Contacts of the helix formed by residues 1483 - 1499 (chain F) in PDB entry 5YWB
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 SER1483 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715F VAL* 4.6 8.5 - - - +
716F GLY 5.1 0.2 - - - -
775F GLN* 4.2 1.3 + - - -
1480F GLU* 5.0 0.6 + - - +
1482F PHE* 1.3 76.5 - - - +
1484F GLN* 1.3 78.4 + - - +
1485F GLY 3.3 6.6 + - - -
1486F GLN* 2.9 18.8 + - - -
1487F ARG* 3.1 21.1 + - - +
2501F ADP 2.4 56.1 + - - -
2503F MG 3.9 1.0 - - - -
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Residues in contact with GLN1484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775F GLN* 3.9 43.5 + - + +
776F LYS* 4.7 16.5 - - - +
1429F PRO* 4.6 11.1 - - + +
1483F SER* 1.3 81.2 + - - +
1485F GLY* 1.3 61.8 + - - +
1487F ARG* 3.2 48.0 + - - +
1488F GLN* 2.9 25.5 + - - +
1511F SER* 3.3 23.3 - - - +
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Residues in contact with GLY1485 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715F VAL* 4.0 14.5 - - - +
1483F SER* 3.3 5.7 + - - -
1484F GLN* 1.3 78.7 - - - +
1486F GLN* 1.3 57.3 + - - +
1488F GLN* 3.2 7.6 + - - +
1489F LEU* 2.9 36.9 + - - +
1511F SER* 3.4 25.3 + - - -
1512F ILE* 4.7 3.8 - - - -
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Residues in contact with GLN1486 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715F VAL* 4.1 17.0 - - + +
716F GLY* 5.1 2.6 - - - -
1460F LEU* 4.7 9.4 - - + -
1463F VAL* 3.3 37.2 - - + +
1481F ASN 4.9 1.2 + - - -
1482F PHE* 3.4 34.2 - - + -
1483F SER* 2.9 31.5 + - - +
1485F GLY* 1.3 73.4 - - - +
1487F ARG* 1.3 60.8 + - - +
1489F LEU* 3.2 10.1 + - + +
1490F PHE* 2.9 35.7 + - - -
2501F ADP 3.7 21.0 + - - -
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Residues in contact with ARG1487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776F LYS* 4.7 17.0 - - - +
1429F PRO* 3.8 28.9 + - + +
1431F LEU* 3.6 32.8 - - + +
1478F GLY* 3.8 24.1 + - - -
1479F GLY 2.5 31.5 + - - +
1480F GLU* 4.9 0.2 - - - +
1482F PHE* 3.1 20.9 + - + +
1483F SER* 3.1 12.7 + - - +
1484F GLN* 3.2 41.5 + - - +
1486F GLN* 1.3 74.2 - - - +
1488F GLN* 1.3 64.6 + - - +
1490F PHE* 3.2 3.1 + - - +
1491F CYS* 3.0 27.0 + - - -
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Residues in contact with GLN1488 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425F ILE* 4.8 4.1 - - + +
1426F LEU 2.9 27.3 + - - -
1427F GLN* 4.0 7.7 + - - +
1429F PRO* 3.2 31.3 - - - +
1484F GLN 2.9 11.8 + - - +
1485F GLY* 3.2 12.8 + - - +
1487F ARG* 1.3 75.3 - - - +
1489F LEU* 1.3 57.2 + - - +
1491F CYS* 3.2 6.3 + - - +
1492F LEU* 2.9 38.1 + - + +
1507F GLU 3.4 18.7 + - - -
1508F ALA* 4.1 24.4 - - - +
1510F ALA* 4.6 7.5 - - - +
1511F SER* 5.2 7.4 - - - +
1512F ILE* 4.5 9.4 - - + -
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Residues in contact with LEU1489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715F VAL* 6.3 2.2 - - + -
1458F ALA* 3.5 19.5 - - - +
1459F GLN* 3.2 29.6 - - + +
1460F LEU* 3.6 25.5 - - + +
1485F GLY 2.9 25.0 + - - +
1486F GLN* 3.5 11.0 - - + +
1488F GLN* 1.3 76.3 - - - +
1490F PHE* 1.3 58.2 + - - +
1492F LEU* 3.2 10.0 + - + +
1493F ALA* 2.9 26.9 + - - +
1512F ILE* 3.6 32.1 - - + -
1520F LEU* 4.3 10.3 - - + -
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Residues in contact with PHE1490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1431F LEU* 4.2 28.7 - - + -
1436F ILE* 3.6 31.6 - - + -
1439F ASN* 5.1 4.5 - - + -
1440F LEU* 3.8 24.1 - - + +
1455F LEU* 4.9 1.1 - - + -
1460F LEU* 3.5 27.8 - - + -
1464F VAL* 4.6 8.7 - - + -
1475F ILE* 6.0 0.9 - - + -
1482F PHE* 3.4 46.2 - + - -
1486F GLN 2.9 27.7 + - - -
1487F ARG* 3.2 9.1 + - - +
1489F LEU* 1.3 74.3 - - - +
1491F CYS* 1.3 60.5 + - - +
1493F ALA* 3.1 7.4 + - - +
1494F ARG* 2.9 31.5 + - - +
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Residues in contact with CYS1491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508F LEU* 5.0 8.1 - - + -
1424F ILE 5.6 0.3 - - - +
1425F ILE* 3.9 22.7 - - + +
1426F LEU* 5.5 4.9 - - - +
1429F PRO* 4.1 26.2 - - - -
1430F VAL 4.3 10.1 - - - -
1431F LEU* 5.7 0.4 - - - -
1487F ARG 3.0 18.9 + - - -
1488F GLN* 3.5 9.2 - - - +
1490F PHE* 1.3 76.2 - - - +
1492F LEU* 1.3 61.1 + - - +
1494F ARG* 3.2 29.0 + - - +
1495F ALA* 3.0 20.8 + - - +
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Residues in contact with LEU1492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425F ILE* 3.6 35.7 - - + -
1458F ALA* 5.0 3.6 - - + +
1488F GLN* 2.9 27.9 + - + +
1489F LEU* 3.3 17.7 - - + +
1491F CYS* 1.3 75.9 - - - +
1493F ALA* 1.3 57.4 + - - +
1495F ALA* 3.2 2.6 + - - +
1496F PHE* 2.8 50.9 + - + -
1505F MET* 5.9 3.1 - - + -
1508F ALA* 3.9 22.2 - - + +
1512F ILE* 5.0 1.1 - - + -
1520F LEU* 3.8 37.5 - - + -
1524F VAL* 5.6 3.8 - - + -
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Residues in contact with ALA1493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440F LEU* 3.6 21.8 - - + -
1454F ALA* 4.8 6.1 - - + +
1455F LEU* 4.3 17.5 - - + -
1458F ALA* 4.6 8.7 - - + +
1460F LEU* 5.3 0.2 - - + -
1489F LEU 2.9 14.0 + - - +
1490F PHE* 3.1 10.2 + - - +
1492F LEU* 1.3 74.1 - - - +
1494F ARG* 1.3 65.4 + - - +
1496F PHE* 3.1 11.0 + - - +
1497F VAL* 3.0 30.1 + - + +
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Residues in contact with ARG1494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508F LEU* 4.0 8.6 - - - +
512F TYR* 3.4 22.2 + - + +
514F TRP* 3.2 41.3 - - + -
1430F VAL* 2.7 31.7 + - - +
1431F LEU* 3.3 23.5 - - - +
1432F PHE* 3.7 11.9 - - - -
1439F ASN* 3.5 24.9 + - - +
1440F LEU* 4.5 6.1 - - + +
1490F PHE 2.9 12.8 + - - +
1491F CYS* 3.3 30.0 - - - +
1493F ALA* 1.3 75.2 - - - +
1495F ALA* 1.3 62.3 + - - +
1497F VAL* 3.2 11.6 - - - +
1498F ARG* 3.0 32.1 + - + +
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Residues in contact with ALA1495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1423F SER* 3.7 22.2 + - - +
1424F ILE 5.4 0.9 - - - +
1425F ILE* 3.6 32.8 - - + -
1491F CYS 3.0 7.0 + - - +
1492F LEU 3.3 8.5 - - - +
1494F ARG* 1.3 77.0 - - - +
1496F PHE* 1.3 66.8 + - + +
1498F ARG* 3.5 13.3 + - - +
1499F LYS 4.0 1.2 + - - -
1503F PHE* 3.6 28.2 - - + -
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Residues in contact with PHE1496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425F ILE* 5.9 1.1 - - + -
1454F ALA* 3.7 27.1 - - + -
1457F ILE* 3.5 26.9 - - + -
1458F ALA* 3.5 32.5 - - + -
1492F LEU* 2.8 43.6 + - + -
1493F ALA* 3.1 8.9 + - - +
1495F ALA* 1.3 81.7 - - + +
1497F VAL* 1.3 62.5 + - - +
1498F ARG 3.4 0.2 + - - -
1499F LYS* 3.7 16.1 + - - +
1503F PHE* 5.7 0.4 - + - -
1520F LEU* 5.2 2.7 - - + -
1523F VAL* 6.4 0.2 - - + -
1524F VAL* 3.5 25.8 - - + -
1528F PHE* 3.3 41.6 - + + -
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Residues in contact with VAL1497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514F TRP* 6.4 0.7 - - + -
1440F LEU* 3.6 27.1 - - + +
1441F ASP* 5.3 5.2 - - + +
1446F CYS* 5.1 10.2 - - - -
1450F THR* 5.2 7.9 - - + +
1451F LEU* 4.1 21.5 - - + -
1454F ALA* 3.6 26.9 - - + -
1493F ALA* 3.0 20.0 + - + +
1494F ARG* 3.2 15.3 - - - +
1496F PHE* 1.3 73.5 - - - +
1498F ARG* 1.3 67.1 + - + +
1499F LYS* 3.3 15.1 + - - +
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Residues in contact with ARG1498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512F TYR* 3.3 54.3 + - - +
514F TRP* 4.0 19.5 - - + +
1419F ARG 3.8 9.3 + - - -
1420F SER* 4.3 8.5 + - - +
1422F LEU 3.3 25.7 + - - -
1423F SER* 4.0 18.0 - - - +
1443F GLU* 5.6 1.8 + - - -
1494F ARG* 3.0 30.3 + - + +
1495F ALA* 3.8 6.7 - - - +
1496F PHE 3.3 1.0 - - - -
1497F VAL* 1.3 80.5 - - + +
1499F LYS* 1.3 69.9 + - - +
1500F THR* 3.6 17.4 - - + +
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Residues in contact with LYS1499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450F THR* 5.0 15.8 - - - +
1495F ALA 4.0 3.6 + - - -
1496F PHE 3.7 16.1 + - - +
1497F VAL* 3.3 14.5 - - - +
1498F ARG* 1.3 81.4 - - - +
1500F THR* 1.3 61.6 - - - +
1503F PHE* 5.5 0.4 - - - -
1531F ARG* 4.3 18.4 - - - +
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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
------------------------------------------------------------
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