Contacts of the helix formed by residues 1481 - 1490 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1477C TYR* 4.6 1.8 - - + -
1478C LYS* 2.9 31.1 + - - +
1480C GLU* 1.3 85.3 - - - +
1482C GLU* 1.3 57.6 + - - +
1483C GLN 3.3 2.2 - - - -
1484C LYS* 3.2 17.3 + - + +
1485C LEU* 2.9 26.9 + - - +
1849C PHE* 3.7 40.3 - - + +
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Residues in contact with GLU1482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477C TYR* 2.8 40.5 + - + +
1478C LYS 3.7 1.8 + - - -
1479C LYS* 3.3 19.5 + - - +
1480C GLU 3.4 0.8 - - - -
1481C ASP* 1.3 78.1 - - - +
1483C GLN* 1.3 65.2 + - + +
1485C LEU* 3.1 14.4 + - + +
1486C VAL* 3.2 15.5 + - + +
1526C LYS* 4.1 3.1 - - - +
1529C SER* 2.2 40.3 + - - -
1530C LEU* 3.4 16.9 + - + -
1533C SER* 3.1 23.5 + - - +
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Residues in contact with GLN1483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1480C GLU 4.9 3.5 + - - +
1481C ASP 3.3 0.8 - - - -
1482C GLU* 1.3 80.3 + - + +
1484C LYS* 1.3 57.0 + - - +
1486C VAL* 3.3 18.6 - - - +
1487C LYS* 2.9 30.1 + - - +
1491C LEU* 5.1 8.3 - - - +
1533C SER* 4.1 16.6 + - - -
1537C SER* 5.7 0.6 + - - -
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Residues in contact with LYS1484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1480C GLU 5.5 0.2 + - - -
1481C ASP* 3.2 21.5 + - - +
1483C GLN* 1.3 75.8 - - - +
1485C LEU* 1.3 65.8 + - - +
1487C LYS* 3.6 16.7 - - - +
1488C ASN* 3.1 38.6 + - - +
1846C GLY 4.8 1.6 - - - -
1849C PHE* 3.6 37.6 - - + +
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Residues in contact with LEU1485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477C TYR* 3.8 47.1 - - + -
1481C ASP 2.9 11.7 + - - +
1482C GLU* 3.1 10.1 + - + +
1484C LYS* 1.3 77.9 - - - +
1486C VAL* 1.3 61.7 + - + +
1488C ASN* 3.9 1.6 - - - +
1489C LEU* 2.9 57.7 + - + +
1511C LEU* 4.3 13.2 - - + -
1514C CYS* 4.2 10.3 - - - -
1530C LEU* 4.6 7.6 - - + -
1847C LEU* 4.2 2.5 - - + +
1849C PHE* 3.7 10.0 - - + -
1850C ILE* 3.7 26.5 - - + -
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Residues in contact with VAL1486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482C GLU* 3.2 11.6 + - + +
1483C GLN* 3.3 36.3 - - - +
1485C LEU* 1.3 84.1 - - + +
1487C LYS* 1.3 60.6 + - - +
1490C ILE* 3.0 28.4 + - + +
1491C LEU* 2.9 28.5 + - + +
1511C LEU* 5.2 1.1 - - + -
1530C LEU* 5.1 7.9 - - + -
1533C SER* 4.0 25.4 - - - -
1534C THR* 4.4 5.4 - - - +
1537C SER* 3.4 23.1 - - - +
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Residues in contact with LYS1487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1483C GLN* 2.9 19.9 + - - +
1484C LYS* 3.6 17.0 - - - +
1485C LEU 3.2 0.2 - - - -
1486C VAL* 1.3 77.6 - - - +
1488C ASN* 1.3 73.9 + - - +
1491C LEU* 3.4 21.2 + - + +
1492C GLU* 2.8 69.6 + - + +
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Residues in contact with ASN1488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1484C LYS* 3.1 39.7 + - - +
1487C LYS* 1.3 99.9 + - - +
1489C LEU* 1.3 61.3 + - - +
1490C ILE 3.5 0.2 - - - -
1492C GLU* 4.5 5.4 - - - +
1493C LEU* 3.7 23.4 + - - +
1845C LEU* 3.7 15.0 - - - +
1846C GLY* 2.8 27.2 + - - -
1847C LEU* 3.7 15.0 - - + -
1849C PHE* 4.0 1.8 - - - -
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Residues in contact with LEU1489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485C LEU* 2.9 27.7 + - + +
1488C ASN* 1.3 77.7 - - - +
1490C ILE* 1.3 63.7 + - + +
1493C LEU* 3.2 28.0 - - + +
1507C PRO* 3.8 28.0 - - + +
1510C ILE* 3.7 31.2 - - + -
1511C LEU* 3.6 34.3 - - + -
1555C TRP* 3.4 6.2 - - - -
1845C LEU* 4.3 8.7 - - + -
1847C LEU* 4.0 20.9 - - + -
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Residues in contact with ILE1490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486C VAL* 3.0 21.4 + - + +
1488C ASN 3.5 0.4 - - - -
1489C LEU* 1.3 91.3 - - + +
1491C LEU* 1.3 69.4 + - - +
1492C GLU 3.4 1.6 + - - -
1493C LEU* 3.5 7.1 + - - +
1511C LEU* 4.1 13.2 - - + -
1534C THR* 4.0 31.9 - - + +
1537C SER* 3.7 42.4 - - - +
1538C ILE* 3.8 10.1 - - + +
1541C VAL* 3.4 14.0 - - + +
1545C ARG* 4.4 2.1 + - - -
1555C TRP* 3.6 32.3 + - + -
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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