Contacts of the helix formed by residues 1601 - 1614 (chain A) in PDB entry 3AU5
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 PRO1601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1546A PRO 4.9 1.6 - - - +
1547A LEU* 3.2 27.6 - - + +
1548A PRO* 3.4 30.0 - - + +
1549A TYR 4.7 7.6 - - - +
1550A GLY* 6.0 0.2 - - - -
1552A ILE* 5.2 9.4 - - + -
1565A LEU* 4.0 24.2 - - + -
1599A LEU* 3.2 8.5 - - + -
1600A ARG* 1.3 94.6 - - + +
1602A LEU* 1.3 57.7 + - - +
1603A ARG 3.5 0.3 + - - -
1604A ASP* 4.2 8.2 + - - +
1605A GLU 4.3 2.1 + - - -
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Residues in contact with LEU1602 (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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1547A LEU* 3.5 26.9 - - + -
1565A LEU* 3.7 8.3 - - + +
1568A GLU* 3.7 17.3 - - + -
1569A ALA* 3.4 47.1 - - + +
1572A ILE* 4.7 5.2 - - + -
1595A THR* 4.1 17.3 - - + -
1596A GLY* 4.7 4.9 - - - -
1599A LEU* 2.8 29.1 + - + +
1601A PRO* 1.3 72.7 - - - +
1603A ARG* 1.3 58.1 + - - +
1604A ASP 3.4 0.7 - - - -
1605A GLU* 3.7 7.4 - - + -
1606A LEU* 2.8 39.4 + - + +
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Residues in contact with ARG1603 (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 GLY 3.0 20.4 + - - +
1597A HIS* 3.0 42.8 + - - -
1599A LEU 3.8 0.2 + - - -
1600A ARG* 2.8 65.8 + - - +
1602A LEU* 1.3 75.8 - - - +
1604A ASP* 1.3 68.8 + - - +
1606A LEU* 3.9 2.3 - - - +
1607A TYR* 3.1 29.7 + - - -
1639A PHE* 3.3 54.3 - - + +
1640A LEU 4.5 11.7 + - - +
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Residues in contact with ASP1604 (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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1545A LEU* 3.7 17.9 - - + -
1600A ARG 4.4 1.0 + - - -
1601A PRO 4.2 6.3 + - - +
1602A LEU 3.4 0.4 - - - -
1603A ARG* 1.3 79.4 - - - +
1605A GLU* 1.3 57.5 + - - +
1607A TYR* 3.2 8.3 + - - +
1608A CYS* 3.0 31.7 + - - -
1641A PRO* 3.2 9.7 - - - +
1642A SER* 2.7 52.5 + - - -
1645A ILE* 3.3 13.7 - - + +
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Residues in contact with GLU1605 (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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1540A LEU* 4.6 0.7 - - - +
1543A PRO* 3.4 14.3 - - - +
1544A LEU* 2.8 26.4 + - - +
1545A LEU* 2.7 40.3 + - + +
1547A LEU* 3.9 17.7 - - + -
1569A ALA* 3.9 16.3 - - + +
1601A PRO 4.3 1.4 + - - -
1602A LEU* 3.6 11.6 - - + +
1603A ARG 3.3 0.2 - - - -
1604A ASP* 1.3 79.9 - - - +
1606A LEU* 1.3 58.4 + - + +
1608A CYS* 3.3 3.5 + - - +
1609A GLN* 2.7 57.7 + - - +
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Residues in contact with LEU1606 (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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1569A ALA* 5.7 1.3 - - - +
1572A ILE* 3.7 42.4 - - + -
1592A ILE* 3.8 33.2 - - + +
1596A GLY* 3.8 22.0 - - - +
1602A LEU* 2.8 26.4 + - + +
1603A ARG* 3.9 4.3 - - - +
1605A GLU* 1.3 74.8 - - + +
1607A TYR* 1.3 63.9 + - - +
1609A GLN* 3.3 13.7 + - + +
1610A LEU* 3.0 34.1 + - + +
1635A LEU* 4.2 13.2 - - + -
1639A PHE* 4.4 10.8 - - + -
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Residues in contact with TYR1607 (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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1603A ARG 3.1 20.8 + - - -
1604A ASP 3.2 8.8 + - - +
1606A LEU* 1.3 77.7 - - - +
1608A CYS* 1.3 62.9 + - - +
1610A LEU* 3.3 4.7 + - - +
1611A ILE* 3.1 30.8 + - + +
1632A LEU* 3.8 25.8 - - + -
1635A LEU* 3.1 32.3 + - + -
1636A SER* 3.3 9.7 - - - -
1639A PHE* 2.7 36.0 + + - -
1640A LEU 4.0 2.0 - - - -
1641A PRO* 3.4 39.6 - - + +
1645A ILE* 3.9 14.1 - - + -
1649A LEU* 3.7 27.1 - - + -
1676A LEU* 4.1 1.7 - - - +
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Residues in contact with CYS1608 (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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1506A THR* 4.7 4.7 - - + -
1510A ILE* 4.4 15.0 - - - -
1544A LEU* 4.0 14.8 - - + +
1545A LEU* 3.5 39.7 - - + -
1604A ASP 3.0 12.6 + - - +
1605A GLU 3.7 4.7 - - - +
1607A TYR* 1.3 77.6 - - - +
1609A GLN* 1.3 58.3 + - - +
1611A ILE* 3.4 8.7 + - - +
1612A LYS* 3.0 28.8 + - - +
1645A ILE* 4.1 20.4 - - - -
1648A TYR* 4.9 6.2 - - + -
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Residues in contact with GLN1609 (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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1540A LEU* 4.1 4.0 - - + +
1544A LEU* 3.6 18.6 - - + -
1569A ALA* 3.1 22.7 + - - +
1572A ILE* 4.0 10.6 - - - +
1573A PHE* 3.3 47.4 + - + +
1605A GLU* 2.7 46.8 + - - +
1606A LEU* 3.5 11.4 - - + +
1607A TYR 3.2 0.2 - - - -
1608A CYS* 1.3 78.0 - - - +
1610A LEU* 1.3 60.5 + - + +
1612A LYS* 3.3 4.3 + - - +
1613A GLN* 3.0 32.3 + - - +
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Residues in contact with LEU1610 (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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1592A ILE* 5.9 0.4 - - + -
1606A LEU* 3.0 35.0 + - + +
1607A TYR 3.8 5.4 - - - +
1609A GLN* 1.3 74.8 - - + +
1611A ILE* 1.3 64.5 + - - +
1613A GLN* 3.3 6.1 + - + +
1614A THR* 2.8 33.6 + - + +
1628A SER* 3.7 38.4 - - - +
1631A ILE* 4.1 21.8 - - + -
1632A LEU* 4.0 25.8 - - + +
1635A LEU* 3.8 21.5 - - + -
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Residues in contact with ILE1611 (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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1527A TYR* 5.3 0.4 - - - +
1533A LEU 5.3 1.6 - - - +
1607A TYR* 3.1 21.7 + - + +
1608A CYS* 3.7 7.6 - - - +
1610A LEU* 1.3 74.9 - - + +
1612A LYS* 1.3 65.9 + - - +
1614A THR* 3.1 10.7 + - - -
1615A ASN* 3.0 27.1 + - + +
1632A LEU* 5.3 2.5 - - + -
1645A ILE* 4.9 5.2 - - + +
1648A TYR* 3.6 42.0 - - + +
1649A LEU* 3.6 47.8 - - + +
1652A HIS* 3.6 26.5 + - + +
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Residues in contact with LYS1612 (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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1531A PRO 3.6 3.4 + - - -
1532A ILE* 3.0 42.7 + - - +
1533A LEU* 3.5 16.6 - - - +
1534A ARG* 3.2 22.5 + - - +
1535A TYR 2.9 22.7 + - - -
1536A THR* 3.4 30.8 - - - +
1540A LEU* 4.4 9.7 - - - +
1544A LEU* 4.0 15.9 - - + -
1573A PHE* 3.5 26.0 - - + -
1608A CYS 3.0 18.2 + - - +
1609A GLN 3.5 2.2 - - - +
1611A ILE* 1.3 77.9 - - - +
1613A GLN* 1.3 58.1 + - - +
1615A ASN 3.1 11.8 + - - +
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Residues in contact with GLN1613 (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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1535A TYR* 3.4 29.5 - - + -
1536A THR 3.0 39.6 + - - -
1573A PHE* 3.5 38.1 - - + -
1577A GLN* 4.4 10.1 - - - +
1609A GLN 3.0 14.3 + - - +
1610A LEU* 3.3 8.0 + - + +
1612A LYS* 1.3 81.8 - - - +
1614A THR* 1.3 60.1 + - - +
1615A ASN 3.4 0.4 - - - -
1617A VAL* 3.2 18.2 - - - +
1625A ASN* 4.4 1.2 + - - -
1628A SER* 4.3 16.7 + - - +
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Residues in contact with THR1614 (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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1610A LEU 2.8 22.9 + - - +
1611A ILE* 3.1 2.9 + - - -
1613A GLN* 1.3 76.5 - - - +
1615A ASN* 1.3 59.0 + - - +
1616A LYS 3.9 1.7 + - - -
1617A VAL* 3.8 12.3 + - - +
1625A ASN* 4.4 1.9 + - - +
1628A SER* 3.6 31.6 - - - +
1629A TRP* 3.6 39.2 + - + +
1632A LEU* 4.8 5.0 - - + +
1652A HIS* 2.9 20.7 + - - -
1656A ILE* 3.8 18.4 - - - +
1660A PHE* 6.0 0.3 - - - -
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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