Contacts of the helix formed by residues 1463 - 1476 (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 SER1463 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1402B ASN* 4.9 8.7 - - - +
1405B LEU* 4.0 28.6 + - - +
1464B TRP* 1.3 67.6 + - - +
1465B ILE* 3.1 21.5 - - - +
1466B HIS* 3.3 15.8 + - - +
1467B ARG* 3.3 24.9 + - - +
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Residues in contact with TRP1464 (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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1463B SER* 1.3 80.0 + - - +
1465B ILE* 1.3 87.6 + - + +
1467B ARG* 3.2 19.3 + - - +
1468B MET* 3.0 49.9 + - + +
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Residues in contact with ILE1465 (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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1267B LEU 5.6 5.4 - - - +
1405B LEU* 5.2 6.7 - - + +
1463B SER* 3.2 23.1 - - - +
1464B TRP* 1.3 117.9 - - + +
1466B HIS* 1.3 58.3 + - - +
1468B MET* 2.9 11.6 + - + +
1469B ILE* 2.8 42.3 + - + +
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Residues in contact with HIS1466 (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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1291B PHE* 4.8 2.0 - + - -
1398B SER 5.9 0.2 - - - -
1401B PHE* 4.0 18.7 - + + -
1402B ASN* 3.4 45.2 + - + -
1405B LEU* 3.4 31.2 - - + +
1463B SER* 3.3 19.8 + - - +
1465B ILE* 1.3 80.4 - - - +
1467B ARG* 1.3 59.8 + - + +
1469B ILE* 3.3 8.2 + - - +
1470B MET* 2.9 63.2 + - + +
1485B ARG* 3.8 12.3 + - - -
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Residues in contact with ARG1467 (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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1463B SER 3.3 15.2 + - - +
1464B TRP* 3.2 18.8 + - - +
1465B ILE 3.1 0.4 - - - -
1466B HIS* 1.3 79.8 - - + +
1468B MET* 1.3 61.1 + - - +
1470B MET* 3.3 7.8 + - - +
1471B ALA* 2.8 30.5 + - - +
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Residues in contact with MET1468 (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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1464B TRP* 3.0 44.9 + - + +
1465B ILE* 2.9 13.1 + - + +
1467B ARG* 1.3 77.0 - - - +
1469B ILE* 1.3 59.6 + - + +
1471B ALA* 3.3 9.5 + - + +
1472B LEU* 2.8 31.1 + - - +
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Residues in contact with ILE1469 (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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1267B LEU* 4.1 38.4 - - + +
1272B VAL* 4.4 22.7 - - + -
1291B PHE* 4.3 9.4 - - + -
1294B ILE* 5.5 3.4 - - + -
1401B PHE* 5.0 3.4 - - + -
1405B LEU* 4.7 8.1 - - + -
1465B ILE* 2.8 25.4 + - + +
1466B HIS* 3.5 14.6 - - - +
1468B MET* 1.3 77.7 - - + +
1470B MET* 1.3 80.9 + - + +
1472B LEU* 3.3 7.8 + - - +
1473B VAL* 2.9 30.7 + - + +
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Residues in contact with MET1470 (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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1291B PHE* 3.1 41.5 - - + -
1466B HIS* 2.9 43.3 + - + +
1467B ARG* 3.7 6.7 - - - +
1469B ILE* 1.3 85.7 - - + +
1471B ALA* 1.3 53.0 + - - +
1473B VAL* 3.1 8.8 + - + +
1474B SER* 2.7 38.9 + - - -
1479B PHE* 4.9 11.4 - - - -
1481B THR* 4.2 20.8 - - - +
1485B ARG* 3.3 25.1 - - - +
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Residues in contact with ALA1471 (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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1467B ARG 2.8 19.1 + - - +
1468B MET* 3.5 13.2 - - + +
1470B MET* 1.3 75.9 - - - +
1472B LEU* 1.3 63.6 + - - +
1474B SER* 2.9 8.0 + - - +
1475B ASP* 2.8 36.6 + - - +
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Residues in contact with LEU1472 (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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1269B PRO* 3.9 30.5 - - + +
1272B VAL* 3.9 24.9 - - + -
1273B LYS* 3.9 32.1 - - + +
1276B VAL* 5.4 2.7 - - + -
1468B MET 2.8 20.7 + - - +
1469B ILE* 3.6 6.5 - - - +
1471B ALA* 1.3 72.1 - - - +
1473B VAL* 1.3 60.9 + - - +
1475B ASP* 3.6 9.6 + - + +
1476B SER* 3.2 33.6 + - - +
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Residues in contact with VAL1473 (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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1272B VAL* 4.5 4.7 - - + -
1276B VAL* 4.1 15.3 - - + -
1294B ILE* 3.8 23.6 - - + -
1469B ILE* 2.9 25.6 + - + +
1470B MET* 3.4 11.0 - - + +
1472B LEU* 1.3 76.0 - - - +
1474B SER* 1.3 64.8 + - - +
1476B SER* 3.1 15.4 + - - -
1477B ALA 3.3 7.6 + - - -
1478B LEU* 3.6 14.7 + - + -
1479B PHE* 3.6 46.6 + - + +
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Residues in contact with SER1474 (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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1470B MET 2.7 18.4 + - - -
1471B ALA* 2.9 7.6 + - - -
1473B VAL* 1.3 72.7 - - - +
1475B ASP* 1.3 67.2 + - - +
1477B ALA* 3.0 14.8 + - - +
1479B PHE 4.1 9.5 + - - -
1480B ASN* 5.9 0.4 - - - -
1481B THR* 3.1 43.6 + - - +
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Residues in contact with ASP1475 (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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1471B ALA* 2.8 30.6 + - - +
1472B LEU* 3.9 9.7 + - + +
1474B SER* 1.3 79.6 - - - +
1476B SER* 1.3 60.7 + - - +
1477B ALA* 3.0 3.7 + - - +
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Residues in contact with SER1476 (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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1273B LYS* 5.9 2.4 - - - +
1276B VAL* 3.3 33.9 - - - +
1280B TRP* 3.0 25.8 + - - -
1472B LEU* 3.2 21.0 + - - +
1473B VAL* 3.1 10.1 + - - -
1475B ASP* 1.3 74.8 - - - +
1477B ALA* 1.3 65.0 + - - +
1478B LEU 3.1 2.7 - - - -
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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