Contacts of the helix formed by residues 1483 - 1494 (chain J) in PDB entry 5IJO
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 TYR1483 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1434J LEU* 4.7 19.2 - - + +
1481J LEU 3.8 1.2 + - - -
1482J GLY* 1.4 73.6 - - - +
1484J LEU* 1.3 63.5 + - - +
1485J CYS 3.2 1.7 + - - -
1486J GLN* 3.3 14.6 + - - +
1487J ALA* 3.6 9.0 + - - +
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Residues in contact with LEU1484 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434J LEU* 5.1 17.2 - - + +
1437J VAL* 5.7 4.2 - - + +
1449J ALA* 5.5 11.9 - - + -
1481J LEU 4.3 9.4 + - - +
1482J GLY 3.2 1.4 + - - -
1483J TYR* 1.3 77.6 - - - +
1485J CYS* 1.3 64.3 + - - +
1487J ALA* 3.0 10.0 + - - +
1488J CYS* 3.0 21.7 + - - +
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Residues in contact with CYS1485 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482J GLY 3.7 8.4 + - - +
1483J TYR 3.2 1.4 + - - -
1484J LEU* 1.3 78.5 - - - +
1486J GLN* 1.3 64.9 + - - +
1488J CYS* 3.2 14.4 + - - +
1489J THR* 3.3 11.6 + - - -
1559J SER* 6.2 5.4 - - - +
1562J LEU* 4.9 18.1 - - + +
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Residues in contact with GLN1486 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482J GLY 4.9 0.6 + - - -
1483J TYR 3.3 9.3 + - - +
1484J LEU 3.3 0.4 - - - -
1485J CYS* 1.3 78.3 - - - +
1487J ALA* 1.3 63.8 + - - +
1489J THR* 3.2 16.0 + - - -
1490J SER* 3.5 10.4 + - - -
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Residues in contact with ALA1487 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434J LEU 4.9 4.3 - - - +
1437J VAL* 3.0 38.9 - - + +
1438J ARG* 5.2 1.1 - - - -
1483J TYR 3.6 6.0 + - - +
1484J LEU* 3.0 13.8 + - - +
1486J GLN* 1.3 78.6 - - - +
1488J CYS* 1.3 63.2 + - - +
1490J SER* 3.3 16.2 + - - -
1491J LEU* 3.5 10.2 + - - +
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Residues in contact with CYS1488 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1437J VAL* 5.7 1.8 - - - +
1484J LEU 3.0 11.4 + - - +
1485J CYS* 3.2 11.9 + - - +
1487J ALA* 1.3 77.7 - - - +
1489J THR* 1.3 62.8 + - - +
1491J LEU* 3.0 9.8 + - - +
1492J LEU* 3.0 20.4 + - - +
1555J LEU* 4.7 27.6 - - + +
1558J LEU* 5.8 3.6 - - + -
1559J SER* 5.4 9.9 - - - +
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Residues in contact with THR1489 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485J CYS 3.3 7.1 + - - -
1486J GLN* 3.2 11.8 + - - -
1488J CYS* 1.3 78.1 - - - +
1490J SER* 1.3 64.4 + - - +
1492J LEU* 3.0 16.5 + - - +
1493J HIS* 3.1 14.9 + - - +
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Residues in contact with SER1490 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486J GLN 3.5 7.0 + - - -
1487J ALA* 3.3 11.1 + - - -
1488J CYS 3.2 1.0 - - - -
1489J THR* 1.3 78.7 - - - +
1491J LEU* 1.3 61.6 + - - +
1493J HIS* 3.6 6.6 + - - +
1494J SER* 3.5 19.2 + - - -
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Residues in contact with LEU1491 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1487J ALA 3.5 7.6 + - - +
1488J CYS* 3.0 12.0 + - - +
1490J SER* 1.3 78.2 - - - +
1492J LEU* 1.3 64.7 + - - +
1494J SER* 3.2 21.9 + - - +
1495J ARG* 4.8 0.3 - - - -
1498J LEU* 4.3 13.0 - - + +
1555J LEU* 5.9 5.4 - - + -
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Residues in contact with LEU1492 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488J CYS 3.0 11.7 + - - +
1489J THR* 3.0 11.2 + - - +
1491J LEU* 1.3 77.0 - - - +
1493J HIS* 1.3 65.2 + - - +
1494J SER 3.3 0.7 + - - -
1495J ARG* 4.1 8.3 + - - +
1555J LEU* 6.6 0.7 - - + -
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Residues in contact with HIS1493 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1489J THR 3.1 11.7 + - - +
1490J SER* 4.0 6.1 - - - +
1491J LEU 3.3 0.2 - - - -
1492J LEU* 1.3 81.5 - - - +
1494J SER* 1.3 58.7 + - - +
1495J ARG* 3.5 4.0 + - - +
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Residues in contact with SER1494 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490J SER 3.5 10.0 + - - -
1491J LEU* 3.2 10.3 + - - +
1492J LEU 3.2 1.0 - - - -
1493J HIS* 1.3 78.5 - - - +
1495J ARG* 1.3 58.3 + - - +
1496J LYS* 3.2 2.0 - - - +
1497J MET* 3.5 25.7 - - - +
1498J LEU* 3.0 25.3 + - - +
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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