Contacts of the helix formed by residues 1603 - 1617 (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 ASP1603 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1509B ALA* 4.0 6.1 - - - -
1510B ARG* 2.6 53.4 + - + +
1586B ILE* 4.5 1.5 - - - +
1601B PHE* 3.2 7.1 - - - +
1602B PRO* 1.3 87.3 - - - +
1604B ALA* 1.3 64.3 + - - +
1605B GLN* 3.4 9.2 + - + +
1606B SER* 2.7 50.1 + - - -
1607B ALA* 3.5 8.8 + - - +
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Residues in contact with ALA1604 (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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1510B ARG 2.9 11.5 + - - +
1511B GLY* 3.9 3.1 - - - +
1512B VAL 3.4 45.1 - - - +
1513B LEU* 3.5 17.6 - - + +
1586B ILE* 4.3 12.3 - - + +
1603B ASP* 1.3 73.3 - - - +
1605B GLN* 1.3 62.0 + - - +
1607B ALA* 3.3 2.8 + - - +
1608B ALA 3.0 18.2 + - - -
1631B GLY* 4.0 7.2 - - - -
1632B GLU 4.6 0.2 - - - +
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Residues in contact with GLN1605 (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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1421B VAL* 4.8 7.5 - - - +
1603B ASP* 3.4 7.6 + - + +
1604B ALA* 1.3 78.8 - - - +
1606B SER* 1.3 55.9 - - - +
1608B ALA* 3.2 9.3 + - - +
1609B ASP* 2.8 65.9 + - - +
1629B VAL 5.4 0.2 + - - -
1630B ARG* 3.7 5.9 - - - +
1631B GLY* 2.6 41.1 + - - +
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Residues in contact with SER1606 (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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1449B PRO 5.9 2.2 - - - -
1452B LEU* 4.3 5.3 - - - +
1601B PHE* 3.8 20.5 - - - -
1602B PRO* 4.4 9.3 - - - +
1603B ASP* 2.7 34.6 + - - -
1605B GLN* 1.3 76.9 - - - +
1607B ALA* 1.3 57.0 + - - +
1609B ASP* 3.3 12.6 + - - +
1610B TYR* 3.0 27.7 + - - +
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Residues in contact with ALA1607 (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* 4.7 4.0 - - + -
1539B LEU* 4.0 16.4 - - + +
1586B ILE* 3.8 26.2 - - + -
1601B PHE* 3.9 26.6 - - + -
1603B ASP 3.5 2.0 + - - +
1604B ALA 3.3 8.4 + - - +
1605B GLN 3.3 0.4 - - - -
1606B SER* 1.3 75.9 - - - +
1608B ALA* 1.3 65.8 + - - +
1610B TYR* 3.3 2.4 + - - +
1611B LEU* 3.0 30.8 + - - +
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Residues in contact with ALA1608 (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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1421B VAL* 3.7 2.5 - - + +
1513B LEU* 3.7 17.6 - - + +
1604B ALA 3.0 13.2 + - - +
1605B GLN* 3.4 14.1 - - - +
1607B ALA* 1.3 78.0 - - - +
1609B ASP* 1.3 55.8 + - - +
1611B LEU* 3.3 3.9 + - - +
1612B GLY* 2.8 25.5 + - - -
1629B VAL* 3.3 29.5 - - + +
1630B ARG* 3.8 19.7 - - - +
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Residues in contact with ASP1609 (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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1421B VAL* 3.4 21.8 - - - +
1423B ASP 5.0 2.6 - - - +
1424B PRO* 3.5 27.9 - - + +
1426B ARG* 5.8 3.0 - - - +
1452B LEU* 4.1 7.5 - - + +
1605B GLN* 2.8 50.4 + - - +
1606B SER* 3.4 12.1 - - - +
1608B ALA* 1.3 76.9 - - - +
1610B TYR* 1.3 51.9 + - - +
1612B GLY* 3.1 2.4 + - - -
1613B ALA* 2.7 34.3 + - - +
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Residues in contact with TYR1610 (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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1437B PHE* 3.7 18.6 - + - -
1452B LEU* 4.1 21.2 - - + +
1455B ASN* 2.7 37.0 + - - -
1456B PHE* 3.3 27.9 - + - -
1538B ILE* 3.6 20.8 + - + -
1539B LEU* 3.6 14.8 - - + -
1601B PHE* 3.6 35.7 - + + -
1606B SER 3.0 6.2 + - - +
1607B ALA 3.6 4.7 - - - +
1608B ALA 3.3 0.2 - - - -
1609B ASP* 1.3 76.0 - - - +
1611B LEU* 1.3 58.3 + - - +
1613B ALA* 3.1 8.0 + - - +
1614B LEU* 2.9 51.4 + - + +
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Residues in contact with LEU1611 (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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1419B LEU* 3.6 20.6 - - + +
1513B LEU* 4.3 21.3 - - + -
1515B LEU* 5.0 1.6 - - + -
1535B LEU* 4.3 18.8 - - + -
1538B ILE* 3.8 29.2 - - + -
1539B LEU* 3.9 21.8 - - + -
1607B ALA 3.0 19.9 + - - +
1608B ALA* 3.6 7.6 - - - +
1610B TYR* 1.3 76.0 - - - +
1612B GLY* 1.3 63.3 + - - +
1614B LEU* 3.2 10.5 + - + +
1615B SER* 3.0 18.5 + - - -
1620B LEU* 4.4 10.2 - - + +
1626B LEU* 5.4 2.9 - - + -
1629B VAL* 4.2 18.6 - - + -
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Residues in contact with GLY1612 (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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1418B SER* 3.3 42.8 - - - -
1419B LEU* 4.1 5.1 - - - +
1421B VAL* 4.2 4.3 - - - -
1424B PRO* 4.2 1.8 - - - -
1608B ALA 2.8 14.1 + - - -
1609B ASP 3.4 4.5 - - - -
1611B LEU* 1.3 77.5 - - - +
1613B ALA* 1.3 57.0 + - - +
1615B SER 3.4 0.5 + - - -
1616B ALA* 3.0 22.5 + - - +
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Residues in contact with ALA1613 (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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1424B PRO* 3.8 12.9 - - + +
1425B TRP* 3.9 13.7 - - + -
1437B PHE* 3.9 12.7 - - + -
1452B LEU* 3.5 24.9 - - + -
1609B ASP 2.7 13.2 + - - +
1610B TYR 3.4 8.3 - - - +
1612B GLY* 1.3 75.0 - - - +
1614B LEU* 1.3 64.9 + - - +
1616B ALA* 3.1 12.1 + - - +
1617B VAL* 3.2 19.1 + - - +
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Residues in contact with LEU1614 (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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1437B PHE* 3.9 7.6 - - + -
1455B ASN* 3.4 25.6 - - - +
1538B ILE* 3.6 23.1 - - + -
1610B TYR* 2.9 44.3 + - + +
1611B LEU* 3.5 9.6 - - - +
1613B ALA* 1.3 75.6 - - - +
1615B SER* 1.3 58.6 + - - +
1617B VAL* 3.4 5.5 + - - +
1618B GLU 3.0 7.3 + - - -
1619B ARG* 2.8 52.0 + - + +
1620B LEU* 3.7 23.1 - - + +
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Residues in contact with SER1615 (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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1401B CYS* 6.0 0.2 - - - -
1406B ASN* 4.5 2.4 + - - -
1417B CYS* 2.7 26.8 + - - +
1419B LEU* 3.8 24.4 - - - +
1611B LEU 3.0 15.7 + - - -
1612B GLY 3.7 3.6 - - - -
1613B ALA 3.2 0.2 - - - -
1614B LEU* 1.3 74.0 - - - +
1616B ALA* 1.3 64.7 + - - +
1618B GLU* 3.2 17.2 + - - +
1620B LEU* 3.9 18.5 - - - +
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Residues in contact with ALA1616 (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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1406B ASN* 2.9 26.1 + - - +
1412B TRP* 3.7 40.3 - - + -
1417B CYS 3.2 7.8 + - - -
1418B SER* 4.1 8.5 - - - -
1424B PRO* 5.2 0.2 - - + -
1425B TRP* 4.9 2.0 - - + -
1612B GLY 3.0 17.3 + - - +
1613B ALA* 3.1 9.8 + - - +
1615B SER* 1.3 76.8 - - - +
1617B VAL* 1.3 61.3 + - + +
1618B GLU* 3.4 1.6 + - - +
5004B NAG 4.8 4.3 - - - +
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Residues in contact with VAL1617 (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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1412B TRP* 5.0 7.4 - - + -
1425B TRP* 4.7 9.9 - - + -
1434B TRP 4.9 9.2 - - - +
1437B PHE* 3.9 23.6 - - + -
1438B ASN* 3.9 20.2 - - + +
1613B ALA 3.2 17.0 + - - +
1614B LEU 3.5 7.4 - - - +
1616B ALA* 1.3 80.9 - - + +
1618B GLU* 1.3 66.0 + - - +
1619B ARG* 3.6 16.6 - - + -
5004B NAG 2.7 43.1 + - + +
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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
------------------------------------------------------------
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