Contacts of the helix formed by residues 1481 - 1490 (chain B) in PDB entry 5JCZ
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 ASP1481 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1477B TYR* 4.2 2.4 - - + -
1478B LYS* 2.9 39.0 + - - +
1480B GLU* 1.3 86.3 - - - +
1482B GLU* 1.3 58.2 + - - +
1483B GLN 3.4 2.2 - - - -
1484B LYS* 3.4 13.9 + - + +
1485B LEU* 2.9 28.1 + - - +
1849B PHE* 3.7 36.1 - - + +
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Residues in contact with GLU1482 (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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1477B TYR* 3.5 34.2 + - + +
1478B LYS 3.6 1.4 + - - -
1479B LYS* 3.6 14.6 + - - +
1480B GLU 3.4 2.0 - - - -
1481B ASP* 1.3 75.9 - - - +
1483B GLN* 1.3 64.7 + - + +
1485B LEU* 3.1 5.3 + - - +
1486B VAL* 3.0 27.1 + - + +
1526B LYS* 4.7 6.4 - - - +
1529B SER* 2.4 39.2 + - - +
1530B LEU* 4.0 13.9 + - + +
1533B SER* 2.6 30.3 + - - +
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Residues in contact with GLN1483 (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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1480B GLU 4.8 4.6 + - - +
1481B ASP* 3.4 0.4 - - - +
1482B GLU* 1.3 80.3 - - + +
1484B LYS* 1.3 57.8 + - - +
1486B VAL* 3.9 5.3 - - - +
1487B LYS* 3.0 30.9 + - - +
1533B SER* 5.9 2.7 - - - +
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Residues in contact with LYS1484 (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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1480B GLU 5.1 1.7 + - - +
1481B ASP* 3.4 24.5 + - + +
1482B GLU 3.2 0.2 - - - -
1483B GLN* 1.3 78.1 - - - +
1485B LEU* 1.3 61.6 + - - +
1487B LYS* 3.7 12.2 - - + +
1488B ASN* 3.3 47.0 + - - +
1846B GLY 5.2 0.2 - - - -
1849B PHE* 3.8 20.1 - - + -
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Residues in contact with LEU1485 (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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1477B TYR* 4.0 40.8 - - + -
1481B ASP 2.9 14.3 + - - +
1482B GLU 3.1 8.7 + - - +
1484B LYS* 1.3 77.6 - - - +
1486B VAL* 1.3 64.2 + - + +
1489B LEU* 3.2 51.8 + - + +
1511B LEU* 5.1 4.9 - - + -
1514B CYS* 4.1 13.5 - - - -
1530B LEU* 4.2 15.7 - - + -
1847B LEU* 4.4 3.9 - - + +
1849B PHE* 3.7 11.6 - - + -
1850B ILE* 3.6 28.7 - - + -
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Residues in contact with VAL1486 (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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1482B GLU* 3.0 14.7 + - + +
1483B GLN* 4.2 5.4 - - - +
1485B LEU* 1.3 77.8 - - - +
1487B LYS* 1.3 60.5 + - - +
1489B LEU* 5.0 0.2 - - - -
1490B ILE* 3.1 22.2 + - + +
1491B LEU* 3.0 23.8 + - - +
1511B LEU* 5.9 1.3 - - + -
1530B LEU* 6.4 2.2 - - + -
1533B SER* 4.4 16.8 - - - +
1534B THR 5.4 0.2 - - - +
1537B SER* 3.5 23.4 + - - +
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Residues in contact with LYS1487 (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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1483B GLN 3.0 19.8 + - - +
1484B LYS* 3.7 17.0 - - + +
1485B LEU 3.2 0.6 - - - -
1486B VAL* 1.3 77.2 - - - +
1488B ASN* 1.3 65.1 + - - +
1491B LEU* 3.1 19.5 + - + +
1492B GLU* 2.6 66.3 + - + +
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Residues in contact with ASN1488 (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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1484B LYS* 3.3 38.7 + - - +
1487B LYS* 1.3 91.1 - - - +
1489B LEU* 1.3 60.2 + - - +
1490B ILE 3.4 0.2 - - - -
1492B GLU* 4.1 12.7 - - - +
1493B LEU* 3.3 28.2 + - - +
1845B LEU 3.9 13.9 - - - +
1846B GLY* 3.0 23.5 + - - -
1847B LEU* 3.7 18.0 - - + +
1849B PHE* 4.1 0.2 - - - -
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Residues in contact with LEU1489 (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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1485B LEU* 3.2 28.4 + - + +
1488B ASN* 1.3 78.4 - - - +
1490B ILE* 1.3 62.6 + - + +
1493B LEU* 3.3 25.0 - - + +
1507B PRO* 3.8 27.4 - - + +
1510B ILE* 3.6 34.3 - - + -
1511B LEU* 3.6 33.4 - - + -
1555B TRP* 3.3 13.0 - - - -
1845B LEU* 4.5 2.9 - - + -
1847B LEU* 3.9 22.0 - - + -
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Residues in contact with ILE1490 (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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1486B VAL* 3.1 16.3 + - + +
1489B LEU* 1.3 89.3 - - + +
1491B LEU* 1.3 67.2 + - - +
1492B GLU 3.4 1.5 + - - -
1493B LEU 3.7 6.2 + - - +
1511B LEU* 3.8 34.8 - - + -
1534B THR* 3.9 20.6 - - + +
1537B SER* 3.6 43.7 - - - +
1538B ILE* 3.8 11.0 - - + +
1541B VAL* 3.5 9.1 - - + +
1555B TRP* 3.3 36.6 + - + -
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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