Contacts of the helix formed by residues 1704 - 1716 (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 ASN1704 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1619B GLU* 3.2 35.4 + - - +
1620B CYS* 3.7 22.7 + - - -
1640B PHE* 3.8 17.1 - - + -
1700B ASN 2.5 28.0 + - - +
1701B THR 3.2 4.2 + - - -
1702B LEU 3.1 0.8 - - - -
1703B ASN* 1.3 83.1 - - - +
1705B ILE* 1.3 63.2 + - - +
1706B ASP* 2.9 14.5 - - - +
1707B VAL* 3.0 25.0 + - + +
1708B ILE* 3.4 9.1 + - - +
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Residues in contact with ILE1705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172B LEU* 4.5 2.9 - - + -
1215B SER* 3.2 33.9 - - - +
1217B ILE* 4.2 18.6 - - + -
1701B THR* 3.6 12.6 - - + +
1702B LEU* 3.4 31.8 + - + +
1704B ASN* 1.3 78.0 - - - +
1706B ASP* 1.3 59.6 + - - +
1708B ILE* 3.3 10.9 + - + +
1709B LYS* 2.9 54.0 + - + +
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Residues in contact with ASP1706 (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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1702B LEU 4.9 0.9 - - - +
1703B ASN 3.6 10.2 - - - +
1704B ASN* 3.6 15.5 - - - +
1705B ILE* 1.3 81.4 + - - +
1707B VAL* 1.3 74.4 + - - +
1709B LYS* 3.2 11.7 + - - +
1710B GLU* 3.1 22.2 + - - +
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Residues in contact with VAL1707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1620B CYS* 4.0 18.6 - - - -
1622B VAL* 3.3 34.8 - - + -
1638B ILE* 3.8 16.8 - - + -
1704B ASN* 3.0 15.8 + - - +
1706B ASP* 1.3 87.6 - - + +
1708B ILE* 1.3 65.3 + - + +
1710B GLU* 3.2 9.8 + - - +
1711B ALA* 3.1 20.1 + - - +
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Residues in contact with ILE1708 (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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1212B LEU* 4.8 10.8 - - + -
1217B ILE* 4.1 36.1 - - + -
1572B ILE* 4.1 36.1 - - + -
1574B PHE* 5.5 0.2 - - + -
1638B ILE* 3.7 20.0 - - + -
1640B PHE* 4.1 19.5 - - + -
1701B THR* 4.9 6.3 - - + +
1704B ASN 3.9 9.6 - - - +
1705B ILE* 3.3 15.1 + - + +
1707B VAL* 1.3 76.2 - - - +
1709B LYS* 1.3 62.1 + - - +
1711B ALA* 3.3 2.8 + - - +
1712B MET* 3.1 38.7 + - + +
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Residues in contact with LYS1709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172B LEU* 3.0 47.6 + - + +
1173B LEU* 3.4 23.2 + - + +
1217B ILE* 5.5 0.2 - - + -
1705B ILE* 2.9 33.8 + - + +
1706B ASP* 3.5 11.7 - - - +
1707B VAL 3.2 0.4 - - - -
1708B ILE* 1.3 76.6 - - - +
1710B GLU* 1.3 56.8 + - - +
1712B MET* 3.2 7.1 + - - +
1713B VAL* 3.0 32.5 + - + +
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Residues in contact with GLU1710 (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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1624B LYS* 3.3 13.9 + - - -
1706B ASP 3.1 10.1 + - - +
1707B VAL* 3.2 10.8 + - - +
1709B LYS* 1.3 74.9 - - - +
1711B ALA* 1.3 56.2 + - - +
1713B VAL* 3.2 9.0 + - + +
1714B GLU* 2.7 63.3 + - + +
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Residues in contact with ALA1711 (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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1570B LEU* 3.7 17.0 - - + -
1622B VAL* 5.7 3.8 - - + -
1636B THR* 4.6 9.3 - - - +
1638B ILE* 3.6 32.5 - - + -
1707B VAL* 3.1 6.9 + - + +
1708B ILE 3.6 4.7 - - - +
1710B GLU* 1.3 75.8 - - - +
1712B MET* 1.3 53.9 + - - +
1714B GLU* 3.7 12.8 - - - +
1715B SER* 2.7 39.4 + - - -
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Residues in contact with MET1712 (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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1169B MET* 3.4 28.8 - - + +
1172B LEU* 3.7 24.7 - - + -
1173B LEU* 4.1 9.4 - - + -
1188B PRO* 5.5 0.2 - - - -
1190B VAL* 3.8 24.9 - - + -
1217B ILE* 4.7 5.8 - - + -
1220B CYS* 3.5 29.8 - - + -
1570B LEU* 3.7 12.6 - - + -
1708B ILE* 3.1 29.7 + - + +
1709B LYS* 3.4 6.3 - - - +
1710B GLU 3.2 0.2 - - - -
1711B ALA* 1.3 74.3 - - - +
1713B VAL* 1.3 55.3 + - - +
1715B SER* 3.1 7.9 + - - -
1716B ILE* 2.7 40.7 + - - +
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Residues in contact with VAL1713 (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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1173B LEU* 3.8 14.8 - - + +
1176B LYS* 3.3 38.6 - - + +
1177B ASN* 5.4 2.2 - - - -
1709B LYS 3.0 22.5 + - - +
1710B GLU* 3.5 10.1 - - + +
1712B MET* 1.3 74.7 - - - +
1714B GLU* 1.3 68.1 + - + +
1716B ILE* 3.0 29.7 + - + +
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Residues in contact with GLU1714 (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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1624B LYS* 2.7 47.1 + - - +
1636B THR* 5.6 4.8 + - + +
1710B GLU* 2.7 37.8 + - + +
1711B ALA* 3.7 10.7 - - - +
1713B VAL* 1.3 78.9 - - + +
1715B SER* 1.3 65.3 + - - +
1716B ILE 3.0 9.0 + - - +
1717B GLU* 3.8 7.4 - - - +
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Residues in contact with SER1715 (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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1188B PRO* 4.2 10.0 - - - +
1569B ASP* 3.7 26.0 + - - +
1570B LEU* 4.0 9.3 - - - +
1636B THR* 3.7 21.8 - - - +
1711B ALA 2.7 27.0 + - - -
1712B MET* 3.1 9.6 + - - -
1714B GLU* 1.3 72.9 - - - +
1716B ILE* 1.3 57.8 + - - +
1717B GLU* 2.8 17.0 + - - +
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Residues in contact with ILE1716 (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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1169B MET* 4.4 2.7 - - + -
1173B LEU* 4.3 10.5 - - + -
1177B ASN* 3.8 20.0 - - + +
1180B GLY* 3.6 30.5 - - - -
1181B LEU* 3.5 36.1 - - + +
1188B PRO* 4.5 19.5 - - + -
1712B MET 2.7 23.1 + - - +
1713B VAL* 3.0 16.1 + - + +
1714B GLU 3.2 5.5 - - - +
1715B SER* 1.3 70.5 - - - +
1717B GLU* 1.3 65.1 + - - +
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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