Contacts of the helix formed by residues 1557 - 1563 (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 PRO1557 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193B LEU* 3.8 26.0 - - + +
1194B GLY 3.5 27.8 - - - +
1225B ALA* 3.9 11.5 - - + +
1226B GLY* 4.0 9.0 - - - +
1227B LEU* 3.5 28.0 - - + -
1330B THR* 4.3 2.0 - - + -
1346B TRP* 4.2 4.7 - - + -
1555B ASN 3.8 1.3 - - - +
1556B LEU* 1.3 81.1 - - + +
1558B TYR* 1.3 65.0 + - - +
1559B PRO* 3.3 6.3 - - + -
1560B LEU* 3.2 29.1 + - + +
1561B ILE* 4.0 2.3 + - - +
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Residues in contact with TYR1558 (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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1193B LEU* 3.8 15.9 - - + -
1554B PHE* 4.8 0.2 - - + -
1556B LEU* 2.8 42.9 + - + +
1557B PRO* 1.3 72.2 - - - +
1559B PRO* 1.3 68.3 - - + +
1561B ILE* 2.8 17.6 + - + +
1562B LEU* 2.9 37.6 + - + +
1571B ILE* 4.0 19.9 - - + +
1573B SER* 3.3 14.3 + - - -
1590B LEU* 4.0 12.5 - - + +
1593B ALA* 3.6 23.6 - - + +
1596B TRP* 5.5 0.4 - - + -
1604B PHE* 3.4 18.2 - + - -
1637B ILE* 3.1 49.1 - - + +
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Residues in contact with PRO1559 (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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1346B TRP* 3.6 47.6 - - + -
1357B ALA* 6.1 0.3 - - - +
1554B PHE* 4.0 13.9 - - + -
1556B LEU 4.0 0.7 - - - +
1557B PRO* 3.3 5.8 - - + -
1558B TYR* 1.3 94.7 - - + +
1560B LEU* 1.3 61.0 + - + +
1561B ILE 3.2 1.0 + - - -
1562B LEU* 3.5 7.9 + - + +
1563B ARG* 3.6 13.0 + - - +
1596B TRP* 3.6 42.0 - - + -
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Residues in contact with LEU1560 (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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1225B ALA* 4.0 14.8 - - + -
1226B GLY 4.0 5.6 - - - +
1328B LEU* 3.9 18.9 - - + +
1329B PHE* 3.3 45.8 - - - +
1330B THR* 3.6 24.5 - - + +
1346B TRP* 5.5 0.7 - - + -
1348B GLU* 3.6 34.8 - - + -
1349B PHE 4.4 0.2 - - - +
1557B PRO* 3.2 12.6 + - + +
1558B TYR 3.0 1.0 + - - -
1559B PRO* 1.3 79.0 - - + +
1561B ILE* 1.3 61.0 + - - +
1562B LEU 3.6 0.2 - - - -
1563B ARG* 4.3 2.4 - - - +
1566B ARG* 3.0 32.0 + - - +
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Residues in contact with ILE1561 (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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1191B ALA* 3.2 32.8 - - + -
1193B LEU* 4.0 21.1 - - + -
1223B TYR* 3.7 17.0 - - + -
1225B ALA* 4.5 7.6 - - + -
1328B LEU* 3.6 29.8 - - + -
1557B PRO 4.7 1.3 - - - +
1558B TYR* 2.8 13.4 + - - +
1560B LEU* 1.3 77.3 - - + +
1562B LEU* 1.3 65.9 + - + +
1563B ARG 3.3 2.2 - - - -
1566B ARG* 4.5 3.6 - - - +
1568B VAL* 2.7 38.1 - - + +
1571B ILE* 3.9 27.5 - - + +
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Residues in contact with LEU1562 (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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1558B TYR* 2.9 44.4 + - + +
1559B PRO* 3.5 5.1 + - + +
1561B ILE* 1.3 79.0 - - - +
1563B ARG* 1.3 65.8 + - - +
1564B PRO* 2.8 12.1 - - - +
1571B ILE* 4.2 17.5 - - + -
1593B ALA 5.3 0.2 - - - +
1596B TRP* 3.8 23.8 - - + -
1597B ALA* 3.9 21.3 - - + -
1602B LEU* 3.9 21.6 - - + +
1603B PRO* 4.0 21.1 - - + +
1604B PHE* 4.0 7.6 - - + -
1635B PRO* 4.7 6.1 - - + -
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Residues in contact with ARG1563 (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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1145B ARG* 5.1 0.6 - - - +
1148B MET 3.0 21.6 + - - -
1149B ALA 3.2 18.8 + - - -
1150B LEU* 3.9 14.0 - - - +
1151B CYS 5.3 0.2 - - - +
1154B GLU* 4.9 0.8 + - - -
1348B GLU* 3.1 29.4 + - - -
1353B GLU* 5.9 1.0 + - - -
1357B ALA* 3.6 24.5 + - + +
1362B PHE* 3.5 26.9 - - - -
1559B PRO 3.6 11.9 + - - +
1560B LEU* 4.3 1.8 - - - +
1561B ILE 3.3 1.1 - - - +
1562B LEU* 1.3 74.7 - - - +
1564B PRO* 1.3 73.6 - - + +
1565B GLN* 3.1 24.1 - - + +
1566B ARG* 2.8 53.9 + - + +
1567B GLY 4.0 0.9 + - - -
1568B VAL* 5.1 0.5 - - - +
1602B LEU* 5.7 0.2 - - - -
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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
------------------------------------------------------------
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