Contacts of the helix formed by residues 1527 - 1540 (chain A) in PDB entry 4ZLP
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 SER1527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1519A LEU* 5.5 1.4 - - - +
1523A GLU 3.7 10.7 + - - -
1524A LEU* 3.2 7.8 + - - -
1525A LEU 3.0 0.4 - - - -
1526A ARG* 1.3 80.7 - - - +
1528A SER* 1.3 60.6 + - - +
1529A ALA* 3.3 3.3 + - - +
1530A ASP* 3.5 8.7 + - - +
1531A PHE* 3.1 23.6 + - - +
1624A TYR* 3.6 22.3 + - - -
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Residues in contact with SER1528 (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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1524A LEU 3.5 5.1 + - - -
1525A LEU* 3.3 20.0 + - - -
1526A ARG 3.7 0.2 - - - -
1527A SER* 1.3 74.6 - - - +
1529A ALA* 1.3 62.5 + - - +
1531A PHE* 4.3 4.5 - - - -
1532A LEU* 2.9 38.8 + - - +
1545A PHE* 3.3 32.5 - - - -
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Residues in contact with ALA1529 (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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1476A ALA 3.6 18.2 - - - +
1477A ASP* 5.3 3.8 - - - +
1479A PHE* 3.8 26.7 - - + +
1527A SER* 3.3 1.4 - - - +
1528A SER* 1.3 82.2 + - - +
1530A ASP* 1.3 57.0 + - - +
1532A LEU* 5.5 0.2 - - - -
1533A GLN* 2.8 34.0 + - - +
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Residues in contact with ASP1530 (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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1473A LYS* 5.8 2.4 - - - +
1476A ALA* 3.5 27.1 + - + +
1477A ASP* 6.0 0.7 - - - +
1527A SER* 3.5 10.9 + - - +
1528A SER 3.4 0.2 - - - -
1529A ALA* 1.3 78.8 - - - +
1531A PHE* 1.3 63.0 + - - +
1533A GLN* 4.0 0.2 - - - +
1534A ARG* 3.0 62.8 + - - +
1623A PRO* 4.7 1.7 - - - +
1624A TYR* 2.5 30.5 + - - +
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Residues in contact with PHE1531 (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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1515A LEU* 4.3 13.9 - - + -
1517A VAL* 4.0 23.8 - - + -
1524A LEU* 3.8 24.5 - - + -
1527A SER 3.1 17.8 + - - +
1528A SER* 3.8 6.1 - - - +
1530A ASP* 1.3 78.6 - - - +
1532A LEU* 1.3 74.9 + - + +
1535A LEU* 3.0 44.0 + - + +
1545A PHE* 4.5 15.7 - + - -
1582A VAL* 4.7 6.1 - - + -
1584A LEU* 4.5 7.2 - - + -
1622A PHE* 3.5 34.3 - + - -
1624A TYR* 3.4 30.2 + + + +
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Residues in contact with LEU1532 (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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1479A PHE* 3.6 22.4 - - + -
1528A SER* 2.9 22.4 + - - +
1529A ALA* 5.5 0.2 - - - -
1531A PHE* 1.3 89.1 - - + +
1533A GLN* 1.3 58.5 + - - +
1535A LEU* 4.1 2.6 - - + +
1536A SER* 2.7 38.3 + - - -
1543A LEU* 4.1 12.8 - - + +
1544A ARG* 3.9 33.7 - - + -
1545A PHE* 3.9 24.9 - - + +
1584A LEU* 4.1 19.1 - - + -
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Residues in contact with GLN1533 (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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1467A CYS* 4.6 0.2 - - - -
1472A GLU* 2.7 40.6 + - - +
1475A CYS* 3.8 14.7 - - + +
1476A ALA* 3.6 22.1 - - - +
1479A PHE* 3.5 29.7 - - + -
1493A CYS* 2.9 33.3 + - - +
1494A GLY* 4.3 1.2 - - - -
1529A ALA 2.8 19.6 + - - +
1530A ASP 4.0 1.1 - - - +
1532A LEU* 1.3 78.1 - - - +
1534A ARG* 1.3 67.6 + - - +
1536A SER* 3.7 1.6 - - - -
1537A ALA* 2.9 32.3 + - - +
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Residues in contact with ARG1534 (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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1472A GLU* 3.3 32.8 + - - +
1473A LYS* 5.9 3.8 - - - +
1476A ALA* 5.5 0.4 - - - +
1530A ASP* 3.0 49.8 + - - +
1533A GLN* 1.3 87.8 - - - +
1535A LEU* 1.3 57.3 + - - +
1537A ALA* 3.4 6.0 + - - +
1538A ILE* 3.1 33.2 + - + +
1621A ASP* 5.4 4.6 + - - +
1622A PHE* 3.7 17.5 - - + -
1623A PRO* 3.6 35.9 - - + +
1624A TYR* 4.3 2.7 - - - -
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Residues in contact with LEU1535 (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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1513A LEU* 5.0 3.1 - - + -
1515A LEU* 3.7 19.5 - - + -
1531A PHE* 3.0 30.0 + - + +
1532A LEU* 4.1 4.5 - - + +
1534A ARG* 1.3 72.4 - - - +
1536A SER* 1.3 65.8 + - - +
1538A ILE* 3.4 8.8 + - + +
1539A LEU* 3.1 33.1 + - + +
1543A LEU* 4.6 9.0 - - + -
1584A LEU* 3.6 31.2 - - + -
1611A LEU* 4.3 29.8 - - + -
1620A LEU* 6.2 0.2 - - + -
1622A PHE* 3.8 20.6 - - + -
1626A LEU* 5.5 2.5 - - + -
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Residues in contact with SER1536 (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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1479A PHE* 4.1 4.9 - - - -
1491A GLU 3.9 1.0 - - - +
1494A GLY* 3.9 21.3 - - - -
1532A LEU 2.7 24.2 + - - -
1533A GLN 3.7 3.6 - - - -
1535A LEU* 1.3 75.4 - - - +
1537A ALA* 1.3 58.6 + - - +
1539A LEU 3.3 0.3 + - - -
1540A ARG* 2.7 28.9 + - - -
1541A THR 3.2 23.2 + - - +
1542A SER* 3.9 1.3 - - - -
1543A LEU* 3.0 33.6 + - - +
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Residues in contact with ALA1537 (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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1465A ARG* 5.8 0.5 + - - -
1467A CYS* 5.2 2.0 - - + -
1472A GLU* 5.5 1.1 - - - +
1491A GLU 3.8 11.4 - - - +
1492A GLU* 3.2 26.8 - - - +
1493A CYS* 4.1 6.3 - - - -
1494A GLY* 4.1 2.4 - - - +
1533A GLN* 2.9 22.5 + - - +
1534A ARG* 3.6 8.5 - - - +
1535A LEU 3.3 0.2 - - - -
1536A SER* 1.3 76.9 - - - +
1538A ILE* 1.3 62.4 + - + +
1540A ARG* 3.3 19.6 + - - +
5009A GOL 5.2 0.9 + - - -
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Residues in contact with ILE1538 (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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1456A PHE* 3.9 4.9 - - - -
1465A ARG* 5.6 1.2 + - - -
1534A ARG* 3.1 19.5 + - + +
1535A LEU* 3.7 10.5 - - + +
1536A SER 3.2 0.4 - - - -
1537A ALA* 1.3 78.3 - - + +
1539A LEU* 1.3 59.5 + - - +
1540A ARG* 3.5 1.7 + - - +
1610A TYR* 3.5 18.5 + - + -
1611A LEU* 3.9 16.8 - - + -
1614A LEU* 3.6 29.8 - - + -
1620A LEU* 4.0 6.7 - - + -
1621A ASP 4.0 14.8 - - - +
1622A PHE* 3.8 30.3 - - + -
5009A GOL 3.8 28.0 + - - +
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Residues in contact with LEU1539 (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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1456A PHE* 3.8 12.0 - - - -
1513A LEU* 4.3 9.0 - - + -
1535A LEU* 3.1 22.0 + - + +
1536A SER 4.2 0.2 - - - +
1538A ILE* 1.3 75.5 - - - +
1540A ARG* 1.3 70.4 + - - +
1541A THR* 3.3 17.7 + - + +
1543A LEU* 3.6 34.3 - - + -
1586A ILE* 5.2 0.9 - - + -
1599A HIS 5.2 1.4 - - - +
1600A CYS* 6.1 0.3 - - - -
1601A PHE* 3.8 22.4 - - + -
1607A ALA* 4.0 29.4 - - + +
1610A TYR* 3.7 26.5 - - + -
1611A LEU* 4.0 16.8 - - + -
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Residues in contact with ARG1540 (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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1456A PHE* 3.4 41.3 - - + -
1460A ALA* 3.5 15.0 - - - +
1464A GLU 2.8 28.3 + - - -
1465A ARG* 3.2 30.3 + - - +
1491A GLU* 2.7 64.2 + - - +
1492A GLU* 3.4 25.1 + - - +
1495A TRP* 4.4 1.6 + - - -
1536A SER 2.7 11.7 + - - -
1537A ALA 3.3 12.0 + - - +
1538A ILE 3.3 2.4 - - - +
1539A LEU* 1.3 80.9 - - - +
1541A THR* 1.3 58.2 + - - +
1599A HIS* 4.3 5.1 + - + +
1600A CYS* 5.0 7.6 - - - -
5011A ACT 3.5 14.6 + - - -
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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