Contacts of the helix formed by residues 1587 - 1600 (chain B) in PDB entry 1CJY
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 PHE1587 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1585B PRO* 3.5 6.3 - - + +
1586B PRO* 1.3 94.5 - - + +
1588B LYS* 1.3 66.2 + - - +
1589B GLU 3.3 3.1 - - - -
1590B LEU* 3.2 20.4 + - + -
1591B LEU* 3.0 37.1 + - + +
1607B ILE* 5.0 2.9 - - + -
1609B PRO* 3.9 36.3 - - + -
1611B VAL* 4.8 2.9 - - + -
1612B PHE* 4.0 19.1 - - + -
1621B TYR* 3.5 38.6 - + - -
1623B PHE* 3.7 22.9 - + - -
1639B HIS* 3.9 25.6 - + - -
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Residues in contact with LYS1588 (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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1585B PRO* 4.8 5.8 + - - +
1586B PRO* 3.6 2.4 - - - +
1587B PHE* 1.3 77.7 - - - +
1589B GLU* 1.3 84.8 + - + +
1591B LEU* 3.4 10.3 + - - +
1592B LEU* 3.3 38.1 + - + +
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Residues in contact with GLU1589 (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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1553B THR 5.4 0.2 - - - +
1554B PHE* 3.1 18.7 - - - +
1555B ASN* 2.6 35.3 + - + +
1556B LEU* 4.1 11.8 - - + +
1575B ASP* 4.0 14.1 + - - +
1577B SER* 3.3 29.4 - - - +
1586B PRO 5.4 0.2 + - - -
1587B PHE 3.3 0.8 - - - -
1588B LYS* 1.3 99.9 + - + +
1590B LEU* 1.3 65.1 + - - +
1592B LEU* 3.1 9.0 + - - +
1593B ALA* 3.1 21.8 + - - +
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Residues in contact with LEU1590 (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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1556B LEU* 4.0 7.6 - - + +
1558B TYR* 4.0 18.2 - - + +
1575B ASP* 4.9 1.0 + - - -
1587B PHE* 3.2 21.6 + - + +
1589B GLU* 1.3 77.5 - - - +
1591B LEU* 1.3 57.8 + - - +
1593B ALA* 3.3 2.8 + - - +
1594B GLU* 3.0 24.5 + - - +
1604B PHE* 3.7 28.7 - - + -
1607B ILE* 3.8 32.5 - - + -
1623B PHE* 3.9 20.0 - - + -
1637B ILE* 4.5 2.5 - - + -
1639B HIS* 3.6 32.3 - - + +
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Residues in contact with LEU1591 (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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1587B PHE* 3.0 27.6 + - + +
1588B LYS* 3.6 8.3 - - - +
1589B GLU 3.1 0.2 - - - -
1590B LEU* 1.3 75.0 - - - +
1592B LEU* 1.3 61.1 + - + +
1594B GLU* 3.3 24.9 + - - +
1595B LYS* 3.0 26.3 + - - +
1607B ILE* 3.8 24.5 - - + +
1609B PRO* 4.5 23.8 - - + -
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Residues in contact with LEU1592 (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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1342B MET* 3.3 22.3 - - + +
1553B THR 4.0 17.9 - - - +
1554B PHE* 3.7 18.4 - - + -
1588B LYS* 3.3 37.4 + - + +
1589B GLU* 3.1 15.9 + - - +
1591B LEU* 1.3 75.8 - - + +
1593B ALA* 1.3 65.1 + - - +
1595B LYS* 3.2 20.4 + - - +
1596B TRP* 3.0 19.1 + - - +
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Residues in contact with ALA1593 (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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1554B PHE* 3.6 32.5 - - + -
1556B LEU* 5.0 1.1 - - + -
1558B TYR* 3.6 32.5 - - + -
1562B LEU* 5.3 0.7 - - - +
1589B GLU 3.1 10.5 + - - +
1590B LEU* 3.6 8.3 - - - +
1591B LEU 3.3 0.2 - - - -
1592B LEU* 1.3 77.1 - - - +
1594B GLU* 1.3 56.9 + - - +
1596B TRP* 3.3 6.2 + - - +
1597B ALA* 2.9 28.1 + - - +
1604B PHE* 4.4 4.7 - - + -
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Residues in contact with GLU1594 (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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1590B LEU 3.0 13.8 + - - +
1591B LEU* 3.6 18.0 - - - +
1592B LEU 3.2 0.2 - - - -
1593B ALA* 1.3 74.5 - - - +
1595B LYS* 1.3 67.0 + - - +
1597B ALA* 3.2 2.4 + - - +
1598B LYS* 3.0 22.8 + - + +
1604B PHE* 3.6 31.0 - - + +
1605B PRO 3.1 12.6 - - - +
1606B LYS* 3.6 4.3 - - - -
1607B ILE* 2.9 45.5 + - + +
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Residues in contact with LYS1595 (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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1342B MET* 3.4 21.7 - - + +
1591B LEU 3.0 13.4 + - - +
1592B LEU* 3.2 21.9 + - - +
1594B GLU* 1.3 76.4 - - - +
1596B TRP* 1.3 60.2 + - - +
1598B LYS* 3.1 8.5 + - - +
1599B MET* 2.8 42.2 + - + +
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Residues in contact with TRP1596 (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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1342B MET* 3.5 38.0 + - + -
1344B ALA 5.0 2.8 + - - -
1346B TRP* 3.9 20.4 - + + +
1553B THR* 5.7 0.2 - - + -
1554B PHE* 3.7 25.4 - + + -
1558B TYR* 5.5 0.2 - - + -
1559B PRO* 3.6 41.7 - - + -
1562B LEU* 3.8 25.4 - - + -
1592B LEU 3.0 8.0 + - - +
1593B ALA 3.4 9.6 - - - +
1595B LYS* 1.3 77.4 - - - +
1597B ALA* 1.3 63.4 + - - +
1599B MET* 3.2 7.5 + - - +
1600B ASN* 2.9 62.1 + - - +
1602B LEU* 4.3 18.4 - - + -
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Residues in contact with ALA1597 (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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1562B LEU* 3.9 12.1 - - + -
1593B ALA 2.9 17.3 + - - +
1594B GLU 3.2 5.3 + - - +
1596B TRP* 1.3 86.3 - - - +
1598B LYS* 1.3 61.5 + - - +
1600B ASN 3.5 0.6 + - - +
1601B LYS 3.1 2.6 + - - -
1602B LEU* 2.7 46.6 + - - +
1604B PHE* 3.6 28.5 - - + -
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Residues in contact with LYS1598 (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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1594B GLU* 3.0 14.2 + - + +
1595B LYS* 3.5 9.0 - - - +
1597B ALA* 1.3 75.5 - - - +
1599B MET* 1.3 65.6 + - - +
1601B LYS* 2.9 15.8 + - - +
1602B LEU 4.9 1.1 - - - -
1604B PHE* 5.7 0.2 - - - +
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Residues in contact with MET1599 (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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1342B MET* 3.6 41.1 - - + +
1343B PHE* 4.2 25.8 - - + -
1595B LYS* 2.8 42.9 + - + +
1596B TRP* 3.2 11.4 - - - +
1598B LYS* 1.3 77.4 - - - +
1600B ASN* 1.3 63.7 + - - +
1601B LYS* 3.5 1.0 + - - +
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Residues in contact with ASN1600 (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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1358B LYS* 4.2 26.9 - - - +
1596B TRP* 2.9 59.3 + - + +
1599B MET* 1.3 81.5 + - - +
1601B LYS* 1.3 69.5 + - - +
1602B LEU* 3.1 29.8 - - + +
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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