Contacts of the helix formed by residues 1686 - 1703 (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 PRO1686 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1260B SER* 4.7 8.3 - - - +
1677B PRO* 5.1 4.5 - - + -
1684B GLN* 3.4 22.2 - - + +
1685B TYR* 1.3 85.3 - - - +
1687B ASN* 1.3 58.8 + - - +
1688B GLN* 2.6 22.6 + - + +
1689B ALA* 2.7 28.2 + - + +
1690B PHE* 2.9 7.4 + - - -
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Residues in contact with ASN1687 (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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1256B MET* 3.9 36.1 + - - +
1257B LYS* 5.4 1.4 - - - +
1260B SER* 4.0 21.0 - - - -
1685B TYR 4.9 0.2 + - - -
1686B PRO* 1.3 69.6 - - - +
1688B GLN* 1.3 57.1 + - - +
1690B PHE* 3.8 8.0 - - - +
1691B LYS* 2.8 41.4 + - + +
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Residues in contact with GLN1688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1665B ILE* 5.1 10.9 - - - +
1686B PRO* 2.6 12.5 + - + +
1687B ASN* 1.3 77.7 - - - +
1689B ALA* 1.3 65.0 + - - +
1691B LYS* 3.4 3.8 + - - +
1692B ARG* 3.1 63.4 + - - +
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Residues in contact with ALA1689 (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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1677B PRO* 3.8 26.7 - - + -
1678B PHE* 3.3 27.2 - - + -
1685B TYR* 4.4 7.0 - - + -
1686B PRO* 2.7 30.0 + - + +
1688B GLN* 1.3 77.1 - - - +
1690B PHE* 1.3 64.1 + - - +
1692B ARG* 3.3 5.5 + - - +
1693B LEU* 3.2 16.8 + - - +
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Residues in contact with PHE1690 (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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1203B VAL* 3.4 30.4 - - + +
1206B SER* 4.1 15.5 - - - -
1252B ASN* 3.8 20.2 - - + -
1255B LEU* 3.2 31.6 - - + -
1256B MET* 3.5 42.4 - - + -
1259B VAL* 5.1 2.5 - - + -
1685B TYR* 4.4 18.5 - - + +
1686B PRO 2.9 12.7 + - - +
1687B ASN* 3.8 7.0 - - - +
1689B ALA* 1.3 78.7 - - - +
1691B LYS* 1.3 69.1 + - + +
1692B ARG 3.0 0.5 + - - -
1693B LEU* 3.8 0.9 - - - +
1694B HIS* 2.8 45.4 + + + +
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Residues in contact with LYS1691 (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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1256B MET* 3.8 31.4 - - - +
1665B ILE* 6.3 3.8 - - + -
1687B ASN* 2.8 28.0 + - + +
1688B GLN* 3.9 4.9 - - - +
1690B PHE* 1.3 77.0 - - + +
1692B ARG* 1.3 57.3 + - + +
1694B HIS* 4.3 3.8 - - + -
1695B ASP* 2.9 49.0 + - - +
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Residues in contact with ARG1692 (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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1647B PHE* 4.3 2.8 - - - -
1664B GLU 3.6 21.6 + - - -
1665B ILE* 3.4 19.6 + - + +
1667B ASP 4.1 6.3 + - - -
1668B PHE* 3.4 54.7 - - + +
1673B ASP* 5.6 1.2 + - - -
1677B PRO* 6.2 1.6 - - - +
1678B PHE* 4.2 9.6 - - + -
1688B GLN* 3.1 53.6 + - - +
1689B ALA* 3.5 10.1 - - - +
1690B PHE 3.1 0.6 - - - -
1691B LYS* 1.3 77.7 - - + +
1693B LEU* 1.3 58.5 + - - +
1695B ASP* 4.0 2.0 - - - +
1696B LEU* 2.8 32.1 + - - +
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Residues in contact with LEU1693 (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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1200B ARG* 3.5 38.4 - - + +
1203B VAL* 3.8 13.2 - - + -
1204B GLY* 3.9 14.3 - - - +
1642B LEU* 3.6 31.2 - - + -
1668B PHE* 5.4 1.6 - - + -
1670B ILE* 5.2 4.0 - - + -
1678B PHE* 3.8 30.2 - - + -
1685B TYR* 4.4 2.5 - - + -
1689B ALA 3.2 9.0 + - - +
1690B PHE 3.2 1.2 + - - -
1692B ARG* 1.3 78.5 - - - +
1694B HIS* 1.3 66.1 + - - +
1696B LEU* 4.4 8.7 - - + -
1697B MET* 3.2 28.5 + - + +
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Residues in contact with HIS1694 (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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1203B VAL* 3.9 11.8 - - + +
1206B SER* 3.4 16.0 + - - -
1207B GLY* 3.5 21.2 - - - -
1210B LYS* 3.5 26.1 + - + +
1252B ASN* 3.6 33.2 - - + -
1690B PHE* 2.8 38.9 + + + +
1691B LYS* 3.9 4.0 - - + +
1693B LEU* 1.3 78.1 - - - +
1695B ASP* 1.3 86.0 + - - +
1698B HIS* 3.1 26.7 + + + +
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Residues in contact with ASP1695 (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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1647B PHE* 3.6 23.2 - - + -
1665B ILE* 6.0 2.1 - - - +
1691B LYS* 2.9 39.6 + - - +
1692B ARG* 5.0 0.2 - - - -
1694B HIS* 1.3 87.9 - - - +
1696B LEU* 1.3 65.6 + - - +
1698B HIS* 3.1 12.2 + - + +
1699B PHE* 2.8 24.4 + - - +
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Residues in contact with LEU1696 (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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1642B LEU* 4.2 12.6 - - + -
1643B ALA 3.4 22.4 - - - +
1644B ASN* 3.5 25.6 - - - +
1647B PHE* 3.6 20.7 - - + -
1668B PHE* 4.5 10.3 - - + -
1670B ILE* 3.7 30.3 - - + -
1692B ARG 2.8 23.6 + - - +
1693B LEU* 3.7 8.5 - - + +
1695B ASP* 1.3 72.2 - - - +
1697B MET* 1.3 59.5 + - - +
1699B PHE* 3.0 5.0 + - - +
1700B ASN* 2.6 53.0 + - - +
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Residues in contact with MET1697 (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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1204B GLY* 3.5 22.0 - - - +
1208B VAL* 3.7 25.8 - - + +
1574B PHE* 4.2 11.4 - - + -
1575B ASP 6.0 0.4 - - - +
1576B PHE* 3.8 24.7 - - + -
1640B PHE* 4.9 6.3 - - + -
1641B VAL 4.4 18.2 - - - +
1642B LEU* 3.7 28.0 - - + -
1693B LEU* 3.2 15.4 + - + +
1694B HIS 4.2 0.9 - - - +
1696B LEU* 1.3 80.9 - - - +
1698B HIS* 1.3 62.9 + - - +
1699B PHE 3.2 0.2 - - - -
1700B ASN* 4.1 15.7 - - + -
1701B THR* 2.9 29.6 + - - +
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Residues in contact with HIS1698 (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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1207B GLY* 3.9 14.9 + - - +
1210B LYS* 3.6 24.2 + - + +
1211B ALA* 3.4 23.6 + - - +
1214B GLU* 2.8 31.3 + - - -
1694B HIS* 3.1 23.3 + - - +
1695B ASP* 3.1 14.3 + - + +
1697B MET* 1.3 77.4 - - - +
1699B PHE* 1.3 67.7 + - - +
1702B LEU* 3.3 42.2 + - + +
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Residues in contact with PHE1699 (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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1619B GLU* 3.9 2.0 - - - -
1646B ASN* 3.4 10.1 - - + -
1647B PHE* 3.3 45.8 - + + -
1650B TYR* 3.6 21.8 - + + -
1652B ALA* 3.2 17.7 - - - -
1653B PRO* 3.2 40.6 - - + -
1695B ASP 2.8 12.8 + - - +
1696B LEU 3.2 7.9 - - - +
1698B HIS* 1.3 77.9 - - - +
1700B ASN* 1.3 80.8 + - - +
1702B LEU* 2.8 7.4 + - - +
1703B ASN* 2.7 51.7 + - - +
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Residues in contact with ASN1700 (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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1619B GLU* 3.9 30.7 - - + +
1640B PHE* 3.5 8.8 - - + -
1641B VAL 4.1 13.1 + - - +
1643B ALA 2.9 25.5 + - - -
1644B ASN 4.2 0.8 + - - +
1696B LEU* 2.6 37.4 + - - +
1697B MET* 4.2 17.1 - - + +
1698B HIS 3.7 0.2 - - - -
1699B PHE* 1.3 85.2 - - - +
1701B THR* 1.3 60.7 + - - +
1703B ASN* 4.2 1.3 - - - -
1704B ASN* 2.5 34.7 + - - +
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Residues in contact with THR1701 (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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1208B VAL* 3.7 6.9 - - - +
1211B ALA* 3.4 28.7 - - + -
1212B LEU* 3.9 30.3 - - + +
1215B SER* 5.4 1.1 - - - +
1217B ILE* 6.1 0.7 - - + -
1574B PHE* 3.5 24.1 - - + -
1640B PHE* 3.9 11.7 - - + -
1697B MET* 2.9 19.4 + - - +
1699B PHE 2.9 4.8 + - - -
1700B ASN* 1.3 77.1 - - - +
1702B LEU* 1.3 62.4 + - + -
1704B ASN* 3.2 12.0 + - - +
1705B ILE* 3.5 13.6 + - + +
1708B ILE* 4.9 4.6 - - + +
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Residues in contact with LEU1702 (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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1211B ALA* 3.8 18.8 - - + +
1214B GLU* 3.9 6.7 - - + +
1215B SER* 3.7 18.4 - - - +
1653B PRO* 4.1 26.3 - - + +
1698B HIS* 3.3 41.4 + - + +
1699B PHE* 2.8 6.8 + - - +
1701B THR* 1.3 77.3 - - - +
1703B ASN* 1.3 57.5 + - - +
1704B ASN 3.1 3.6 + - - -
1705B ILE* 3.4 38.0 + - + +
1706B ASP* 4.9 1.4 - - - +
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Residues in contact with ASN1703 (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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1619B GLU* 3.1 17.5 - - - +
1646B ASN* 3.5 16.4 + - - +
1653B PRO* 3.0 29.6 - - + +
1654B GLY 4.7 1.4 - - - +
1699B PHE* 2.7 48.1 + - + +
1700B ASN 3.8 4.7 - - - +
1702B LEU* 1.3 71.1 - - - +
1704B ASN* 1.3 67.3 + - - +
1705B ILE 3.8 0.7 - - - -
1706B ASP* 3.6 11.4 - - - +
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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