Contacts of the helix formed by residues 1505 - 1521 (chain C) in PDB entry 5JCZ
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 GLY1505 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1500C VAL 5.6 0.8 + - - -
1503C ILE 3.8 0.4 + - - -
1504C PRO* 1.3 73.5 - - - +
1506C LEU* 1.3 59.0 + - - +
1507C PRO* 4.8 0.6 - - - +
1508C ALA* 3.1 5.5 + - - +
1509C TYR* 3.0 32.1 + - - -
1554C PHE* 6.0 1.4 - - - -
1557C SER* 5.5 1.3 - - - -
1558C ASN* 3.2 29.6 + - - +
1561C ARG* 4.2 17.0 - - - -
1676C HIS 4.6 3.8 + - - -
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Residues in contact with LEU1506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1499C ALA 3.6 25.8 - - - +
1500C VAL* 4.6 6.3 + - + -
1502C LEU* 5.7 1.8 - - + -
1503C ILE* 3.8 31.4 + - + +
1504C PRO 3.3 2.8 - - - -
1505C GLY* 1.3 74.9 - - - +
1507C PRO* 1.3 75.4 - - + +
1509C TYR* 3.2 7.2 + - + -
1510C ILE* 2.9 50.8 + - + +
1839C ILE* 4.1 21.8 - - + -
1840C GLN 4.5 4.5 - - - +
1842C PRO* 4.2 23.3 - - + -
1845C LEU* 4.4 6.3 - - + -
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Residues in contact with PRO1507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1489C LEU* 3.8 28.7 - - + +
1493C LEU* 3.5 27.6 - - + -
1500C VAL* 4.4 9.2 - - + +
1505C GLY* 4.4 0.7 - - - +
1506C LEU* 1.3 94.7 - - + +
1508C ALA* 1.3 55.8 + - - +
1510C ILE* 3.7 1.6 - - + +
1511C LEU* 2.9 38.5 + - + +
1554C PHE* 3.9 12.8 - - + -
1555C TRP* 4.2 17.5 - - + -
1558C ASN* 3.2 17.0 - - - +
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Residues in contact with ALA1508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505C GLY 3.1 9.9 + - - +
1507C PRO* 1.3 76.4 - - - +
1509C TYR* 1.3 61.0 + - - +
1511C LEU* 3.3 9.1 + - - +
1512C PHE* 2.9 29.5 + - - +
1555C TRP* 5.9 0.2 - - - -
1558C ASN* 3.3 34.0 + - - +
1561C ARG* 3.8 10.5 - - + -
1562C PHE* 3.5 25.6 - - + +
1565C CYS* 4.7 1.5 - - - -
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Residues in contact with TYR1509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A HIS 5.4 1.0 + - - -
1503C ILE* 4.5 8.7 - - + -
1504C PRO 3.7 16.4 - - - -
1505C GLY 3.0 27.4 + - - -
1506C LEU* 3.7 11.2 - - + +
1508C ALA* 1.3 75.8 - - - +
1510C ILE* 1.3 57.3 + - - +
1512C PHE* 3.3 2.3 + - - +
1513C MET* 3.0 36.0 + - - +
1561C ARG* 3.5 25.9 + - + -
1565C CYS* 3.6 26.0 - - - -
1568C GLN* 5.9 0.9 - - - -
1569C TYR* 5.6 3.6 - + - -
1832C SER* 2.6 32.3 + - - -
1834C LEU* 3.7 29.6 - - + +
1836C LEU* 4.0 19.0 - - + +
1839C ILE* 3.8 20.2 - - + -
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Residues in contact with ILE1510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475C LEU* 3.6 24.6 - - + +
1489C LEU* 3.7 23.6 - - + -
1506C LEU* 2.9 40.3 + - + +
1507C PRO 3.7 3.8 - - - +
1509C TYR* 1.3 77.0 - - - +
1511C LEU* 1.3 61.7 + - - +
1513C MET* 3.2 4.6 + - - +
1514C CYS* 3.1 28.2 + - - -
1839C ILE* 5.1 5.6 - - + -
1841C ILE* 4.3 19.7 - - + -
1845C LEU* 3.7 30.3 - - + -
1847C LEU* 4.4 9.2 - - + -
1850C ILE* 5.0 2.9 - - + -
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Residues in contact with LEU1511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485C LEU* 4.3 13.7 - - + -
1486C VAL* 5.2 1.6 - - + -
1489C LEU* 3.6 20.2 - - + -
1490C ILE* 4.1 18.8 - - + -
1507C PRO* 2.9 29.9 + - + +
1508C ALA* 3.6 7.4 - - - +
1510C ILE* 1.3 78.3 - - - +
1512C PHE* 1.3 57.1 + - - +
1514C CYS* 3.3 7.1 + - + +
1515C VAL* 3.1 28.6 + - - +
1530C LEU* 4.2 13.7 - - + +
1534C THR* 3.7 39.9 - - + +
1538C ILE* 5.7 0.9 - - + -
1555C TRP* 5.3 5.2 - - + -
1562C PHE* 3.8 17.0 - - + -
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Residues in contact with PHE1512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508C ALA 2.9 17.5 + - - +
1509C TYR 3.8 3.4 - - - +
1510C ILE 3.3 0.2 - - - -
1511C LEU* 1.3 73.4 - - - +
1513C MET* 1.3 61.9 + - - +
1515C VAL* 3.0 7.5 + - + +
1516C ARG* 2.8 51.5 + - + +
1562C PHE* 3.7 8.0 - - + -
1565C CYS* 3.7 33.0 - - + -
1566C LEU* 3.7 33.2 - - + -
1569C TYR* 3.3 44.2 - + + -
1588C LEU* 4.1 21.1 - - + -
1836C LEU* 3.9 15.3 - - + -
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Residues in contact with MET1513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473C GLY* 3.5 27.4 - - - +
1474C MET* 3.6 1.2 - - - +
1475C LEU* 3.0 51.5 + - + +
1509C TYR 3.0 24.6 + - - +
1510C ILE* 3.2 5.8 + - - +
1512C PHE* 1.3 76.2 - - - +
1514C CYS* 1.3 60.8 + - - +
1516C ARG* 3.4 8.0 - - - +
1517C HIS 3.4 13.0 + - - -
1836C LEU* 3.4 36.3 - - + +
1839C ILE* 3.9 43.3 - - + +
1841C ILE* 6.3 0.4 - - + -
1852C ARG* 5.5 2.9 - - + +
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Residues in contact with CYS1514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475C LEU* 3.6 29.2 - - - +
1477C TYR* 4.3 14.0 - - + -
1485C LEU* 4.2 24.2 - - - -
1510C ILE* 3.1 23.8 + - - -
1511C LEU* 3.4 11.7 - - - +
1513C MET* 1.3 75.2 - - - +
1515C VAL* 1.3 64.9 + - - +
1517C HIS* 3.4 4.2 + - - +
1518C ALA* 3.2 21.0 + - - +
1526C LYS* 5.6 0.2 - - - +
1530C LEU* 3.7 18.7 - - + +
1850C ILE* 4.6 6.3 - - - -
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Residues in contact with VAL1515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1511C LEU 3.1 15.8 + - - +
1512C PHE* 3.0 20.1 + - + +
1514C CYS* 1.3 75.4 - - - +
1516C ARG* 1.3 58.3 + - - +
1518C ALA* 3.3 5.5 + - - +
1519C ASP* 2.8 29.7 + - + +
1527C VAL* 4.8 9.8 - - + +
1530C LEU* 3.7 18.8 - - + -
1531C LEU* 3.9 23.3 - - + -
1562C PHE* 4.2 8.1 - - + -
1566C LEU* 4.6 0.9 - - + -
1588C LEU* 4.3 11.9 - - + -
1593C LEU* 4.0 26.7 - - + -
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Residues in contact with ARG1516 (chain C).
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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1472C GLN* 2.9 23.6 + - - +
1473C GLY* 2.9 24.9 + - - -
1474C MET* 3.3 39.5 - - + +
1512C PHE* 2.8 34.0 + - + +
1513C MET* 3.4 10.5 - - - +
1515C VAL* 1.3 76.7 - - - +
1517C HIS* 1.3 56.8 + - - +
1519C ASP* 3.3 4.5 + - - +
1520C TYR* 2.8 27.9 + - - +
1585C GLU 4.2 4.2 + - - -
1586C HIS* 3.0 57.9 + - - +
1587C CYS 5.1 1.6 + - - -
1588C LEU* 4.1 10.8 - - + -
1836C LEU* 3.7 19.9 - - - +
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Residues in contact with HIS1517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474C MET* 3.8 22.4 - - + -
1475C LEU 3.3 24.0 - - - +
1476C GLU* 3.3 37.1 - - + +
1477C TYR 5.1 0.4 + - - -
1513C MET 3.4 1.8 + - - +
1514C CYS 3.4 3.4 + - - +
1515C VAL 3.3 0.4 - - - -
1516C ARG* 1.3 75.8 - - - +
1518C ALA* 1.3 60.7 + - - +
1520C TYR* 3.3 11.6 + + - +
1521C LEU* 2.9 65.5 + - + +
1526C LYS* 5.2 3.6 + - - +
1853C VAL* 4.0 26.8 - - + +
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Residues in contact with ALA1518 (chain C).
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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1514C CYS 3.2 10.3 + - - +
1515C VAL* 3.6 10.1 - - - +
1517C HIS* 1.3 78.8 + - - +
1519C ASP* 1.3 62.5 + - - +
1521C LEU* 3.4 4.9 + - - +
1522C ASN 3.3 2.9 + - - -
1523C ASP* 3.1 27.5 + - - +
1526C LYS* 3.7 37.6 - - + +
1527C VAL* 3.6 22.0 - - + +
1530C LEU* 5.2 2.0 - - + -
1591C PHE* 4.0 0.3 - - - -
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Residues in contact with ASP1519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515C VAL* 2.8 15.0 + - + +
1516C ARG 3.4 9.2 - - - +
1518C ALA* 1.3 73.8 - - - +
1520C TYR* 1.3 56.7 + - - +
1522C ASN 2.9 8.8 + - - -
1527C VAL* 4.0 1.9 - - + +
1588C LEU* 3.6 23.3 - - + +
1589C THR* 3.0 28.4 + - - +
1590C ASN* 2.7 37.3 + - - +
1591C PHE* 2.9 47.9 + - + +
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Residues in contact with TYR1520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474C MET* 3.8 26.0 - - + -
1516C ARG 2.8 19.3 + - - +
1517C HIS* 3.3 18.1 + + - +
1519C ASP* 1.3 76.8 + - - +
1521C LEU* 1.3 82.8 + - + +
1522C ASN* 3.1 1.8 + - - +
1589C THR* 5.3 2.5 - - - -
1590C ASN* 3.9 9.1 + - - +
1853C VAL* 6.3 1.3 - - + -
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Residues in contact with LEU1521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517C HIS* 2.9 44.7 + - + +
1518C ALA* 3.7 8.3 - - - +
1519C ASP 3.2 0.4 - - - -
1520C TYR* 1.3 101.1 - - + +
1522C ASN* 1.3 68.5 + - - +
1523C ASP* 3.2 17.4 + - + +
1526C LYS* 4.5 15.7 - - - +
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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
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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