Contacts of the helix formed by residues 1527 - 1540 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1519B LEU* 5.1 2.1 - - - +
1523B GLU 3.8 7.3 + - - -
1524B LEU* 3.1 10.2 + - - +
1525B LEU 3.0 0.2 - - - -
1526B ARG* 1.3 80.4 - - - +
1528B SER* 1.3 62.8 + - - +
1529B ALA 3.3 3.1 - - - +
1530B ASP* 3.6 8.2 + - - +
1531B PHE* 3.2 22.3 + - - +
1624B TYR* 3.7 23.9 + - - -
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Residues in contact with SER1528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524B LEU 3.6 4.0 + - - -
1525B LEU* 2.7 36.0 + - - +
1526B ARG 3.7 0.2 - - - -
1527B SER* 1.3 71.5 - - - +
1529B ALA* 1.3 60.7 + - - +
1531B PHE* 3.4 3.8 + - - +
1532B LEU* 2.9 39.0 + - - +
1545B PHE* 3.5 29.6 - - - -
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Residues in contact with ALA1529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476B ALA 3.3 18.3 - - - +
1477B ASP* 4.5 9.4 - - - +
1479B PHE* 3.9 24.8 - - - +
1527B SER 3.3 0.8 - - - -
1528B SER* 1.3 79.1 - - - +
1530B ASP* 1.3 57.5 + - - +
1532B LEU* 4.9 0.9 - - - -
1533B GLN* 2.9 33.8 + - - +
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Residues in contact with ASP1530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473B LYS* 5.0 10.8 + - - +
1476B ALA* 3.5 25.7 + - + +
1477B ASP* 5.5 3.8 - - - +
1527B SER* 3.6 11.9 + - - +
1528B SER 3.4 0.2 - - - -
1529B ALA* 1.3 78.4 - - - +
1531B PHE* 1.3 62.3 + - - +
1534B ARG* 2.9 63.5 + - - +
1623B PRO* 4.5 1.4 - - - +
1624B TYR* 2.5 30.9 + - - +
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Residues in contact with PHE1531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515B LEU* 4.3 12.8 - - + -
1517B VAL* 3.9 28.7 - - + -
1524B LEU* 4.0 16.2 - - + -
1527B SER 3.2 17.5 + - - +
1528B SER* 3.7 5.4 - - - +
1530B ASP* 1.3 79.4 - - - +
1532B LEU* 1.3 73.1 + - + +
1535B LEU* 3.2 38.7 + - + +
1545B PHE* 4.8 8.1 - + - -
1582B VAL* 4.7 14.1 - - + -
1584B LEU* 4.4 11.7 - - + -
1622B PHE* 3.4 35.7 - + - -
1624B TYR* 3.3 34.7 + + + -
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Residues in contact with LEU1532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479B PHE* 3.5 21.1 - - + -
1480B ALA* 6.3 0.7 - - + -
1528B SER* 2.9 21.7 + - - +
1529B ALA* 5.5 0.4 - - - -
1531B PHE* 1.3 85.0 - - + +
1533B GLN* 1.3 58.2 + - - +
1535B LEU* 3.4 3.6 + - + +
1536B SER* 2.7 38.4 + - - -
1543B LEU* 4.2 15.7 - - + +
1544B ARG* 4.2 15.3 - - + -
1545B PHE* 3.8 29.8 - - + -
1584B LEU* 3.7 35.4 - - + -
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Residues in contact with GLN1533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1472B GLU* 2.6 40.4 + - - +
1475B CYS* 3.8 14.0 - - - +
1476B ALA* 3.6 23.3 - - - +
1479B PHE* 3.6 35.6 - - + -
1493B CYS* 2.8 31.3 + - - +
1529B ALA 2.9 19.5 + - - +
1530B ASP 4.0 0.9 - - - +
1532B LEU* 1.3 78.0 - - - +
1534B ARG* 1.3 62.2 + - - +
1536B SER* 3.3 2.3 + - - -
1537B ALA* 2.9 29.2 + - - +
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Residues in contact with ARG1534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1472B GLU* 3.5 33.0 + - - +
1473B LYS* 5.4 7.5 - - - +
1476B ALA* 5.3 1.2 - - - +
1530B ASP* 2.9 49.0 + - - +
1533B GLN* 1.3 87.8 - - - +
1535B LEU* 1.3 61.4 + - - +
1537B ALA* 3.3 6.5 + - - +
1538B ILE* 3.1 32.0 + - + +
1621B ASP* 5.3 8.1 + - - +
1622B PHE* 3.7 15.5 - - + -
1623B PRO* 3.6 32.9 - - + +
1624B TYR* 4.3 2.0 - - - -
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Residues in contact with LEU1535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513B LEU* 4.9 2.7 - - + -
1515B LEU* 3.7 21.5 - - + -
1531B PHE* 3.2 26.4 + - + +
1532B LEU* 3.9 3.1 - - + +
1534B ARG* 1.3 80.7 - - - +
1536B SER* 1.3 61.5 + - - +
1538B ILE* 3.4 7.1 + - + +
1539B LEU* 3.1 27.3 + - + +
1543B LEU* 3.5 15.9 - - + -
1584B LEU* 3.6 31.6 - - + -
1611B LEU* 4.3 27.8 - - + -
1620B LEU* 5.9 0.7 - - + -
1622B PHE* 3.8 24.4 - - + -
1626B LEU* 5.3 2.7 - - + -
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Residues in contact with SER1536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479B PHE* 3.6 13.8 - - - -
1491B GLU 4.2 0.5 - - - +
1494B GLY* 3.9 15.9 - - - -
1532B LEU 2.7 23.3 + - - -
1533B GLN 3.3 4.2 + - - -
1535B LEU* 1.3 73.7 - - - +
1537B ALA* 1.3 54.9 + - - +
1539B LEU* 3.3 1.8 + - - -
1540B ARG* 2.7 30.8 + - - -
1541B THR 3.1 26.0 + - - +
1542B SER* 4.5 0.4 - - - -
1543B LEU* 3.1 30.2 + - - +
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Residues in contact with ALA1537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1465B ARG 5.2 2.9 - - - +
1467B CYS* 5.1 3.1 - - + +
1472B GLU* 5.4 1.6 - - - +
1491B GLU 4.0 8.0 - - - +
1492B GLU* 3.2 29.0 - - - +
1493B CYS* 4.2 6.7 - - - -
1494B GLY* 4.2 2.2 - - - +
1533B GLN* 2.9 22.6 + - - +
1534B ARG* 3.6 7.9 - - - +
1536B SER* 1.3 75.2 - - - +
1538B ILE* 1.3 64.1 + - + +
1540B ARG* 3.3 17.8 + - - +
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Residues in contact with ILE1538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456B PHE* 4.8 0.2 - - - -
1534B ARG* 3.1 19.3 + - + +
1535B LEU* 3.7 9.6 - - + +
1537B ALA* 1.3 80.1 - - + +
1539B LEU* 1.3 58.6 + - - +
1540B ARG* 3.2 7.5 + - - +
1610B TYR* 3.6 17.0 + - + -
1611B LEU* 3.8 17.3 - - + -
1614B LEU* 3.6 30.7 - - + -
1620B LEU* 4.0 17.0 - - + -
1621B ASP 3.9 22.9 - - - +
1622B PHE* 4.0 17.3 - - + -
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Residues in contact with LEU1539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456B PHE* 4.2 3.9 - - - -
1513B LEU* 4.4 6.5 - - + -
1535B LEU* 3.1 13.3 + - + +
1536B SER* 4.0 2.2 - - - +
1538B ILE* 1.3 74.2 - - - +
1540B ARG* 1.3 71.7 + - - +
1541B THR* 3.2 20.1 + - + +
1543B LEU* 3.5 32.1 - - + -
1586B ILE* 5.2 0.7 - - + -
1599B HIS 5.0 1.9 - - - +
1600B CYS* 6.1 0.2 - - - -
1601B PHE* 3.6 36.2 - - + -
1607B ALA* 4.0 20.4 - - + +
1610B TYR* 3.6 18.8 - - + -
1611B LEU* 3.9 31.9 - - + -
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Residues in contact with ARG1540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456B PHE* 3.5 39.0 - - + -
1459B HIS* 3.9 9.9 + - - -
1460B ALA* 3.6 17.0 - - - +
1464B GLU* 3.0 31.1 + - - +
1465B ARG* 3.1 26.2 + - - +
1491B GLU* 2.8 74.8 + - - +
1492B GLU* 3.8 8.9 + - - +
1495B TRP* 4.5 0.9 + - - -
1536B SER 2.7 9.9 + - - -
1537B ALA 3.3 11.6 + - - +
1538B ILE 3.2 6.2 - - - +
1539B LEU* 1.3 81.8 - - - +
1541B THR* 1.3 58.6 + - - +
1591B CYS* 4.4 8.1 - - - -
1599B HIS* 5.1 5.6 + - - +
1600B CYS* 5.1 1.9 - - - -
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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