Contacts of the helix formed by residues 1579 - 1592 (chain A) in PDB entry 3H6N
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 THR1579 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1577A THR 3.4 4.6 + - - +
1578A ASP* 1.3 75.4 - - - +
1580A LEU* 1.3 60.2 + - - +
1581A THR* 3.6 6.8 + - - -
1582A GLN* 3.0 39.6 + - - +
1583A VAL* 2.9 23.6 + - - +
1622A ASP* 3.6 12.6 - - - -
1636A LEU* 3.7 30.3 - - + -
1637A ASN 3.5 9.2 - - - +
1638A THR* 4.3 4.7 - - + +
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Residues in contact with LEU1580 (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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1579A THR* 1.3 69.2 - - - +
1581A THR* 1.3 58.9 + - - +
1582A GLN 3.3 0.2 - - - -
1583A VAL* 3.5 13.3 - - + +
1584A LYS* 2.9 36.6 + - + +
1608A LEU* 4.4 12.3 - - + -
1620A LEU* 3.1 40.8 - - + +
1621A ARG* 3.3 22.2 - - - +
1622A ASP* 2.9 11.9 + - - +
1637A ASN* 3.4 8.8 + - + +
1638A THR 3.9 13.7 - - - +
1639A LEU* 4.6 7.4 - - + +
1642A TYR* 3.0 38.1 - - + -
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Residues in contact with THR1581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1579A THR* 3.8 4.7 - - - -
1580A LEU* 1.3 76.1 - - - +
1582A GLN* 1.3 57.8 + - + +
1584A LYS* 3.2 12.8 + - - +
1585A GLU* 2.8 47.0 + - - +
1603A ALA* 4.0 19.0 - - + +
1622A ASP* 2.4 33.5 + - - -
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Residues in contact with GLN1582 (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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1577A THR 4.3 1.6 - - - +
1578A ASP* 3.3 21.8 - - + +
1579A THR* 3.0 42.0 + - - +
1581A THR* 1.3 78.1 - - + +
1583A VAL* 1.3 63.5 + - - +
1585A GLU* 3.4 20.3 + - - +
1586A LYS* 3.0 32.2 + - - +
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Residues in contact with VAL1583 (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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1558A LEU* 4.3 16.4 - - + -
1574A ALA* 4.1 13.2 - - + -
1578A ASP* 3.8 20.4 - - + +
1579A THR 2.9 16.5 + - - +
1580A LEU* 3.5 14.8 - - + +
1581A THR 3.3 0.2 - - - -
1582A GLN* 1.3 76.3 - - - +
1584A LYS* 1.3 62.4 + - - +
1586A LYS* 3.2 9.7 + - - +
1587A ILE* 3.0 30.3 + - + +
1608A LEU* 3.7 26.2 - - + -
1639A LEU* 4.2 20.6 - - + -
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Residues in contact with LYS1584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1580A LEU* 2.9 22.7 + - - +
1581A THR* 3.2 8.3 + - - +
1583A VAL* 1.3 77.0 - - - +
1585A GLU* 1.3 56.9 + - - +
1587A ILE* 3.2 2.3 + - - +
1588A LEU* 2.8 38.1 + - + +
1603A ALA* 3.6 33.4 + - + +
1604A GLU* 5.6 0.4 - - - +
1606A VAL* 2.9 28.4 + - + +
1607A ASP* 4.4 6.1 + - - +
1608A LEU* 4.1 25.8 - - + +
1620A LEU 4.1 16.4 + - - -
1621A ARG* 4.8 9.7 - - - +
1652A MSE 4.1 20.9 - - + -
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Residues in contact with GLU1585 (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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1581A THR* 2.8 34.6 + - + +
1582A GLN* 3.5 23.8 - - - +
1584A LYS* 1.3 75.7 - - - +
1586A LYS* 1.3 58.5 + - + +
1588A LEU* 3.4 8.7 + - + +
1589A GLU* 2.9 42.3 + - - +
1600A TRP* 5.1 0.5 - - - -
1603A ALA* 5.0 6.9 - - + +
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Residues in contact with LYS1586 (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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1572A VAL* 4.1 15.3 - - + +
1573A ARG 3.9 16.9 + - - +
1574A ALA* 4.3 6.8 - - + +
1575A MSE 4.1 16.2 - - - +
1578A ASP* 2.5 42.4 + - - +
1582A GLN* 3.0 18.0 + - - +
1583A VAL* 3.2 8.0 + - - +
1585A GLU* 1.3 73.4 - - + +
1587A ILE* 1.3 65.4 + - - +
1589A GLU* 3.5 12.4 + - - +
1590A ALA* 3.1 22.5 + - - +
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Residues in contact with ILE1587 (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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1558A LEU* 5.0 1.6 - - + -
1560A VAL* 3.7 26.9 - - + -
1572A VAL* 4.0 20.4 - - + -
1583A VAL* 3.0 23.1 + - + +
1584A LYS 3.6 6.5 - - - +
1586A LYS* 1.3 76.0 - - - +
1588A LEU* 1.3 57.8 + - - +
1590A ALA* 3.1 4.2 + - - +
1591A PHE* 3.0 54.3 + - + -
1608A LEU* 3.7 35.9 - - + -
1650A LEU* 4.6 1.6 - - + -
1652A MSE 3.4 24.0 - - + -
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Residues in contact with LEU1588 (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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1562A PHE* 4.1 8.7 - - + -
1584A LYS 2.8 28.1 + - - +
1585A GLU* 3.9 7.9 - - + +
1587A ILE* 1.3 72.5 - - - +
1589A GLU* 1.3 56.7 + - - +
1591A PHE* 4.5 1.8 - - - +
1592A CYS* 2.8 41.8 + - - +
1600A TRP* 4.0 14.5 - - + -
1601A PRO* 3.5 50.0 - - + +
1602A ARG 4.0 18.4 - - - +
1603A ALA* 4.1 6.3 - - - +
1606A VAL* 4.5 7.4 - - + -
1652A MSE 4.0 21.1 - - - -
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Residues in contact with GLU1589 (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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1585A GLU* 2.9 28.8 + - - +
1586A LYS* 3.7 10.6 - - - +
1587A ILE 3.3 0.2 - - - -
1588A LEU* 1.3 76.3 - - - +
1590A ALA* 1.3 61.7 + - - +
1593A LYS* 3.3 26.0 + - - +
1600A TRP* 3.5 27.4 - - + -
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Residues in contact with ALA1590 (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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1570A LEU* 3.6 19.3 - - + +
1571A SER 5.5 1.8 - - - +
1572A VAL* 3.9 24.0 - - + -
1586A LYS 3.1 14.1 + - - +
1587A ILE 3.4 8.1 - - - +
1589A GLU* 1.3 79.7 - - - +
1591A PHE* 1.3 61.9 + - - +
1593A LYS* 3.8 14.7 - - - +
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Residues in contact with PHE1591 (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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1A ARS 4.1 5.0 - - - -
1560A VAL* 3.3 49.1 - - + -
1561A SER* 4.3 0.2 - - - -
1562A PHE* 3.8 44.9 - + + -
1567A MSE 3.4 34.7 - - + +
1568A ASP 3.8 19.3 - - - -
1570A LEU* 3.6 25.8 - - + -
1572A VAL* 5.2 1.3 - - + -
1587A ILE* 3.0 34.3 + - + +
1588A LEU* 4.2 2.5 - - - +
1590A ALA* 1.3 78.3 - - + +
1592A CYS* 1.3 65.7 + - - +
1593A LYS* 3.5 2.6 + - - +
1594A ASN 5.1 0.7 + - - -
1595A VAL* 5.8 0.5 - - - +
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Residues in contact with CYS1592 (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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1A ARS 2.3 39.9 - - - -
1562A PHE* 5.0 2.7 - - - -
1588A LEU* 2.8 33.1 + - - +
1591A PHE* 1.3 77.5 - - - +
1593A LYS* 1.3 64.7 + - - +
1594A ASN 3.2 3.4 - - - -
1595A VAL* 3.0 10.3 + - - -
1600A TRP* 2.9 41.7 + - + +
1601A PRO* 4.0 21.8 - - - -
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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