Contacts of the helix formed by residues 1617 - 1630 (chain A) in PDB entry 4C6C
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 ARG1617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1592A GLU* 2.9 32.9 + - - +
1593A GLN* 3.3 43.7 - - - +
1615A VAL 3.9 0.2 - - - -
1616A ALA* 1.3 85.5 - - + +
1618A LYS* 1.3 66.3 + - - +
1619A GLU* 3.9 13.9 - - + +
1620A GLU* 2.9 40.6 + - + +
1621A ILE* 3.0 23.9 + - - +
1662A PRO* 3.9 11.3 - - - +
1663A GLU* 3.8 34.2 + - - +
1665A GLY* 5.8 1.8 - - - -
1669A ASP* 3.5 17.3 - - - +
1673A LEU* 4.1 7.4 - - - +
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Residues in contact with LYS1618 (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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1617A ARG* 1.3 70.4 - - - +
1619A GLU* 1.3 63.5 + - - +
1620A GLU 3.2 0.2 + - - -
1621A ILE* 3.5 2.0 - - - +
1622A LEU* 3.0 53.8 + - + +
1668A GLN* 4.6 14.0 - - + +
1669A ASP* 2.9 23.5 + - - +
1672A ALA* 3.5 33.4 - - + -
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Residues in contact with GLU1619 (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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1593A GLN* 3.2 54.9 - - - +
1594A GLN* 4.1 4.5 + - - +
1596A VAL* 6.2 0.7 - - + -
1617A ARG* 3.2 10.4 - - + +
1618A LYS* 1.3 80.5 - - - +
1620A GLU* 1.3 59.6 + - - +
1622A LEU* 4.0 4.5 - - - +
1623A LEU* 3.1 27.6 + - + +
1669A ASP* 4.6 0.6 + - - -
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Residues in contact with GLU1620 (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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1591A ALA 4.8 3.1 - - - +
1592A GLU* 3.4 6.8 - - - +
1593A GLN* 2.8 41.5 + - - +
1596A VAL* 4.6 11.9 - - + -
1612A ILE* 6.4 0.4 - - + -
1614A HIS 4.5 1.4 - - - +
1615A VAL* 3.8 15.3 - - + -
1616A ALA* 2.8 30.0 + - - +
1617A ARG* 2.9 41.9 + - + +
1619A GLU* 1.3 74.8 - - + +
1621A ILE* 1.3 67.8 + - - +
1623A LEU* 3.2 5.8 + - - +
1624A ILE* 3.0 30.4 + - + +
1662A PRO* 5.9 0.7 - - - -
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Residues in contact with ILE1621 (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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1615A VAL* 3.8 17.9 - - + +
1617A ARG 3.0 10.7 + - - +
1618A LYS* 3.5 15.7 - - - +
1620A GLU* 1.3 76.9 - - - +
1622A LEU* 1.3 63.6 + - + +
1624A ILE* 3.4 3.0 + - + +
1625A LYS* 2.9 28.6 + - - +
1636A CYS* 4.1 11.4 - - - -
1672A ALA* 4.1 5.4 - - + +
1673A LEU* 3.8 23.6 - - + -
1676A ASN* 3.9 38.8 - - + +
1679A VAL* 3.7 22.8 - - + +
1680A ILE* 4.0 22.9 - - + -
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Residues in contact with LEU1622 (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 LYS* 3.0 50.8 + - + +
1619A GLU* 4.1 4.0 - - - +
1621A ILE* 1.3 76.4 - - + +
1623A LEU* 1.3 64.4 + - - +
1625A LYS* 3.4 14.5 + - + +
1626A ALA* 3.0 23.7 + - - +
1676A ASN* 3.8 31.2 - - - +
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Residues in contact with LEU1623 (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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1596A VAL* 4.0 24.0 - - + -
1597A ALA* 4.2 19.3 - - + -
1600A LEU* 3.3 31.6 - - + -
1619A GLU* 3.1 19.6 + - + +
1620A GLU 3.6 4.7 - - - +
1622A LEU* 1.3 77.2 - - - +
1624A ILE* 1.3 63.7 + - - +
1626A ALA* 3.2 10.9 + - + +
1627A ALA* 3.0 19.0 + - + +
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Residues in contact with ILE1624 (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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1596A VAL* 4.1 26.0 - - + -
1600A LEU* 4.9 0.9 - - + -
1612A ILE* 4.2 7.9 - - + -
1615A VAL* 3.5 32.8 - - + -
1620A GLU* 3.0 20.5 + - + +
1621A ILE* 3.8 4.7 - - - +
1623A LEU* 1.3 76.8 - - + +
1625A LYS* 1.3 58.3 + - - +
1627A ALA* 3.1 7.9 + - - +
1628A LYS* 2.9 45.6 + - + +
1634A VAL* 4.5 14.4 - - + -
1636A CYS* 4.0 17.3 - - + -
1679A VAL* 3.8 17.3 - - + -
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Residues in contact with LYS1625 (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 ILE 2.9 18.8 + - - +
1622A LEU* 3.6 19.3 - - + +
1624A ILE* 1.3 76.1 - - - +
1626A ALA* 1.3 55.4 + - - +
1628A LYS* 3.3 6.0 + - - +
1629A ALA* 3.0 28.9 + - + +
1676A ASN* 3.5 24.3 + - - +
1678A ALA* 6.2 1.8 - - - +
1679A VAL* 3.8 25.7 - - + +
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Residues in contact with ALA1626 (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 LEU 3.0 13.7 + - - +
1623A LEU* 3.2 15.2 + - + +
1625A LYS* 1.3 76.6 - - - +
1627A ALA* 1.3 62.1 + - - +
1629A ALA* 3.2 9.1 + - - +
1630A ARG* 3.2 26.9 + - + +
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Residues in contact with ALA1627 (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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1600A LEU* 4.1 16.6 - - + -
1623A LEU* 3.0 13.4 + - + +
1624A ILE 3.5 7.6 - - - +
1626A ALA* 1.3 76.1 - - - +
1628A LYS* 1.3 63.4 + - - +
1630A ARG* 3.1 9.3 + - - -
1632A LEU* 3.1 46.5 + - + +
1634A VAL* 3.9 17.3 - - + -
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Residues in contact with LYS1628 (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 ILE* 2.9 31.2 + - - +
1625A LYS* 3.7 5.8 - - - +
1627A ALA* 1.3 76.1 - - - +
1629A ALA* 1.3 58.2 + - - +
1631A GLY* 2.9 20.0 + - - +
1632A LEU 4.4 7.9 - - - +
1634A VAL* 3.3 32.3 - - + +
1635A THR* 5.3 0.2 - - - -
1678A ALA 4.8 2.4 + - - -
1679A VAL* 2.8 43.4 + - + +
1681A ASP* 2.8 27.9 + - - -
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Residues in contact with ALA1629 (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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1625A LYS* 3.0 14.7 + - + +
1626A ALA* 3.5 11.9 - - - +
1627A ALA 3.2 0.4 - - - -
1628A LYS* 1.3 76.3 - - - +
1630A ARG* 1.3 62.5 + - + +
1631A GLY 3.2 1.1 + - - -
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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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1626A ALA* 3.2 13.2 + - + +
1627A ALA* 3.1 10.1 + - - +
1629A ALA* 1.3 78.7 - - + +
1631A GLY* 1.3 61.0 + - - +
1632A LEU* 3.3 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