Contacts of the helix formed by residues 1458 - 1472 (chain B) in PDB entry 5DKD
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 LEU1458 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1542A GLU* 5.5 3.8 + - - -
1457B ASN* 1.3 69.8 - - - +
1459B THR* 1.3 68.0 + - - +
1461B LYS* 3.2 16.5 + - + +
1462B MET* 3.0 48.0 + - + +
1519B TYR 4.7 2.2 - - - +
1520B ARG 3.5 25.4 - - - +
1521B SER* 4.2 4.9 - - - -
1522B LEU* 4.5 20.9 - - + +
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Residues in contact with THR1459 (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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1537A GLN* 6.2 0.2 - - - +
1542A GLU* 4.9 3.6 + - - -
1547A TYR* 5.6 2.0 - - - -
1457B ASN 3.4 0.6 - - - -
1458B LEU* 1.3 78.2 - - - +
1460B LYS* 1.3 58.4 + - - +
1462B MET* 3.3 9.4 + - - +
1463B LYS* 3.0 50.6 + - - +
1514B ILE* 3.6 26.5 + - + +
1515B ARG* 4.8 3.8 - - - +
1517B HIS* 3.0 36.4 + - + +
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Residues in contact with LYS1460 (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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1457B ASN* 3.3 17.9 + - + +
1458B LEU 3.3 1.0 - - - -
1459B THR* 1.3 78.6 - - - +
1461B LYS* 1.3 57.4 + - - +
1463B LYS* 3.4 30.0 - - + +
1464B LYS* 3.0 28.1 + - - +
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Residues in contact with LYS1461 (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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1457B ASN 3.4 19.6 + - - +
1458B LEU* 3.2 18.1 + - + +
1460B LYS* 1.3 78.7 - - - +
1462B MET* 1.3 65.2 + - - +
1464B LYS* 3.4 10.5 + - + +
1465B ILE* 3.2 26.1 + - + +
1522B LEU* 4.0 31.9 - - + -
1564B ILE* 4.2 30.2 - - + +
1565B GLU* 5.1 7.6 - - + +
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Residues in contact with MET1462 (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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1458B LEU* 3.0 39.5 + - + +
1459B THR* 3.6 9.4 - - - +
1461B LYS* 1.3 77.2 - - - +
1463B LYS* 1.3 63.7 + - - +
1464B LYS 3.3 0.3 + - - -
1465B ILE* 3.4 2.8 + - - +
1466B VAL* 3.0 26.7 + - - +
1514B ILE* 3.9 19.3 - - + +
1519B TYR* 3.4 39.9 - - + +
1521B SER 3.2 35.7 - - - +
1522B LEU* 3.6 19.1 - - + +
1525B LEU* 3.7 19.0 - - + +
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Residues in contact with LYS1463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459B THR* 3.0 38.8 + - - +
1460B LYS* 3.4 31.0 - - - +
1462B MET* 1.3 77.1 - - - +
1464B LYS* 1.3 57.2 + - - +
1466B VAL* 3.8 2.3 - - - +
1467B ASP* 2.9 43.0 + - - +
1514B ILE* 4.0 18.7 - - + +
1515B ARG* 5.7 4.9 - - - +
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Residues in contact with LYS1464 (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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1460B LYS 3.0 14.4 + - - +
1461B LYS* 3.6 10.3 - - + +
1462B MET 3.2 0.2 - - - -
1463B LYS* 1.3 80.0 - - - +
1465B ILE* 1.3 62.2 + - - +
1467B ASP* 3.6 7.5 + - - +
1468B ALA* 3.2 24.4 + - - +
1564B ILE* 3.5 37.0 - - + +
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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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1461B LYS* 3.2 18.7 + - + +
1462B MET* 3.6 4.9 - - - +
1464B LYS* 1.3 74.4 - - - +
1466B VAL* 1.3 65.4 + - - +
1468B ALA 3.2 1.4 + - - -
1469B VAL* 2.9 23.4 + - - +
1522B LEU* 4.0 27.6 - - + -
1525B LEU* 4.7 4.3 - - + -
1557B PHE* 3.7 34.3 - - + -
1560B VAL* 3.6 18.9 - - + +
1561B ARG* 3.9 29.6 - - + +
1564B ILE* 3.9 27.8 - - + -
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Residues in contact with VAL1466 (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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1462B MET 3.0 17.9 + - - +
1463B LYS* 4.0 2.9 - - - +
1465B ILE* 1.3 78.9 - - + +
1467B ASP* 1.3 62.7 + - - +
1469B VAL* 3.3 5.7 + - - +
1470B ILE* 2.9 43.0 + - + +
1507B PHE* 4.2 15.0 - - + -
1510B ILE* 4.1 7.4 - - + -
1511B LYS* 4.2 18.6 - - + -
1514B ILE* 3.7 20.0 - - + -
1525B LEU* 4.0 20.4 - - + -
1529B VAL* 5.3 3.4 - - + -
1557B PHE* 5.2 4.0 - - + -
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Residues in contact with ASP1467 (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 LYS* 2.9 32.6 + - - +
1464B LYS* 3.9 7.6 - - - +
1465B ILE 3.3 0.2 - - - -
1466B VAL* 1.3 75.6 - - - +
1468B ALA* 1.3 58.0 + - - +
1470B ILE* 3.4 9.1 + - - +
1471B LYS* 2.9 30.9 + - - +
1511B LYS* 5.0 12.5 - - - +
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Residues in contact with ALA1468 (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 LYS 3.2 14.4 + - - +
1465B ILE 3.2 4.8 + - - +
1466B VAL 3.1 0.2 - - - -
1467B ASP* 1.3 79.3 - - - +
1469B VAL* 1.3 64.7 + - - +
1471B LYS* 3.8 6.5 - - - +
1472B TYR* 3.1 22.7 + - - +
1560B VAL* 3.8 22.8 - - + +
1563B LYS* 6.1 2.9 - - - +
1564B ILE* 5.9 3.1 - - + -
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Residues in contact with VAL1469 (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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1465B ILE 2.9 19.6 + - - +
1466B VAL* 3.8 6.3 - - - +
1468B ALA* 1.3 76.9 - - - +
1470B ILE* 1.3 64.7 + - - +
1472B TYR* 3.4 14.2 + - - +
1482B SER* 4.1 5.9 - - - -
1507B PHE* 4.1 22.9 - - + -
1529B VAL* 5.7 1.1 - - + -
1553B LEU* 3.9 26.7 - - + +
1556B VAL* 4.2 10.1 - - + -
1557B PHE* 3.7 44.4 - - + +
1560B VAL* 4.0 13.9 - - + -
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Residues in contact with ILE1470 (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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1466B VAL* 2.9 37.7 + - + +
1467B ASP* 3.6 9.2 - - - +
1469B VAL* 1.3 77.7 - - - +
1471B LYS* 1.3 62.8 + - + +
1472B TYR 3.3 1.2 + - - +
1480B GLN* 3.1 19.6 + - - +
1482B SER* 2.6 29.7 + - - +
1486B ILE* 3.8 28.5 - - + -
1507B PHE* 4.0 24.7 - - + -
1511B LYS* 4.1 20.0 - - + +
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Residues in contact with LYS1471 (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 ASP 2.9 17.7 + - - +
1468B ALA* 4.0 7.4 - - - +
1469B VAL 3.3 0.2 - - - -
1470B ILE* 1.3 78.9 - - + +
1472B TYR* 1.3 65.2 + - - +
1473B LYS* 3.2 36.4 + - - +
1480B GLN* 4.4 7.6 - - - +
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Residues in contact with TYR1472 (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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1468B ALA 3.1 13.3 + - - +
1469B VAL 3.5 14.5 - - - +
1470B ILE 3.2 2.7 - - - +
1471B LYS* 1.3 77.8 - - - +
1473B LYS* 1.3 82.6 + - - +
1474B ASP* 3.9 8.6 + - - -
1475B SER* 4.6 3.5 + - - -
1480B GLN* 3.4 19.1 - - - +
1481B LEU* 3.5 34.4 + - + +
1482B SER 4.8 0.3 + - - -
1552B VAL* 5.0 2.3 - - + +
1553B LEU* 5.1 1.3 - - + -
1556B VAL* 3.8 37.4 - - + +
1560B VAL* 6.0 2.2 - - + -
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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
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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