.6 - - - -
1627A GLU* 1.3 80.7 - - - +
1629A LEU* 1.3 65.8 + - + +
1631A LYS* 3.4 5.1 + - + +
1632A VAL* 3.0 38.5 + - + +
1654A LEU* 5.5 3.6 - - + -
1658A LEU* 4.0 17.9 - - + +
1661A ARG* 3.5 39.0 - - + +
1662A LEU* 3.7 39.3 - - + -
1665A GLU* 4.0 11.2 - - - +
1666A TYR* 3.6 15.6 + - + -
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Residues in contact with LEU1629 (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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1559A LEU* 4.1 21.5 - - + -
1625A ILE* 3.2 19.9 + - + +
1626A ARG 3.2 2.0 + - - -
1628A LEU* 1.3 85.4 - - + +
1630A ARG* 1.3 67.9 + - - +
1632A VAL* 4.4 4.5 - - + +
1633A GLY* 3.0 20.6 + - - -
1644A HIS* 5.8 0.3 + - - -
1646A PRO* 3.5 31.9 - - + +
1647A ILE* 4.9 2.0 - - + -
1652A TRP* 3.7 56.2 - - + -
1654A LEU* 3.9 18.8 - - + -
1658A LEU* 4.3 8.5 - - + -
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Residues in contact with ARG1630 (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 GLU* 3.7 18.4 + - - -
1626A ARG* 2.8 58.6 + - - +
1627A GLU* 3.8 9.2 - - - +
1629A LEU* 1.3 74.9 - - - +
1631A LYS* 1.3 58.3 + - - +
1633A GLY* 3.4 1.0 + - - -
1634A GLU* 3.0 29.0 + - - +
1638A GLN* 5.3 2.4 - - - +
1642A PRO 5.1 1.6 - - - +
1643A ASP* 4.1 14.9 + - - +
1644A HIS* 2.7 51.4 + - + +
1645A ASP* 4.5 1.6 - - - +
1646A PRO* 3.8 8.0 - - + +
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Residues in contact with LYS1631 (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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1627A GLU 3.3 10.3 + - - +
1628A LEU* 3.5 10.1 - - - +
1629A LEU 3.3 0.4 - - - -
1630A ARG* 1.3 76.4 - - - +
1632A VAL* 1.3 67.0 + - + +
1634A GLU* 3.3 9.1 + - - +
1635A GLU* 3.2 33.5 + - - +
1661A ARG* 5.0 6.7 - - - +
1665A GLU* 6.1 0.7 - - - +
1666A TYR* 5.7 1.8 - - - +
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Residues in contact with VAL1632 (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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1628A LEU* 3.0 36.1 + - + +
1629A LEU* 4.1 8.7 - - + +
1630A ARG 3.4 0.2 - - - -
1631A LYS* 1.3 75.4 - - - +
1633A GLY* 1.3 63.7 + - - +
1635A GLU* 3.1 32.0 + - - +
1636A GLN* 3.8 1.7 + - - +
1652A TRP* 3.9 21.8 - - + -
1658A LEU* 4.6 21.1 - - + -
1661A ARG* 4.2 18.6 - - - +
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Residues in contact with GLY1633 (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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1629A LEU 3.0 15.9 + - - -
1630A ARG 3.8 0.9 - - - -
1632A VAL* 1.3 77.4 - - - +
1634A GLU* 1.3 56.8 + - - +
1636A GLN* 2.9 23.0 + - - +
1637A GLY 3.3 12.5 + - - +
1638A GLN* 4.6 4.5 - - - -
1652A TRP* 3.7 21.9 - - - -
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Residues in contact with GLU1634 (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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1630A ARG 3.0 14.1 + - - +
1631A LYS* 3.3 11.8 + - - +
1633A GLY* 1.3 69.8 - - - +
1635A GLU* 1.3 58.3 + - + +
1636A GLN 3.0 9.6 + - - -
1637A GLY* 3.1 11.4 + - - -
1638A GLN* 3.9 24.7 + - + +
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Residues in contact with GLU1635 (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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1631A LYS* 3.2 22.0 + - - +
1632A VAL* 3.1 24.6 + - - +
1634A GLU* 1.3 76.9 - - - +
1636A GLN* 1.3 57.5 + - - +
1661A ARG* 4.0 27.5 + - - -
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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