Contacts of the helix formed by residues 1603 - 1617 (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 ASP1603 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1509A ALA* 3.9 6.7 - - - -
1510A ARG* 3.2 49.6 + - + +
1586A ILE* 4.7 0.7 - - - -
1601A PHE* 3.2 6.1 + - - +
1602A PRO* 1.3 84.2 - - - +
1604A ALA* 1.3 62.2 + - - +
1605A GLN* 3.8 1.4 - - - +
1606A SER* 2.6 54.8 + - - -
1607A ALA* 3.5 3.8 + - - +
5010A ACT 3.4 17.6 - - - +
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Residues in contact with ALA1604 (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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1509A ALA* 4.7 0.4 - - - +
1510A ARG 2.8 10.5 + - - +
1511A GLY 3.9 1.6 - - - +
1512A VAL 3.3 42.8 - - - +
1513A LEU* 3.5 12.7 - - + +
1586A ILE* 3.9 15.2 - - + +
1603A ASP* 1.3 72.0 - - - +
1605A GLN* 1.3 63.9 + - - +
1607A ALA* 3.1 6.1 + - - +
1608A ALA 3.0 18.0 + - - -
1631A GLY* 3.7 4.7 - - - -
5010A ACT 3.5 10.9 + - - +
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Residues in contact with GLN1605 (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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1421A VAL* 4.7 5.9 - - - +
1426A ARG* 3.3 26.6 - - - +
1603A ASP* 3.4 2.4 - - - +
1604A ALA* 1.3 78.4 - - - +
1606A SER* 1.3 56.7 + - - +
1608A ALA* 3.2 9.2 + - - +
1609A ASP* 2.8 60.6 + - - +
1630A ARG* 3.8 6.3 - - - +
1631A GLY* 2.8 36.5 + - - +
5010A ACT 3.2 23.3 + - - +
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Residues in contact with SER1606 (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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1427A GLN* 5.1 6.6 + - - -
1452A LEU* 4.6 3.8 - - - +
1601A PHE* 3.7 26.8 - - - -
1602A PRO* 4.2 10.5 - - - +
1603A ASP* 2.6 39.4 + - - -
1605A GLN* 1.3 73.2 - - - +
1607A ALA* 1.3 63.7 + - - +
1609A ASP* 3.4 12.2 + - - +
1610A TYR* 3.2 16.3 + - - +
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Residues in contact with ALA1607 (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* 4.6 4.0 - - + -
1539A LEU* 4.0 17.0 - - + +
1586A ILE* 3.8 24.7 - - + -
1601A PHE* 3.9 28.8 - - + -
1603A ASP 3.5 2.0 + - - +
1604A ALA 3.1 9.3 + - - +
1606A SER* 1.3 76.2 - - - +
1608A ALA* 1.3 64.9 + - - +
1610A TYR* 3.2 3.6 + - - +
1611A LEU* 3.1 28.0 + - - +
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Residues in contact with ALA1608 (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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1421A VAL* 3.6 3.8 - - + +
1513A LEU* 3.9 9.7 - - + +
1604A ALA 3.0 13.1 + - - +
1605A GLN* 3.2 15.7 + - - +
1607A ALA* 1.3 76.2 - - - +
1609A ASP* 1.3 52.7 + - - +
1611A LEU* 3.2 2.8 + - - -
1612A GLY 2.8 30.3 + - - -
1629A VAL* 3.4 23.9 - - + +
1630A ARG* 3.8 31.2 - - - -
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Residues in contact with ASP1609 (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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1421A VAL* 3.3 9.6 - - - +
1424A PRO* 3.4 30.7 - - + +
1426A ARG* 2.3 47.9 + - - +
1427A GLN* 4.9 7.4 - - - +
1452A LEU* 4.1 7.8 - - + +
1605A GLN* 2.8 31.8 + - - +
1606A SER* 3.6 11.0 - - - +
1607A ALA 3.3 0.2 - - - -
1608A ALA* 1.3 77.4 - - - +
1610A TYR* 1.3 56.9 + - - +
1612A GLY* 3.1 1.2 + - - -
1613A ALA* 2.9 24.4 + - - +
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Residues in contact with TYR1610 (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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1437A PHE* 3.5 23.8 - + - -
1452A LEU* 4.2 19.0 - - + +
1455A ASN* 2.7 36.9 + - - -
1456A PHE* 3.5 26.3 - + - -
1465A ARG* 3.9 4.3 + - - -
1538A ILE* 3.5 21.1 + - + -
1539A LEU* 3.7 21.8 - - + -
1601A PHE* 3.6 28.3 - + + -
1606A SER 3.2 3.6 + - - +
1607A ALA 3.2 5.8 + - - +
1609A ASP* 1.3 78.5 - - - +
1611A LEU* 1.3 63.1 + - - +
1613A ALA* 3.1 5.8 + - - +
1614A LEU* 3.0 46.4 + - + +
5009A GOL 4.0 2.4 - - - -
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Residues in contact with LEU1611 (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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1419A LEU* 3.5 21.1 - - + +
1513A LEU* 4.5 18.2 - - + -
1515A LEU* 5.1 2.5 - - + -
1535A LEU* 4.3 23.1 - - + -
1538A ILE* 3.9 28.3 - - + -
1539A LEU* 4.0 16.2 - - + -
1607A ALA 3.1 19.2 + - - +
1608A ALA 3.5 5.4 - - - +
1610A TYR* 1.3 76.1 - - - +
1612A GLY* 1.3 63.3 + - - +
1614A LEU* 3.3 10.5 + - + +
1615A SER* 3.1 17.3 + - - -
1620A LEU* 4.5 10.5 - - + +
1626A LEU* 5.3 3.8 - - + -
1629A VAL* 4.1 22.9 - - + -
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Residues in contact with GLY1612 (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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1418A SER* 3.3 35.2 - - - -
1419A LEU* 4.2 3.9 - - - +
1421A VAL* 4.1 7.0 - - - -
1424A PRO* 4.1 7.2 - - - -
1608A ALA 2.8 15.1 + - - -
1609A ASP 3.1 4.0 + - - -
1611A LEU* 1.3 74.9 - - - +
1613A ALA* 1.3 56.4 + - - +
1615A SER 3.3 1.4 + - - -
1616A ALA* 2.9 24.8 + - - +
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Residues in contact with ALA1613 (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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1424A PRO* 3.8 6.0 - - + +
1425A TRP* 3.6 25.4 - - + -
1437A PHE* 3.9 10.3 - - + -
1452A LEU* 3.6 23.1 - - + -
1609A ASP 2.9 12.6 + - - +
1610A TYR 3.1 9.4 + - - +
1612A GLY* 1.3 74.1 - - - +
1614A LEU* 1.3 64.0 + - - +
1616A ALA* 3.1 12.8 + - - +
1617A VAL* 3.2 19.4 + - - +
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Residues in contact with LEU1614 (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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1437A PHE* 3.8 10.5 - - + -
1455A ASN* 3.5 23.1 - - - +
1538A ILE* 3.6 21.8 - - + -
1610A TYR* 3.0 47.2 + - + +
1611A LEU* 3.3 11.2 + - + +
1613A ALA* 1.3 75.8 - - - +
1615A SER* 1.3 61.1 + - - +
1617A VAL* 3.6 3.3 + - - +
1618A GLU 3.3 2.1 + - - -
1619A ARG* 2.8 42.3 + - + -
1620A LEU* 3.1 20.1 + - + +
5009A GOL 3.9 21.8 - - - -
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Residues in contact with SER1615 (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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1401A CYS* 6.1 0.2 - - - -
1406A ASN* 5.0 1.2 + - - -
1417A CYS* 2.7 26.1 + - - +
1419A LEU* 3.8 26.6 + - - +
1611A LEU 3.1 13.4 + - - -
1612A GLY 3.5 7.6 - - - -
1614A LEU* 1.3 77.1 - - - +
1616A ALA* 1.3 64.0 + - - +
1618A GLU* 3.2 16.1 + - - +
1619A ARG 5.0 0.2 - - - +
1620A LEU* 4.0 13.8 - - - +
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Residues in contact with ALA1616 (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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1406A ASN* 2.8 29.5 + - - +
1412A TRP* 3.7 35.0 - - + -
1417A CYS 3.3 8.5 + - - -
1418A SER* 4.2 7.6 - - - -
1424A PRO* 5.2 0.2 - - + -
1425A TRP* 4.5 7.2 - - + -
1612A GLY 2.9 16.5 + - - +
1613A ALA* 3.1 10.2 + - - +
1615A SER* 1.3 76.3 - - - +
1617A VAL* 1.3 59.9 + - + +
1618A GLU* 3.4 0.8 + - - +
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Residues in contact with VAL1617 (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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1412A TRP* 5.5 0.4 - - + -
1425A TRP* 4.2 19.3 - - + -
1434A TRP* 4.5 20.2 - - + +
1437A PHE* 3.9 18.8 - - + -
1438A ASN* 3.8 20.0 - - + +
1613A ALA 3.2 16.8 - - - +
1614A LEU 3.7 6.5 - - - +
1616A ALA* 1.3 79.9 - - + +
1618A GLU* 1.3 61.3 + - - +
1619A ARG* 3.7 15.3 - - + -
1C NAG 2.7 35.3 + - - +
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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