Contacts of the helix formed by residues 1600 - 1618 (chain A) in PDB entry 5XJY
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 HIS1600 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A GLU* 4.7 2.9 + - + -
565A ARG 3.9 12.3 + - - -
566A THR* 3.8 11.1 - - - +
568A LYS 3.7 19.3 - - - -
569A ILE* 3.7 18.0 - - + +
588A TYR* 3.0 29.6 + - - -
1378A GLU* 3.1 38.3 + - - -
1380A GLN* 4.0 15.4 + - - +
1383A MET* 4.4 9.1 - - - +
1384A TYR* 3.3 11.9 + - + +
1598A GLY 3.2 0.6 - - - -
1599A TRP* 1.3 90.5 - - + +
1601A ALA* 1.3 63.3 + - - +
1602A ILE 3.5 1.3 - - - -
1603A SER 4.7 1.1 - - - -
1604A SER* 3.2 20.2 + - - -
1633A ASN* 4.5 2.2 - - - -
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Residues in contact with ALA1601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384A TYR* 4.3 4.2 + - + +
1532A TYR* 4.0 20.2 - - + +
1594A PHE* 4.3 3.8 - - + -
1595A ASN 3.2 26.2 - - - +
1598A GLY* 3.8 11.1 + - - +
1599A TRP 3.5 3.0 + - - -
1600A HIS* 1.3 77.9 - - - +
1602A ILE* 1.3 60.9 + - + +
1603A SER 3.3 0.2 - - - -
1604A SER* 2.4 36.7 + - - +
1605A PHE* 3.1 16.8 + - + +
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Residues in contact with ILE1602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A ARG* 6.3 0.2 - - - +
585A ASP 5.9 1.6 - - - +
586A MET* 5.5 7.9 - - - -
588A TYR* 3.9 28.0 - - + -
589A VAL* 4.1 24.9 - - + -
594A ALA* 4.9 4.5 - - + -
619A MET* 3.6 16.0 - - + +
1592A VAL* 5.8 0.2 - - - +
1594A PHE* 3.6 50.9 - - + -
1596A ASN* 3.5 22.7 - - - +
1598A GLY 5.0 0.4 - - - +
1599A TRP 4.1 10.5 - - - +
1601A ALA* 1.3 79.1 - - + +
1603A SER* 1.3 62.7 + - - +
1605A PHE* 4.3 1.0 + - - +
1606A LEU* 3.5 18.2 + - - +
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Residues in contact with SER1603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A TYR* 3.2 35.4 - - - +
593A PHE* 3.3 24.0 - - - -
594A ALA* 5.3 3.4 - - - +
597A GLN* 4.4 9.1 - - - +
1380A GLN* 3.3 24.4 - - - +
1600A HIS 4.7 1.1 - - - -
1601A ALA 3.3 0.2 - - - -
1602A ILE* 1.3 77.9 - - - +
1604A SER* 1.3 57.6 + - - +
1606A LEU* 3.3 8.6 - - - +
1607A ASN* 3.0 26.0 + - - +
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Residues in contact with SER1604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1380A GLN* 4.2 17.1 - - - +
1381A PRO 3.2 27.1 - - - +
1382A TRP* 4.8 4.3 + - - -
1383A MET* 5.6 0.7 - - - -
1600A HIS 3.2 15.5 + - - -
1601A ALA* 2.4 38.0 + - - -
1603A SER* 1.3 72.6 - - - +
1605A PHE* 1.3 72.8 + - - -
1607A ASN* 3.0 8.0 + - - +
1608A VAL* 3.0 27.4 + - - +
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Residues in contact with PHE1605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382A TRP* 4.7 14.6 - - + -
1387A GLN* 4.7 8.1 - - - -
1389A THR* 3.8 18.2 - - + -
1414A PHE* 4.2 9.0 - + - -
1532A TYR* 3.7 15.3 - - + -
1533A GLY* 3.1 52.3 - - - -
1535A PHE* 4.3 15.9 - + + -
1592A VAL* 3.7 22.9 - - + -
1594A PHE* 4.8 4.5 - - + -
1601A ALA* 3.1 14.1 + - + +
1602A ILE* 5.2 1.1 - - - +
1604A SER* 1.3 91.1 + - - +
1606A LEU* 1.3 59.9 + - - +
1608A VAL* 3.0 14.3 + - + +
1609A ILE* 2.8 32.6 + - - +
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Residues in contact with LEU1606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A MET* 3.7 32.3 - - + -
594A ALA* 4.0 8.5 - - + +
597A GLN* 3.7 21.1 - - + -
598A ASP* 4.3 6.3 - - - +
617A VAL* 3.7 25.8 - - + -
619A MET* 3.7 19.6 - - + +
1592A VAL* 4.7 2.0 - - + -
1602A ILE 3.5 13.6 + - - +
1603A SER* 3.3 9.8 + - - +
1604A SER 3.1 0.2 - - - -
1605A PHE* 1.3 78.1 - - - +
1607A ASN* 1.3 54.2 + - - +
1609A ILE* 3.4 2.6 + - + -
1610A ASN* 2.7 56.3 + - - +
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Residues in contact with ASN1607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A GLN* 4.2 10.7 - - - +
601A GLU* 3.7 13.3 - - - +
1380A GLN* 3.0 25.8 + - + +
1416A THR* 4.9 5.5 - - - +
1603A SER 3.0 12.6 + - - +
1604A SER* 3.0 10.7 + - - +
1606A LEU* 1.3 76.0 - - - +
1608A VAL* 1.3 57.1 + - + +
1610A ASN* 4.5 2.0 - - - +
1611A ASN* 3.0 26.9 + - - +
1629A ILE* 2.9 17.0 + - - +
1630A THR* 3.4 9.6 - - - +
1631A ALA* 3.3 33.1 - - + +
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Residues in contact with VAL1608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381A PRO* 5.1 3.8 - - + -
1382A TRP* 4.8 17.0 - - + +
1408A LEU* 5.9 1.3 - - + -
1414A PHE* 3.3 39.3 - - + +
1415A GLY* 4.8 7.2 - - - -
1416A THR* 5.4 3.6 - - + -
1535A PHE* 4.2 25.4 - - + -
1604A SER 3.0 15.2 + - - +
1605A PHE* 3.0 21.7 + - + +
1607A ASN* 1.3 77.1 - - + +
1609A ILE* 1.3 58.0 + - - +
1611A ASN* 3.2 9.1 - - - +
1612A ALA* 3.0 25.7 + - + +
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Residues in contact with ILE1609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A VAL* 4.1 11.2 - - + -
1404A LEU* 6.0 1.1 - - + -
1408A LEU* 5.3 3.6 - - + -
1535A PHE* 3.6 44.2 - - + -
1537A LEU* 5.6 0.2 - - + -
1590A VAL* 3.6 33.9 - - + -
1592A VAL* 3.5 27.6 - - + -
1605A PHE 2.8 13.9 + - - +
1606A LEU* 4.1 4.0 - - - +
1608A VAL* 1.3 75.9 - - - +
1610A ASN* 1.3 60.3 + - - +
1612A ALA* 2.7 24.7 + - + +
1613A ILE* 2.9 29.0 + - + +
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Residues in contact with ASN1610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A GLN* 4.7 0.2 - - - +
598A ASP* 3.9 10.0 + - - +
601A GLU* 3.4 49.0 - - + +
602A GLN* 3.3 18.9 + - - -
605A ILE* 3.5 14.7 - - + +
617A VAL* 4.2 8.5 - - - +
1606A LEU* 2.7 41.0 + - - +
1607A ASN 4.3 0.7 - - - +
1609A ILE* 1.3 75.3 - - - +
1611A ASN* 1.3 62.1 + - - +
1613A ILE* 3.4 11.3 + - - +
1614A LEU* 3.1 19.9 + - - +
1629A ILE* 5.1 0.4 - - - +
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Residues in contact with ASN1611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A GLU* 4.8 1.0 + - - -
1415A GLY* 2.4 38.0 + - - -
1416A THR* 3.5 15.2 - - - +
1607A ASN* 3.0 21.4 + - - +
1608A VAL* 3.2 7.4 - - - +
1610A ASN* 1.3 76.9 - - - +
1612A ALA* 1.3 56.4 + - - +
1614A LEU* 3.2 6.4 + - - +
1615A ARG* 3.0 49.4 + - - +
1628A GLY* 3.4 12.1 - - - -
1629A ILE* 4.2 18.9 + - - +
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Residues in contact with ALA1612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1404A LEU* 4.1 10.4 - - + +
1407A ALA* 5.0 3.5 - - - +
1408A LEU* 3.9 38.1 - - + -
1608A VAL* 3.0 12.7 + - + +
1609A ILE* 2.7 19.8 + - + +
1611A ASN* 1.3 70.7 - - - +
1613A ILE* 1.3 57.9 + - + +
1615A ARG* 3.2 13.5 + - - +
1616A ALA* 2.9 26.9 + - - +
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Residues in contact with ILE1613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A GLN* 3.5 28.0 - - - +
605A ILE* 4.4 9.6 - - + -
613A LYS 5.8 1.1 - - - +
615A THR* 3.6 35.9 - - + +
617A VAL* 4.5 0.7 - - + -
1404A LEU* 4.3 16.2 - - + -
1590A VAL* 5.8 0.9 - - + -
1609A ILE* 2.9 23.0 + - + +
1610A ASN* 3.6 18.2 - - - +
1611A ASN 3.3 0.2 - - - -
1612A ALA* 1.3 76.3 - - - +
1614A LEU* 1.3 57.6 + - - +
1616A ALA* 3.0 5.4 + - - +
1617A ASN* 3.0 55.5 + - - +
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Residues in contact with LEU1614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A ILE* 4.1 21.2 - - + +
608A LEU* 4.0 25.6 - - + -
609A THR* 3.7 21.0 + - - +
1610A ASN 3.1 14.0 + - - +
1611A ASN* 3.4 9.2 - - - +
1613A ILE* 1.3 78.9 - - - +
1615A ARG* 1.3 61.4 + - - +
1616A ALA 3.1 0.9 + - - -
1617A ASN* 3.8 3.2 + - - -
1618A LEU* 3.4 17.2 + - + +
1627A TYR* 4.0 17.6 - - + -
1628A GLY* 3.4 35.4 - - - +
1629A ILE* 3.8 22.0 - - + -
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Residues in contact with ARG1615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1407A ALA* 3.5 26.9 - - + +
1412A PRO* 4.1 21.2 + - + +
1413A GLY 3.8 15.2 + - - -
1414A PHE 5.2 0.6 - - - -
1415A GLY 2.7 29.9 + - - +
1416A THR* 4.0 2.8 - - - +
1417A ARG 3.5 22.0 + - - -
1611A ASN* 3.0 48.5 + - - +
1612A ALA* 3.2 11.3 + - - +
1614A LEU* 1.3 76.6 - - - +
1616A ALA* 1.3 57.6 + - - +
1618A LEU* 3.3 17.5 - - - +
1624A PRO* 3.3 35.7 + - + +
1625A SER 4.5 0.6 + - - -
1627A TYR* 4.1 9.5 + - + -
1628A GLY* 4.1 12.7 - - - +
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Residues in contact with ALA1616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403A GLU* 4.3 32.1 - - + +
1404A LEU* 3.7 22.9 - - + -
1407A ALA* 4.2 6.5 - - + -
1612A ALA 2.9 12.2 + - - +
1613A ILE* 3.0 9.1 + - + +
1615A ARG* 1.3 80.1 - - - +
1617A ASN* 1.3 70.9 + - - +
1618A LEU* 3.1 11.1 + - - +
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Residues in contact with ASN1617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A ILE* 4.3 10.3 - - + +
609A THR* 3.4 17.6 - - + +
611A THR* 3.5 37.6 + - + +
613A LYS 5.5 1.6 + - - -
614A LYS* 4.3 19.5 - - - +
615A THR* 5.3 0.4 + - - -
1613A ILE* 3.0 37.4 + - - +
1614A LEU 3.8 0.8 + - - +
1616A ALA* 1.3 80.5 - - - +
1618A LEU* 1.3 63.6 + - - +
1619A GLN* 3.6 1.2 + - - -
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Residues in contact with LEU1618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A THR* 3.7 15.4 - - + +
1614A LEU 3.4 16.2 + - - +
1615A ARG* 3.3 30.5 - - - +
1616A ALA 3.1 9.8 + - - +
1617A ASN* 1.3 79.7 - - - +
1619A GLN* 1.3 67.4 + - - +
1620A LYS* 3.4 3.7 + - - +
1621A GLY* 4.4 17.7 - - - +
1623A ASN 4.1 18.8 - - - +
1624A PRO* 4.2 11.4 - - + -
1627A TYR* 3.7 35.7 - - + +
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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
------------------------------------------------------------
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