Contacts of the helix formed by residues 1459 - 1473 (chain B) in PDB entry 2ZEJ
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 GLU1459 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1457B SER 4.1 0.4 + - - -
1458B ASP* 1.3 72.5 - - - +
1460B LYS* 1.3 58.2 + - - +
1461B GLN 3.4 0.2 + - - -
1462B ARG* 3.5 12.9 + - - +
1463B LYS* 3.2 29.3 + - + +
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Residues in contact with LYS1460 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1458B ASP* 3.0 30.8 + - + +
1459B GLU* 1.3 75.1 - - - +
1461B GLN* 1.3 80.5 + - - +
1462B ARG 2.8 8.0 + - - -
1463B LYS* 4.1 9.2 - - - +
1464B ALA* 3.4 20.1 + - - +
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Residues in contact with GLN1461 (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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1421B LEU* 3.1 22.4 - - + +
1422B SER* 3.1 28.5 + - - +
1423B LYS 4.5 0.8 - - - -
1424B GLY* 3.7 18.8 - - - +
1425B GLN 4.7 0.5 + - - -
1456B VAL 5.7 0.2 + - - -
1457B SER* 4.2 4.4 - - - +
1458B ASP* 3.0 36.0 + - + +
1460B LYS* 1.3 100.1 + - - +
1462B ARG* 1.3 59.8 + - + +
1464B ALA* 3.7 7.1 - - - +
1465B CYS* 3.2 29.3 + - - -
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Residues in contact with ARG1462 (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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1421B LEU* 3.9 22.2 - - + -
1454B LEU* 4.4 15.5 - - + +
1458B ASP 3.4 18.6 - - - +
1459B GLU* 3.5 13.3 + - - +
1460B LYS 2.8 1.6 + - - -
1461B GLN* 1.3 76.2 - - - +
1463B LYS* 1.3 82.2 + - - +
1464B ALA 3.4 0.8 - - - +
1465B CYS* 3.8 8.7 - - - +
1466B MSE 3.0 38.7 + - - +
1487B PHE* 4.2 33.1 - - + +
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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
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1459B GLU* 3.2 17.7 - - + +
1460B LYS* 4.2 7.6 - - - +
1462B ARG* 1.3 93.7 - - - +
1464B ALA* 1.3 59.1 + - - +
1466B MSE 2.9 33.2 - - + +
1467B SER* 2.9 35.7 + - - -
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Residues in contact with ALA1464 (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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1425B GLN* 3.8 28.3 - - + +
1460B LYS* 3.4 17.0 + - - +
1461B GLN* 3.7 7.4 - - - +
1462B ARG 3.4 3.2 - - - +
1463B LYS* 1.3 77.6 - - - +
1465B CYS* 1.3 58.5 + - - +
1467B SER* 3.6 5.5 - - - -
1468B LYS* 2.9 29.6 + - - +
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Residues in contact with CYS1465 (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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1419B TYR* 4.2 19.1 - - - +
1421B LEU* 4.6 8.7 - - + -
1424B GLY* 3.9 8.7 - - - -
1425B GLN* 3.9 18.8 - - - -
1428B VAL* 3.7 26.5 - - + -
1461B GLN 3.2 23.7 + - - +
1462B ARG* 3.8 8.3 + - - +
1463B LYS 3.3 0.4 - - - -
1464B ALA* 1.3 75.5 - - - +
1466B MSE 1.3 55.9 + - - +
1468B LYS* 3.2 3.7 + - - +
1469B ILE* 2.7 40.3 + - - +
1487B PHE* 4.4 4.7 - - + -
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Residues in contact with MSE1466 (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 ARG* 3.0 30.4 + - - +
1463B LYS* 2.9 48.0 + - + +
1464B ALA 3.4 0.2 - - - -
1465B CYS* 1.3 75.9 - - - +
1467B SER* 1.3 53.8 + - - +
1469B ILE* 3.6 9.6 - - - +
1470B THR* 2.8 38.2 + - - +
1485B TYR* 3.5 34.5 - - + +
1487B PHE* 4.1 12.5 - - + -
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Residues in contact with SER1467 (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 21.7 + - - +
1464B ALA* 3.6 6.7 - - - -
1466B MSE 1.3 77.5 - - - +
1468B LYS* 1.3 55.6 + - - +
1470B THR* 3.2 9.6 + - - +
1471B LYS* 3.0 44.3 + - - +
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Residues in contact with LYS1468 (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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1425B GLN* 3.9 38.1 + - + +
1428B VAL* 3.4 18.2 - - + -
1429B ASP* 2.8 46.5 + - - +
1432B LYS* 5.1 0.4 - - - +
1464B ALA 2.9 17.7 + - - +
1465B CYS* 3.4 6.3 - - - +
1467B SER* 1.3 73.4 - - - +
1469B ILE* 1.3 66.1 + - - +
1471B LYS* 5.2 0.4 - - - -
1472B GLU* 2.9 61.6 + - + +
1473B LEU* 4.4 0.7 - - - +
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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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1419B TYR* 3.4 28.3 - - + +
1428B VAL* 4.2 14.1 - - + -
1449B LEU* 3.8 28.7 - - + -
1465B CYS 2.7 28.1 + - - +
1466B MSE 3.6 4.7 - - - +
1468B LYS* 1.3 71.3 - - - +
1470B THR* 1.3 64.1 + - - +
1473B LEU* 3.0 29.7 + - + +
1474B LEU* 3.1 28.9 + - + -
1485B TYR* 3.8 35.2 - - + -
1487B PHE* 4.2 3.8 - - + -
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Residues in contact with THR1470 (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 MSE 2.8 19.5 + - - +
1467B SER* 3.2 11.4 + - - +
1469B ILE* 1.3 77.8 - - - +
1471B LYS* 1.3 77.2 + - + +
1474B LEU* 3.4 37.8 + - - +
1475B ASN 5.1 0.5 + - - -
1476B LYS* 5.5 0.5 - - - -
1485B TYR* 4.4 8.7 + - - -
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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 SER* 3.0 22.0 + - - +
1468B LYS* 5.2 0.2 - - - -
1470B THR* 1.3 92.9 - - + +
1472B GLU* 1.3 67.9 + - + +
1476B LYS* 3.2 21.8 + - - -
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Residues in contact with GLU1472 (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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1429B ASP* 3.9 0.2 - - - +
1432B LYS* 2.8 35.0 + - - +
1468B LYS* 2.9 55.7 + - + +
1471B LYS* 1.3 87.3 - - + +
1473B LEU* 1.3 63.5 + - + +
1476B LYS* 3.7 15.3 - - - +
1479B PHE* 3.5 16.3 - - - -
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Residues in contact with LEU1473 (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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1428B VAL* 4.0 30.1 - - + +
1431B MSE 4.6 5.6 - - + -
1432B LYS* 3.7 34.3 - - + -
1435B LEU* 4.0 20.2 - - + -
1449B LEU* 3.9 23.3 - - + -
1468B LYS 4.4 2.0 - - - +
1469B ILE* 3.0 21.5 + - + +
1472B GLU* 1.3 88.3 - - + +
1474B LEU* 1.3 68.1 + - - +
1475B ASN 3.6 1.3 + - - -
1476B LYS* 4.0 7.2 + - - +
1479B PHE* 3.8 17.0 - - + +
1482B ILE* 3.3 26.1 - - + +
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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