Contacts of the helix formed by residues 1521 - 1540 (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 SER1521 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1458B LEU* 4.2 3.8 - - - -
1462B MET* 3.2 15.0 - - - +
1520B ARG* 1.4 95.8 + - - +
1522B LEU* 1.3 65.9 + - - +
1523B ASN* 3.5 14.2 - - - +
1524B ASP* 2.7 41.1 + - - +
1525B LEU 3.1 9.2 + - - -
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Residues in contact with LEU1522 (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* 4.5 13.6 - - + +
1461B LYS* 4.0 24.0 - - + -
1462B MET* 3.6 29.5 - - + +
1465B ILE* 4.0 23.3 - - + -
1521B SER* 1.3 72.2 - - - +
1523B ASN* 1.3 57.2 + - - +
1525B LEU* 3.2 9.1 + - + +
1526B GLU* 2.9 28.9 + - - +
1557B PHE* 4.7 2.6 - - + -
1561B ARG* 3.6 23.9 + - - +
1565B GLU* 3.6 36.1 - - + +
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Residues in contact with ASN1523 (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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1520B ARG* 5.3 1.9 - - - +
1521B SER* 3.1 13.2 - - - +
1522B LEU* 1.3 74.8 - - - +
1524B ASP* 1.3 61.8 + - - +
1526B GLU* 3.4 4.6 + - - +
1527B LYS* 2.9 28.1 + - - +
1561B ARG* 2.9 34.4 + - - +
1604B EDO 3.6 33.4 + - - -
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Residues in contact with ASP1524 (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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1518B LYS 5.6 0.2 - - - +
1519B TYR* 3.7 25.8 - - + -
1520B ARG* 2.5 39.7 + - - +
1521B SER* 2.7 32.2 + - - +
1523B ASN* 1.3 73.7 - - - +
1525B LEU* 1.3 66.5 + - - +
1527B LYS* 3.5 30.5 + - - +
1528B ASP* 3.4 14.0 + - - +
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Residues in contact with LEU1525 (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* 3.7 44.0 - - + +
1465B ILE* 4.7 4.5 - - + -
1466B VAL* 4.0 11.9 - - + -
1510B ILE* 3.5 31.9 - - + -
1514B ILE* 4.3 1.3 - - + -
1519B TYR* 3.7 24.7 - - + -
1521B SER 3.1 12.7 + - - +
1522B LEU* 3.2 16.6 + - + +
1524B ASP* 1.3 74.3 - - - +
1526B GLU* 1.3 63.2 + - - +
1528B ASP* 2.9 12.6 + - - +
1529B VAL* 3.1 15.5 + - + +
1557B PHE* 4.1 17.3 - - + -
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Residues in contact with GLU1526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1522B LEU 2.9 17.9 + - - +
1523B ASN* 3.6 6.7 - - - +
1525B LEU* 1.3 73.2 - - - +
1527B LYS* 1.3 58.3 + - - +
1528B ASP 3.2 0.3 + - - -
1529B VAL* 3.2 2.1 + - - +
1530B MET* 2.8 55.0 + - + +
1557B PHE* 3.4 36.9 - - + -
1558B THR* 4.4 10.5 - - - +
1561B ARG* 2.8 32.0 + - - +
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Residues in contact with LYS1527 (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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1503B LYS* 5.9 5.4 - - - +
1523B ASN 2.9 18.6 + - - +
1524B ASP* 3.5 30.0 + - - +
1526B GLU* 1.3 77.4 - - - +
1528B ASP* 1.3 59.3 + - - +
1530B MET* 3.9 5.6 - - - +
1531B LEU* 3.0 29.0 + - + +
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Residues in contact with ASP1528 (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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1503B LYS* 5.6 0.7 - - - -
1505B VAL* 4.1 17.1 - - - +
1510B ILE* 4.0 7.8 - - + +
1513B ARG* 3.4 21.5 + - - -
1519B TYR* 2.6 39.7 + - + +
1524B ASP 3.4 1.7 + - - +
1525B LEU 2.9 8.9 + - - +
1527B LYS* 1.3 79.3 - - - +
1529B VAL* 1.3 62.7 + - - +
1531B LEU* 3.4 22.3 + - - +
1532B LEU* 3.0 26.7 + - - +
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Residues in contact with VAL1529 (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* 5.3 2.7 - - + -
1469B VAL* 5.7 1.3 - - + -
1507B PHE* 4.5 21.1 - - + -
1510B ILE* 3.9 21.5 - - + -
1525B LEU* 3.1 20.5 + - + +
1526B GLU 3.6 6.1 - - - +
1528B ASP* 1.3 77.4 - - - +
1530B MET* 1.3 64.4 + - - +
1532B LEU* 3.2 6.1 + - - +
1533B CYS* 3.1 31.4 + - - -
1553B LEU* 5.1 3.4 - - + +
1557B PHE* 3.8 46.9 - - + -
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Residues in contact with MET1530 (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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1526B GLU* 2.8 37.8 + - + +
1527B LYS* 4.0 5.2 - - - +
1529B VAL* 1.3 74.5 - - + +
1531B LEU* 1.3 57.3 + - - +
1533B CYS* 3.3 4.6 + - - +
1534B GLN* 2.9 29.0 + - - +
1554B GLN* 3.4 55.2 - - + +
1557B PHE* 4.1 16.8 - - + -
1558B THR* 3.9 18.6 - - + -
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Residues in contact with LEU1531 (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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1503B LYS* 3.5 50.0 - - + +
1505B VAL* 4.2 4.7 - - + -
1527B LYS* 3.0 19.8 + - + +
1528B ASP* 3.5 23.6 - - - +
1530B MET* 1.3 74.1 - - - +
1532B LEU* 1.3 66.3 + - - +
1534B GLN* 3.6 21.2 - - - +
1535B ASN* 2.8 49.3 + - - +
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Residues in contact with LEU1532 (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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1485B PHE* 3.8 35.7 - - + +
1505B VAL* 3.6 26.5 - - + +
1506B ASP* 3.6 10.8 - - - -
1507B PHE* 3.6 48.2 - - + +
1510B ILE* 4.0 12.3 - - + -
1528B ASP 3.0 13.8 + - - +
1529B VAL* 3.2 10.5 + - - +
1531B LEU* 1.3 73.0 - - - +
1533B CYS* 1.3 73.4 + - - +
1535B ASN* 3.4 4.2 + - - +
1536B ALA* 3.0 19.2 + - - +
1550B SER* 6.3 0.2 - - - -
1553B LEU* 6.2 0.4 - - + -
1605B 5BW 3.9 5.6 - - + -
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Residues in contact with CYS1533 (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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1507B PHE* 6.0 1.8 - - - -
1529B VAL* 3.1 25.9 + - - -
1530B MET* 3.7 6.5 - - - +
1531B LEU 3.1 0.4 - - - -
1532B LEU* 1.3 87.1 - - - +
1534B GLN* 1.3 62.5 + - - +
1536B ALA* 3.1 4.2 + - - +
1537B GLN* 3.0 29.9 + - - +
1550B SER* 3.3 38.1 - - - +
1553B LEU* 4.2 11.0 - - - -
1554B GLN* 3.6 30.1 - - + +
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Residues in contact with GLN1534 (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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1530B MET 2.9 16.9 + - - +
1531B LEU* 3.6 23.0 - - - +
1533B CYS* 1.3 75.4 - - - +
1535B ASN* 1.3 64.9 + - - +
1537B GLN* 3.1 14.3 + - + +
1538B THR* 3.0 30.7 + - - +
1554B GLN* 4.7 1.5 + - - -
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Residues in contact with ASN1535 (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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1497B TYR* 3.5 15.0 - - - +
1501B ILE* 3.6 32.5 - - + +
1503B LYS 2.9 29.5 + - - -
1504B PRO* 4.0 2.8 - - - +
1505B VAL* 3.9 13.3 - - - +
1531B LEU* 2.8 37.4 + - - +
1532B LEU* 3.5 4.9 - - - +
1534B GLN* 1.3 75.4 - - - +
1536B ALA* 1.3 62.6 + - - +
1538B THR* 3.2 3.7 + - - -
1539B PHE* 3.0 26.0 + - - +
1605B 5BW 4.0 2.5 - - + -
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Residues in contact with ALA1536 (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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1485B PHE* 3.8 16.6 - - + -
1532B LEU 3.0 12.8 + - - +
1533B CYS* 3.1 8.3 + - - +
1535B ASN* 1.3 76.0 - - - +
1537B GLN* 1.3 57.6 + - - +
1540B ASN* 2.8 41.1 + - - +
1546B ILE* 5.0 2.0 - - + +
1547B TYR* 4.6 1.7 - - - -
1550B SER* 3.7 21.1 - - - -
1605B 5BW 3.2 20.5 + - - +
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Residues in contact with GLN1537 (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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1533B CYS 3.0 19.2 + - - -
1534B GLN* 3.1 10.1 + - - +
1536B ALA* 1.3 73.2 - - - +
1538B THR* 1.3 61.0 + - - +
1540B ASN 3.2 14.7 - - - +
1547B TYR* 3.3 41.6 + - + +
1550B SER* 2.9 25.7 + - - +
1551B ILE* 3.4 26.2 - - + +
1554B GLN* 2.9 28.7 + - - +
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Residues in contact with THR1538 (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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1500B LEU* 3.8 23.1 - - + +
1501B ILE* 3.6 22.4 - - + -
1534B GLN* 3.0 18.7 + - - +
1535B ASN* 3.2 9.0 + - - -
1537B GLN* 1.3 79.3 - - - +
1539B PHE* 1.3 62.3 + - - +
1540B ASN 4.2 1.6 - - - +
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Residues in contact with PHE1539 (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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1494B LEU* 4.0 30.7 - - + -
1496B GLU* 4.3 11.9 - - + -
1497B TYR* 3.5 53.8 - + + -
1500B LEU* 3.9 19.5 - - + +
1501B ILE* 4.5 4.5 - - + -
1535B ASN 3.0 15.5 + - - +
1538B THR* 1.3 79.2 - - - +
1540B ASN* 1.3 80.8 + - - +
1541B LEU* 4.3 1.6 + - - +
1605B 5BW 3.9 16.6 - - - -
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Residues in contact with ASN1540 (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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1536B ALA* 2.8 28.0 + - - +
1537B GLN 3.2 18.7 - - - +
1538B THR 4.2 1.6 - - - +
1539B PHE* 1.3 93.3 - - - +
1541B LEU* 1.3 66.2 + - - +
1542B GLU 3.7 0.5 + - - -
1544B SER* 3.8 3.8 - - - +
1546B ILE* 3.3 40.2 - - + +
1547B TYR* 3.5 6.7 - - + +
1605B 5BW 2.9 39.9 + - - -
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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