Contacts of the helix formed by residues 1505 - 1524 (chain B) in PDB entry 5WBY
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 ASN1505 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474B PRO* 4.0 21.4 - - - +
1503B LEU 3.6 5.3 + - - +
1504B VAL* 1.3 75.4 - - - +
1506B ASP* 1.3 57.2 + - - +
1507B GLU* 3.3 7.2 - - + +
1508B THR* 3.2 20.9 + - - +
1509B GLN* 2.7 37.6 + - - +
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Residues in contact with ASP1506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505B ASN* 1.3 73.9 - - - +
1507B GLU* 1.3 65.5 + - + +
1509B GLN* 3.6 13.6 + - - +
1510B ALA* 3.4 22.9 + - - +
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Residues in contact with GLU1507 (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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1505B ASN* 3.3 4.9 - - + +
1506B ASP* 1.3 78.6 - - + +
1508B THR* 1.3 63.6 + - - +
1510B ALA* 3.9 8.9 + - - +
1511B LYS* 4.1 24.7 + - - +
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Residues in contact with THR1508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474B PRO* 3.8 19.4 - - + +
1477B MET* 4.2 16.2 - - + -
1478B LEU* 4.0 28.3 - - + +
1504B VAL* 4.3 2.5 - - + -
1505B ASN* 3.2 29.4 + - - +
1507B GLU* 1.3 77.8 - - - +
1509B GLN* 1.3 58.3 + - - +
1511B LYS* 3.4 6.1 + - - +
1512B MET* 2.9 49.1 + - + +
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Residues in contact with GLN1509 (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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1501B TRP* 3.3 40.4 - - + +
1504B VAL* 4.2 16.0 - - + +
1505B ASN 2.7 22.6 + - - +
1506B ASP* 3.9 15.7 - - - +
1508B THR* 1.3 70.6 - - - +
1510B ALA* 1.3 63.9 + - - +
1512B MET* 3.4 7.3 - - - +
1513B ALA* 3.2 23.9 + - - +
1535B MET* 3.4 26.6 - - + +
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Residues in contact with ALA1510 (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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1506B ASP 3.4 13.7 + - - +
1507B GLU* 4.1 7.6 - - - +
1508B THR 3.3 1.0 - - - -
1509B GLN* 1.3 77.9 - - - +
1511B LYS* 1.3 63.6 + - + +
1513B ALA* 3.9 8.9 + - - +
1514B ARG* 3.2 25.9 + - - +
1535B MET 5.8 3.4 - - - -
1536B ILE* 5.3 1.6 - - - +
1537B PRO* 5.5 8.7 - - + +
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Residues in contact with LYS1511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1478B LEU* 3.9 35.6 - - + +
1482B ARG* 5.1 11.0 - - - +
1507B GLU* 4.1 16.2 + - - +
1508B THR 3.4 6.1 + - - +
1510B ALA* 1.3 75.9 - - + +
1512B MET* 1.3 66.2 + - - +
1514B ARG* 3.2 30.9 + - - +
1515B MET* 3.6 17.2 + - - +
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Residues in contact with MET1512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477B MET* 4.2 11.7 - - + -
1478B LEU* 4.1 10.7 - - + +
1481B MET* 3.6 38.0 - - - +
1496B GLN 5.5 0.4 - - - +
1497B CYS* 3.7 18.3 - - - +
1500B LYS 5.1 1.3 - - - +
1501B TRP* 3.7 27.8 - - + -
1504B VAL* 3.8 16.2 - - + -
1508B THR* 2.9 40.1 + - + +
1509B GLN* 3.3 12.5 + - - +
1511B LYS* 1.3 76.5 - - - +
1513B ALA* 1.3 60.7 + - - +
1515B MET* 3.7 5.5 + - - +
1516B ALA* 3.4 23.2 + - - +
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Residues in contact with ALA1513 (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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1501B TRP* 5.6 1.9 - - + -
1509B GLN 3.2 12.1 + - - +
1510B ALA* 4.1 4.5 - - - +
1511B LYS 3.3 0.4 - - - -
1512B MET* 1.3 77.2 - - - +
1514B ARG* 1.3 65.8 + - - +
1517B ALA* 3.2 24.8 + - - +
1532B TYR* 3.6 22.7 - - + +
1535B MET* 3.5 34.5 - - + +
1536B ILE* 3.6 13.3 - - + +
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Residues in contact with ARG1514 (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 GLU* 5.3 0.5 - - - +
1510B ALA* 3.2 28.0 + - - +
1511B LYS* 3.2 22.5 + - - +
1513B ALA* 1.3 79.0 - - - +
1515B MET* 1.3 63.4 + - + +
1517B ALA* 3.9 2.8 - - - +
1518B ALA* 4.5 0.3 - - - +
1536B ILE* 3.7 25.2 - - + +
1537B PRO* 4.3 6.9 - - - +
1540B THR* 3.6 29.9 + - - +
1542B ASP* 3.6 42.5 - - + +
1546B TYR* 3.7 27.0 + - + +
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Residues in contact with MET1515 (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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1478B LEU* 4.1 12.8 - - - +
1481B MET* 3.3 32.5 - - + +
1482B ARG* 3.2 50.3 - - + +
1485B GLU* 3.6 29.4 - - + +
1493B LEU* 3.7 20.0 - - + +
1511B LYS* 3.6 20.7 + - - +
1512B MET* 3.7 3.8 + - - +
1513B ALA 3.3 0.2 - - - -
1514B ARG* 1.3 76.2 - - + +
1516B ALA* 1.3 61.4 + - - +
1517B ALA 3.2 1.8 - - - -
1518B ALA* 3.2 19.9 + - - +
1519B ALA 3.2 9.5 + - - -
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Residues in contact with ALA1516 (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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1481B MET* 5.3 0.9 - - + +
1493B LEU* 5.1 3.3 - - - +
1494B HIS* 4.1 6.7 - - + -
1497B CYS* 3.5 36.6 - - + -
1512B MET 3.4 9.8 + - - +
1513B ALA 4.3 0.2 - - - +
1515B MET* 1.3 76.2 - - - +
1517B ALA* 1.3 62.4 + - - +
1519B ALA* 3.9 10.1 - - - +
1520B ALA* 3.2 23.2 + - - +
1532B TYR* 3.7 25.0 - - + -
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Residues in contact with ALA1517 (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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1513B ALA 3.2 17.3 + - - +
1514B ARG 3.9 4.7 - - - +
1515B MET 3.2 0.4 - - - -
1516B ALA* 1.3 77.4 - - - +
1518B ALA* 1.3 57.8 + - - +
1520B ALA* 3.6 3.6 + - - +
1521B TRP* 3.1 27.0 + - - +
1529B MET* 3.8 11.5 - - + +
1532B TYR* 4.2 8.7 - - + +
1533B THR* 4.4 11.0 - - - +
1536B ILE* 3.8 19.1 - - + -
1546B TYR* 3.9 17.9 - - + -
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Residues in contact with ALA1518 (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 GLU* 4.9 8.1 - - - +
1490B TRP* 4.0 22.4 - - + -
1493B LEU* 5.4 0.2 - - + -
1514B ARG 4.5 0.7 - - - +
1515B MET* 3.2 13.6 + - - +
1517B ALA* 1.3 76.9 - - - +
1519B ALA* 1.3 64.1 + - - +
1521B TRP* 3.3 11.9 + - + +
1522B GLY* 3.1 19.8 + - - -
1546B TYR* 3.5 23.5 + - + +
1635B LYS* 5.4 9.0 - - - +
1638B MET* 4.2 5.5 - - + +
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Residues in contact with ALA1519 (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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1490B TRP* 3.7 34.1 - - - +
1493B LEU* 4.0 12.8 - - + -
1494B HIS* 3.8 20.6 - - + +
1515B MET 3.2 10.1 + - - +
1516B ALA* 3.9 7.9 - - - +
1518B ALA* 1.3 78.9 - - - +
1520B ALA* 1.3 61.2 + - - +
1522B GLY 3.4 0.7 + - - -
1523B LEU* 3.3 32.3 + - - +
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Residues in contact with ALA1520 (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 HIS* 4.2 9.5 - - + -
1516B ALA 3.2 16.7 + - - +
1517B ALA 3.9 0.9 - - - +
1518B ALA 3.4 0.2 - - - -
1519B ALA* 1.3 79.5 - - - +
1521B TRP* 1.3 59.5 + - - +
1523B LEU* 3.8 0.6 + - - -
1524B GLY* 3.1 2.9 + - - -
1525B GLN* 2.9 52.1 + - - +
1526B TRP* 5.9 0.2 - - - -
1528B SER* 3.9 11.2 - - - -
1529B MET* 3.6 24.4 - - + +
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Residues in contact with TRP1521 (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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1517B ALA 3.1 17.7 + - - +
1518B ALA* 3.5 7.9 - - + +
1519B ALA 3.3 0.2 - - - -
1520B ALA* 1.3 74.1 - - - +
1522B GLY* 1.3 64.4 + - - +
1524B GLY* 3.3 12.0 + - - -
1526B TRP* 4.1 23.8 - + - -
1529B MET* 3.8 13.2 - - + -
1545B PHE* 4.1 25.6 - + - -
1546B TYR* 4.2 17.9 - + - -
1549B VAL* 3.6 31.0 - - + +
1595B MET* 4.2 7.9 - - + -
1635B LYS* 4.2 7.9 - - + -
1638B MET* 3.5 58.8 + - + +
1639B VAL* 3.9 25.1 - - + -
1642B LEU* 4.6 6.1 - - + +
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Residues in contact with GLY1522 (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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1490B TRP* 4.0 21.0 - - - -
1518B ALA 3.1 14.0 + - - -
1519B ALA 3.4 2.8 + - - -
1521B TRP* 1.3 78.4 - - - +
1523B LEU* 1.3 59.8 + - - +
1524B GLY 3.5 0.3 + - - -
1638B MET* 4.0 20.5 - - - +
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Residues in contact with LEU1523 (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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1490B TRP* 3.9 24.0 - - + +
1491B GLY* 4.0 23.1 - - - +
1494B HIS* 4.2 10.8 - - + +
1519B ALA 3.3 17.9 + - - +
1520B ALA 4.3 2.7 - - - +
1522B GLY* 1.3 77.5 - - - +
1524B GLY* 1.3 59.0 + - - +
1525B GLN* 3.7 30.1 - - + +
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Residues in contact with GLY1524 (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 ALA 3.1 6.0 + - - -
1521B TRP 3.3 7.8 + - - -
1522B GLY 3.3 3.6 - - - -
1523B LEU* 1.3 79.0 - - - +
1525B GLN* 1.3 61.7 + - - +
1526B TRP* 3.2 36.7 + - - -
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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
------------------------------------------------------------
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