Contacts of the helix formed by residues 1448 - 1457 (chain A) in PDB entry 5CZV
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 SER1448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1429A GLU* 3.2 29.2 + - - -
1446A CYS 3.5 1.0 - - - -
1447A SER* 1.3 80.5 - - - +
1449A PRO* 1.4 74.6 - - - +
1450A ALA 3.7 1.9 + - - -
1451A CYS* 3.1 30.3 + - - -
1452A LEU 3.3 0.2 + - - -
1453A TYR 3.1 10.3 + - - -
101H PHE* 3.7 7.4 - - - -
91L TYR 5.3 0.2 - - - -
92L LEU 3.5 8.9 + - - -
93L GLN* 4.2 4.5 - - - -
94L TYR* 3.4 16.4 - - - -
96L MET* 5.4 0.2 - - - -
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Residues in contact with PRO1449 (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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1448A SER* 1.4 81.2 - - - +
1450A ALA* 1.4 53.9 + - - +
1452A LEU* 3.1 25.1 + - - +
1453A TYR* 3.5 34.7 - - + +
1598A ASP 5.3 0.2 - - - +
101H PHE* 3.6 19.4 - - + -
32L TYR* 3.2 42.8 + - + +
91L TYR* 3.4 28.9 - - + +
92L LEU* 3.4 9.2 - - - +
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Residues in contact with ALA1450 (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 4.6 2.3 - - - +
1425A TRP* 4.5 5.9 - - - -
1427A GLN* 3.4 32.6 + - + +
1428A CYS* 3.5 16.7 + - - +
1429A GLU* 3.9 7.0 - - - +
1448A SER* 3.2 4.9 - - - +
1449A PRO* 1.4 78.0 - - - +
1451A CYS* 1.3 56.1 + - - +
1452A LEU* 3.3 10.3 + - - +
32L TYR* 5.9 0.2 - - - -
92L LEU* 3.5 38.2 + - + +
93L GLN* 4.2 0.2 - - + -
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Residues in contact with CYS1451 (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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1425A TRP* 4.5 9.4 + - - -
1428A CYS* 2.0 53.2 - - - -
1429A GLU* 3.7 13.5 - - - -
1430A ALA 4.4 1.3 - - - -
1433A CYS* 4.1 8.1 - - + +
1437A PHE* 4.8 1.2 - - - -
1445A ALA 4.5 4.0 - - - -
1446A CYS* 3.1 30.0 - - - +
1448A SER* 3.1 20.1 + - - +
1450A ALA* 1.3 72.8 - - - +
1452A LEU* 1.3 68.5 + - - +
1453A TYR 3.3 2.9 - - - -
1454A ASP* 3.4 5.2 + - - -
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Residues in contact with LEU1452 (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* 3.5 33.7 - - + +
1425A TRP* 4.0 14.8 - - + +
1437A PHE* 3.7 12.6 - - + -
1449A PRO 3.1 16.5 + - - +
1450A ALA 4.3 4.5 - - - +
1451A CYS* 1.3 78.4 - - - +
1453A TYR* 1.4 66.9 + - + +
1454A ASP 3.0 7.1 + - - -
1455A ASN* 3.0 15.1 + - - -
1601A PHE* 5.5 2.2 - - + -
1606A SER* 4.4 4.9 - - - +
1609A ASP* 4.0 8.3 - - + +
1610A TYR* 3.9 33.7 - - + +
1613A ALA* 3.5 29.8 - - + -
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Residues in contact with TYR1453 (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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1446A CYS 3.9 1.1 - - - -
1447A SER* 3.3 17.7 - - - -
1448A SER 3.1 6.5 + - - -
1449A PRO* 3.5 38.3 - - + +
1452A LEU* 1.4 75.6 - - - +
1454A ASP* 1.4 69.8 + - - +
1455A ASN 3.2 0.2 - - - -
1456A PHE* 3.0 43.1 + + + +
1457A ASP 3.9 1.9 + - - -
1458A CYS* 4.5 4.2 + - - +
1598A ASP 4.0 8.5 + - - -
1599A HIS* 3.7 30.9 + - - +
1600A CYS 3.4 19.8 + - - -
1601A PHE* 3.6 30.7 - + - -
1602A PRO* 4.4 8.3 - - - +
1606A SER* 5.9 0.2 - - - -
1610A TYR* 5.5 0.2 - + - -
101H PHE* 3.6 27.6 - + - -
32L TYR* 4.4 2.8 + - - -
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Residues in contact with ASP1454 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1436A LEU 3.0 15.1 - - - +
1437A PHE* 3.9 7.0 - - - -
1441A ARG 3.0 4.0 - - - +
1442A CYS* 3.6 2.8 - - - -
1443A ASP* 2.8 35.1 + - - +
1446A CYS* 3.0 32.4 + - - +
1447A SER* 4.2 2.5 - - - -
1451A CYS 3.4 3.6 + - - -
1452A LEU 3.0 2.2 + - - -
1453A TYR* 1.4 75.9 - - - +
1455A ASN* 1.4 67.3 + - - +
1457A ASP* 3.0 15.8 + - - +
1458A CYS* 4.1 5.7 - - - -
5002A CA 2.4 31.0 - - - -
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Residues in contact with ASN1455 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1437A PHE* 3.2 44.2 - - + +
1438A ASN* 5.1 0.2 - - - -
1452A LEU 3.0 9.8 + - - -
1454A ASP* 1.4 74.6 - - - +
1456A PHE* 1.4 62.3 + - - +
1457A ASP* 3.2 7.6 + - - +
1465A ARG* 2.8 28.8 + - - +
1610A TYR* 2.6 38.7 + - - -
1614A LEU* 3.3 16.7 - - - +
1619A ARG* 3.4 32.7 + - - +
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Residues in contact with PHE1456 (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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1453A TYR* 3.0 34.3 + + + +
1455A ASN* 1.4 73.5 - - - +
1457A ASP* 1.3 55.8 + - - +
1458A CYS 3.2 5.6 - - - -
1459A HIS* 3.7 22.9 - - - +
1460A ALA* 2.8 31.2 + - + +
1465A ARG* 4.2 8.3 - - - +
1538A ILE 4.4 0.7 - - - -
1539A LEU 4.0 7.9 - - - -
1540A ARG* 3.7 33.0 - - + +
1599A HIS* 3.5 31.4 - - + -
1601A PHE* 3.8 26.7 - + - -
1610A TYR* 3.4 44.2 - + - -
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Residues in contact with ASP1457 (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 4.0 6.9 - - - +
1440A SER* 3.5 33.0 + - - -
1441A ARG* 3.5 26.1 + - - +
1442A CYS* 3.5 15.1 + - - +
1453A TYR 3.9 0.4 + - - -
1454A ASP* 3.0 17.0 + - - +
1455A ASN 3.7 5.4 - - - +
1456A PHE* 1.3 75.8 - - - +
1458A CYS* 1.3 58.2 + - - +
1460A ALA 4.2 5.8 - - - +
1461A GLY* 3.9 15.9 - - - -
1465A ARG* 3.3 30.1 + - - +
1619A ARG* 3.7 9.7 + - - -
5002A CA 4.2 1.0 - - - -
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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