Contacts of the helix formed by residues 1507 - 1523 (chain B) in PDB entry 4J5L
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 GLY1507 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1506B PRO* 1.3 72.4 + - - -
1508B LEU* 1.3 64.4 + - - -
1509B PRO* 3.5 3.4 - - - -
1510B ALA* 3.4 13.7 + - - +
1511B TYR* 3.2 26.8 + - - -
1556B PHE* 6.0 2.2 - - - -
1559B SER 6.3 0.4 - - - -
1560B ASN* 3.5 20.4 - - - +
1563B ARG* 4.5 9.5 - - - +
1678B HIS 4.6 5.1 + - - -
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Residues in contact with LEU1508 (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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1504B LEU* 4.6 16.6 - - + -
1505B ILE* 2.7 36.9 + - + +
1507B GLY* 1.3 69.6 - - - -
1509B PRO* 1.4 75.3 - - + +
1511B TYR* 3.1 12.8 + - + -
1512B ILE* 2.9 45.4 + - + +
1841B ILE* 3.8 29.4 - - + -
1842B GLN 4.6 2.0 - - - +
1844B PRO* 3.6 37.0 - - + -
1847B LEU* 4.4 6.1 - - + -
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Residues in contact with PRO1509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491B LEU* 3.7 33.3 - - + +
1495B LEU* 4.5 5.6 - - + -
1504B LEU* 6.5 0.7 - - + -
1507B GLY* 4.4 0.2 - - - -
1508B LEU* 1.4 93.9 - - + +
1510B ALA* 1.3 56.9 + - - +
1512B ILE* 3.4 1.0 + - - +
1513B LEU* 2.9 39.4 + - + +
1556B PHE* 3.9 26.9 - - + -
1557B TRP* 4.1 21.1 - - + -
1560B ASN* 3.3 16.6 - - - +
1847B LEU* 6.3 0.7 - - + -
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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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1507B GLY 3.4 9.5 + - - +
1508B LEU 3.3 0.6 - - - -
1509B PRO* 1.3 79.3 - - - +
1511B TYR* 1.3 58.8 + - - +
1513B LEU* 4.5 3.6 - - - -
1514B PHE* 3.0 26.5 + - - +
1560B ASN* 3.2 32.9 + - - +
1563B ARG* 3.8 12.8 - - + -
1564B PHE* 3.5 33.5 - - - +
1567B CYS* 4.8 1.1 - - - -
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Residues in contact with TYR1511 (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 ILE* 5.3 2.0 - - + -
1506B PRO 4.3 3.7 + - - -
1507B GLY 3.2 36.9 + - - -
1508B LEU* 3.1 13.5 + - + +
1510B ALA* 1.3 74.2 - - - +
1512B ILE* 1.3 64.8 + - - +
1514B PHE* 3.5 5.3 + - - +
1515B MET* 3.1 31.6 + - - +
1563B ARG* 3.5 20.3 + - + -
1567B CYS* 3.8 26.5 - - - -
1571B TYR* 6.0 0.9 - + - -
1834B SER* 3.2 34.6 - - - -
1836B LEU* 3.6 32.3 - - + +
1838B LEU* 3.9 18.8 - - + -
1841B ILE* 4.0 20.2 - - + -
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Residues in contact with ILE1512 (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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1477B LEU* 3.7 14.3 - - + +
1487B LEU* 5.1 2.7 - - + -
1491B LEU* 3.7 22.2 - - + -
1508B LEU* 2.9 43.7 + - + +
1509B PRO 3.7 3.6 - - - +
1511B TYR* 1.3 73.3 - - - +
1513B LEU* 1.3 65.6 + - - +
1515B MET* 3.2 13.3 + - + +
1516B CYS* 3.0 29.1 + - - -
1843B ILE* 3.6 29.2 - - + -
1847B LEU* 3.7 23.8 - - + -
1849B LEU* 4.4 8.3 - - + -
1852B ILE* 5.7 2.0 - - + -
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Residues in contact with LEU1513 (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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1487B LEU* 5.3 8.1 - - + -
1488B VAL* 5.3 3.8 - - + -
1491B LEU* 3.8 19.5 - - + -
1492B ILE* 4.2 17.3 - - + -
1509B PRO* 2.9 27.8 + - + +
1510B ALA* 3.8 5.6 - - - +
1512B ILE* 1.3 74.2 - - - +
1514B PHE* 1.3 58.4 + - - +
1516B CYS* 3.1 8.8 + - + +
1517B VAL* 2.9 30.1 + - + +
1532B LEU* 4.3 16.2 - - + +
1536B THR* 3.8 39.7 - - + +
1540B ILE* 5.7 1.3 - - + -
1557B TRP* 5.5 3.4 - - + -
1564B PHE* 3.7 21.1 - - + -
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Residues in contact with PHE1514 (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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1510B ALA 3.0 17.0 + - - +
1511B TYR 3.9 5.6 - - - +
1512B ILE 3.2 0.2 - - - -
1513B LEU* 1.3 76.6 - - - +
1515B MET* 1.3 59.4 + - - +
1517B VAL* 3.0 7.7 + - + +
1518B ARG* 2.8 56.7 + - + +
1564B PHE* 3.5 11.2 - - + -
1567B CYS* 3.9 27.1 - - + -
1568B LEU* 3.5 29.6 - - + -
1571B TYR* 3.3 43.5 - + + -
1588B HIS 4.4 0.4 - - - -
1590B LEU* 4.5 16.4 - - + -
1838B LEU* 3.7 17.5 - - + -
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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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1475B GLY* 3.2 28.7 - - - +
1476B MET* 3.6 0.3 - - - -
1477B LEU* 3.1 52.6 + - + +
1511B TYR 3.1 20.2 + - - +
1512B ILE* 3.2 11.4 + - + +
1514B PHE* 1.3 77.6 - - + +
1516B CYS* 1.3 60.3 + - - +
1518B ARG* 3.5 7.0 + - - +
1519B HIS 3.3 14.2 + - - -
1838B LEU* 3.6 37.7 - - + +
1841B ILE* 3.7 36.3 - - + +
1843B ILE* 4.8 1.1 - - + -
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Residues in contact with CYS1516 (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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1477B LEU* 3.7 28.1 - - - +
1479B TYR* 4.0 18.5 - - + -
1487B LEU* 4.1 21.1 - - + -
1512B ILE* 3.0 26.1 + - - -
1513B LEU* 3.3 11.2 - - - +
1515B MET* 1.3 77.0 - - - +
1517B VAL* 1.3 61.4 + - - +
1519B HIS* 3.5 3.6 + - - +
1520B ALA* 3.3 20.8 + - - +
1532B LEU* 3.7 19.0 - - + +
1852B ILE* 4.6 6.3 - - - -
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Residues in contact with VAL1517 (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 LEU* 2.9 19.0 + - + +
1514B PHE* 3.0 19.5 + - + +
1516B CYS* 1.3 74.0 - - - +
1518B ARG* 1.3 64.6 + - - +
1520B ALA* 3.3 6.0 + - - +
1521B ASP* 3.0 22.2 + - + +
1529B VAL* 4.8 11.2 - - + +
1532B LEU* 3.8 15.5 - - + -
1533B LEU* 3.8 26.7 - - + -
1564B PHE* 4.0 12.6 - - + -
1568B LEU* 5.0 1.1 - - + -
1590B LEU* 4.8 8.5 - - + -
1595B LEU* 4.1 25.4 - - + -
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Residues in contact with ARG1518 (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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1474B GLN* 3.1 26.5 + - - +
1475B GLY* 3.0 24.0 + - - -
1476B MET* 3.5 29.2 - - + +
1514B PHE* 2.8 46.8 + - + +
1515B MET* 3.6 10.5 - - - +
1517B VAL* 1.3 74.4 - - - +
1519B HIS* 1.3 57.7 + - - +
1521B ASP* 3.3 4.5 + - - +
1522B TYR* 2.9 27.7 + - - +
1587B GLU 4.3 4.0 + - - -
1588B HIS* 3.1 55.6 + - - +
1589B CYS 5.1 1.8 + - - -
1590B LEU* 4.1 13.0 - - + -
1838B LEU* 4.2 4.9 - - - +
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Residues in contact with HIS1519 (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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1476B MET* 3.6 29.1 - - + +
1477B LEU 3.2 21.3 - - - +
1478B GLU* 3.3 37.7 - - + +
1479B TYR* 6.3 0.2 - + - -
1515B MET 3.3 5.3 + - - +
1516B CYS 3.9 2.2 - - - +
1517B VAL 3.3 0.6 - - - -
1518B ARG* 1.3 76.9 - - - +
1520B ALA* 1.3 60.7 + - - +
1522B TYR* 3.3 8.0 + + - +
1523B LEU* 3.0 61.6 + - + +
1528B LYS* 4.6 7.2 - - - -
1855B VAL* 4.1 21.7 - - + +
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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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1479B TYR* 5.8 0.4 - - + +
1516B CYS 3.3 12.7 + - - +
1517B VAL* 3.7 7.4 - - - +
1519B HIS* 1.3 78.1 - - - +
1521B ASP* 1.3 61.1 + - - +
1523B LEU* 3.5 5.5 + - - +
1524B ASN 3.2 2.6 + - - -
1525B ASP* 3.0 29.4 + - - +
1528B LYS* 4.2 31.6 - - + +
1529B VAL* 3.6 25.4 - - + +
1532B LEU* 5.6 2.7 - - + -
1593B PHE* 4.0 0.3 - - - -
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Residues in contact with ASP1521 (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 VAL* 3.0 14.1 + - + +
1518B ARG 3.4 9.0 - - - +
1520B ALA* 1.3 77.4 - - - +
1522B TYR* 1.3 53.2 + - - +
1524B ASN* 3.0 6.8 + - - -
1529B VAL* 4.2 1.0 - - + +
1589B CYS 4.9 0.7 - - - +
1590B LEU* 3.6 23.5 - - + +
1591B THR* 3.0 26.8 + - - -
1592B ASN* 2.5 39.3 + - - +
1593B PHE* 2.9 50.7 + - + +
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Residues in contact with TYR1522 (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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1476B MET* 3.9 32.8 - - + -
1518B ARG 2.9 16.8 + - - +
1519B HIS* 3.6 9.2 - + - +
1520B ALA 3.3 0.4 - - - -
1521B ASP* 1.3 79.1 + - - +
1523B LEU* 1.3 78.7 + - + +
1524B ASN* 3.2 1.8 + - - +
1591B THR* 5.4 2.0 - - - -
1592B ASN* 4.2 7.0 + - - +
1855B VAL* 5.8 2.2 - - + -
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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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1478B GLU* 5.9 0.4 - - + -
1519B HIS* 3.0 44.7 + - + +
1520B ALA 3.8 5.6 - - - +
1521B ASP 3.2 0.2 - - - -
1522B TYR* 1.3 98.9 - - + +
1524B ASN* 1.3 69.4 + - - +
1525B ASP* 3.3 16.1 + - + +
1528B LYS* 4.7 14.6 - - + +
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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