Contacts of the helix formed by residues 1481 - 1490 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1477E TYR* 4.6 5.6 - - + -
1478E LYS* 2.9 30.5 + - + +
1480E GLU* 1.3 85.7 - - - +
1482E GLU* 1.3 51.4 + - - +
1483E GLN 3.2 3.4 - - - -
1484E LYS* 3.1 19.9 + - + +
1485E LEU* 2.7 34.3 + - - +
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Residues in contact with GLU1482 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477E TYR* 2.7 38.1 + - + +
1478E LYS 3.6 2.2 + - - -
1479E LYS* 3.5 30.1 + - - +
1480E GLU 3.4 1.6 - - - -
1481E ASP* 1.3 78.6 - - - +
1483E GLN* 1.3 60.9 + - - +
1485E LEU* 3.2 12.2 + - + +
1486E VAL* 3.2 24.6 + - + +
1526E LYS 4.2 0.7 - - - +
1529E SER* 2.2 30.9 + - - -
1530E LEU* 3.7 14.9 + - + -
1533E SER* 3.1 22.8 + - - +
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Residues in contact with GLN1483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1480E GLU 4.7 5.6 + - - +
1481E ASP* 3.2 0.8 - - - +
1482E GLU* 1.3 79.6 - - - +
1484E LYS* 1.3 61.8 + - - +
1486E VAL* 3.3 11.8 - - + +
1487E LYS* 3.1 26.0 + - + +
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Residues in contact with LYS1484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1480E GLU 5.3 0.6 + - - +
1481E ASP* 3.1 24.1 + - + +
1483E GLN* 1.3 75.6 - - - +
1485E LEU* 1.3 67.1 + - - +
1487E LYS* 4.0 17.7 - - - +
1488E ASN* 3.0 45.6 + - - +
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Residues in contact with LEU1485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477E TYR* 3.9 46.9 - - + -
1481E ASP 2.7 13.7 + - - +
1482E GLU* 3.2 11.2 - - - +
1483E GLN 3.2 0.2 - - - -
1484E LYS* 1.3 77.9 - - - +
1486E VAL* 1.3 61.5 + - + +
1488E ASN* 4.1 1.4 - - - +
1489E LEU* 3.1 52.8 + - + +
1510E ILE* 5.4 2.5 - - + -
1511E LEU* 5.4 2.2 - - + -
1514E CYS* 4.4 13.9 - - - -
1530E LEU* 4.0 18.4 - - + -
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Residues in contact with VAL1486 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482E GLU* 3.5 12.3 - - + +
1483E GLN* 3.3 20.4 - - + +
1485E LEU* 1.3 83.8 - - + +
1487E LYS* 1.3 59.5 + - - +
1489E LEU* 4.6 1.6 - - - -
1490E ILE* 3.0 27.6 + - + +
1491E LEU* 2.9 28.8 + - + +
1511E LEU* 5.2 2.2 - - + -
1530E LEU* 5.0 6.7 - - + -
1533E SER* 4.0 31.2 - - - +
1534E THR* 4.3 5.8 - - - +
1537E SER* 3.5 21.5 - - - +
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Residues in contact with LYS1487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1483E GLN* 3.1 21.0 + - + +
1484E LYS* 3.6 19.8 - - - +
1485E LEU 3.1 0.4 - - - -
1486E VAL* 1.3 77.2 - - - +
1488E ASN* 1.3 76.0 + - - +
1491E LEU* 3.3 25.1 + - + +
1492E GLU* 2.7 69.4 + - - +
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Residues in contact with ASN1488 (chain E).
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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1484E LYS* 3.0 47.1 + - - +
1485E LEU* 4.5 0.9 - - - +
1487E LYS* 1.3 98.5 + - - +
1489E LEU* 1.3 58.7 + - - +
1490E ILE 3.5 0.2 - - - -
1492E GLU* 4.4 7.7 - - - +
1493E LEU* 3.3 26.5 - - - +
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Residues in contact with LEU1489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485E LEU* 3.1 32.8 + - + +
1486E VAL* 4.6 0.2 - - - -
1488E ASN* 1.3 77.4 - - - +
1490E ILE* 1.3 62.5 + - + +
1493E LEU* 3.3 29.2 - - + +
1507E PRO* 3.9 22.4 - - + +
1510E ILE* 3.7 37.9 - - + -
1511E LEU* 3.7 33.9 - - + -
1514E CYS* 5.9 0.2 - - - -
1555E TRP* 3.4 13.7 - - - -
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Residues in contact with ILE1490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486E VAL* 3.0 21.3 + - + +
1489E LEU* 1.3 91.2 - - + +
1491E LEU* 1.3 69.0 + - - +
1492E GLU 3.3 2.9 + - - -
1493E LEU* 3.6 7.0 + - - +
1511E LEU* 4.1 21.5 - - + -
1534E THR* 4.0 24.2 - - + +
1537E SER* 3.8 40.2 - - - -
1538E ILE* 3.9 10.8 - - + +
1541E VAL* 3.5 12.1 - - + +
1545E ARG* 4.3 1.6 + - - -
1555E TRP* 3.5 37.2 + - + -
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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