Contacts of the helix formed by residues 1595 - 1618 (chain A) in PDB entry 2YIN
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 LEU1595 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524A ILE* 5.0 5.2 - - + -
1525A ASN* 4.3 13.5 - - - +
1528A SER* 5.2 6.7 - - - +
1591A VAL* 3.9 16.2 - - + -
1592A SER* 3.2 16.2 + - - +
1593A ASP 3.1 0.8 - - - -
1594A ASN* 1.3 76.2 + - - +
1596A ARG* 1.3 63.2 + - - +
1597A PRO* 3.3 3.4 - - - -
1598A PHE* 3.0 21.0 + - + +
1599A HIS* 2.9 19.4 + - - +
5C LYS* 4.7 8.3 - - - +
70C LEU 4.0 10.5 - - - +
71C SER* 4.8 1.6 - - - -
73C PRO* 3.5 34.8 - - + -
74C GLN* 3.4 34.5 - - + +
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Residues in contact with ARG1596 (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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1591A VAL* 4.9 7.6 - - + -
1592A SER 3.6 4.1 + - - +
1593A ASP* 3.0 25.7 + - - +
1595A LEU* 1.3 75.6 - - - +
1597A PRO* 1.4 64.7 - - + +
1599A HIS* 3.1 9.0 + - - +
1600A ASP* 2.7 41.2 + - - +
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Residues in contact with PRO1597 (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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1593A ASP 3.9 2.7 - - - +
1594A ASN 3.2 19.7 - - - +
1595A LEU* 3.3 2.2 - - - -
1596A ARG* 1.4 92.2 - - + +
1598A PHE* 1.3 59.6 + - - +
1600A ASP* 3.1 9.1 + - + +
1601A ARG* 3.1 24.8 + - - +
70C LEU* 4.2 21.1 - - + +
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Residues in contact with PHE1598 (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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1528A SER* 4.0 15.9 - - - -
1532A ASN* 3.8 34.1 - - + -
1587A HIS* 4.1 6.7 - - - -
1595A LEU* 3.0 25.3 + - + +
1597A PRO* 1.3 75.5 - - - +
1599A HIS* 1.3 71.0 + - - +
1601A ARG* 3.5 5.7 + - + +
1602A MET* 3.1 50.6 + - + +
56C TRP* 4.2 12.3 - + - -
70C LEU* 3.4 34.2 + - + +
71C SER* 3.7 33.2 - - - -
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Residues in contact with HIS1599 (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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1584A ILE* 3.6 17.2 + - + +
1587A HIS* 2.9 39.7 - + + +
1588A GLU* 3.4 36.4 + - + +
1591A VAL* 4.4 11.0 - - + +
1595A LEU 2.9 11.5 + - - +
1596A ARG* 3.6 11.6 - - - +
1598A PHE* 1.3 80.9 - - - +
1600A ASP* 1.3 70.1 + - - +
1602A MET* 3.0 11.7 + - + +
1603A GLU* 3.0 53.1 + - + +
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Residues in contact with ASP1600 (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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1596A ARG* 2.7 38.2 + - - +
1597A PRO* 3.4 8.7 - - + +
1599A HIS* 1.3 79.9 + - - +
1601A ARG* 1.3 62.2 + - - +
1603A GLU* 3.2 13.4 + - - +
1604A GLU* 3.1 30.1 + - - +
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Residues in contact with ARG1601 (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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1532A ASN* 6.1 1.1 - - - +
1536A ASP* 2.9 29.9 + - - -
1597A PRO 3.1 14.8 + - - +
1598A PHE* 3.7 6.5 - - + +
1600A ASP* 1.3 75.3 - - - +
1602A MET* 1.3 63.3 + - - +
1604A GLU* 3.2 20.9 + - - +
1605A CYS* 3.0 48.3 + - - +
64C TYR* 4.9 2.6 - - - -
67C LEU* 3.6 34.7 - - + +
70C LEU* 3.8 24.0 - - + -
131D GLU* 3.4 26.2 + - - +
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Residues in contact with MET1602 (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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1528A SER 4.5 3.1 - - - +
1531A LEU* 4.0 26.2 - - - -
1532A ASN* 3.7 25.6 - - + +
1535A VAL* 3.6 18.8 - - + +
1536A ASP* 6.4 0.2 - - - -
1584A ILE* 4.6 14.8 - - - -
1587A HIS* 4.0 21.1 - - + +
1598A PHE* 3.1 51.6 + - + +
1599A HIS* 3.0 15.8 + - + +
1601A ARG* 1.3 76.9 - - - +
1603A GLU* 1.3 57.0 + - - +
1605A CYS* 3.6 2.5 + - - -
1606A PHE* 3.0 27.4 + - - +
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Residues in contact with GLU1603 (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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1584A ILE* 3.8 19.6 - - + +
1588A GLU* 4.5 12.2 - - - +
1599A HIS* 3.0 44.2 + - + +
1600A ASP* 3.2 14.8 + - - +
1602A MET* 1.3 74.3 - - - +
1604A GLU* 1.3 55.6 + - + +
1606A PHE* 3.1 12.2 + - - +
1607A LYS* 2.6 38.3 + - - +
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Residues in contact with GLU1604 (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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1600A ASP* 3.1 18.5 + - - +
1601A ARG* 3.2 25.4 + - - +
1603A GLU* 1.3 77.4 - - + +
1605A CYS* 1.3 57.3 + - - +
1607A LYS* 3.0 9.2 + - - +
1608A ASN* 2.8 34.2 + - - +
131D GLU* 6.1 0.9 - - - -
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Residues in contact with CYS1605 (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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1535A VAL* 3.6 23.6 - - + +
1536A ASP* 4.1 14.6 - - - -
1601A ARG* 3.0 56.4 + - - +
1602A MET* 3.7 4.7 - - - +
1604A GLU* 1.3 74.2 - - - +
1606A PHE* 1.3 56.6 + - - +
1608A ASN* 3.2 9.1 + - - +
1609A LEU* 2.7 37.9 + - - +
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Residues in contact with PHE1606 (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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1535A VAL* 4.0 10.5 - - + +
1577A ILE* 3.3 41.7 - - + -
1580A LEU* 3.6 24.9 - - + -
1581A GLY* 3.4 20.0 - - - -
1584A ILE* 3.4 30.1 - - + -
1602A MET 3.0 7.5 + - - +
1603A GLU* 3.1 11.2 + - - +
1605A CYS* 1.3 79.1 - - - +
1607A LYS* 1.3 56.3 + - + +
1609A LEU* 2.8 10.4 + - + +
1610A LYS* 2.6 65.0 + - + +
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Residues in contact with LYS1607 (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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1603A GLU 2.6 20.4 + - - +
1604A GLU* 3.3 8.7 - - - +
1606A PHE* 1.3 78.1 - - + +
1608A ASN* 1.3 62.8 + - - +
1610A LYS* 3.4 5.9 + - - +
1611A MET* 3.2 23.6 + - - +
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Residues in contact with ASN1608 (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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1604A GLU 2.8 14.3 + - - +
1605A CYS* 3.2 12.3 - - - +
1607A LYS* 1.3 77.4 - - - +
1609A LEU* 1.3 53.1 + - - +
1611A MET* 3.4 12.0 + - - +
1612A LYS* 2.8 72.1 + - - +
131D GLU* 4.3 13.6 + - - +
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Residues in contact with LEU1609 (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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1534A ILE 4.7 3.8 - - - +
1535A VAL* 4.0 26.5 - - + +
1543A PHE* 4.2 18.6 - - + -
1576A GLN* 6.1 0.9 - - - +
1577A ILE* 4.3 13.0 - - + -
1580A LEU* 4.5 20.6 - - + -
1605A CYS 2.7 16.6 + - - +
1606A PHE* 2.8 12.0 + - + +
1608A ASN* 1.3 71.5 - - - +
1610A LYS* 1.3 66.3 + - - +
1612A LYS* 4.6 9.9 - - + -
1613A VAL* 2.9 43.0 + - + +
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Residues in contact with LYS1610 (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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1577A ILE* 3.5 39.1 + - + +
1578A PRO* 4.8 4.8 - - - +
1581A GLY* 5.3 1.8 - - - -
1606A PHE* 2.6 43.0 + - + +
1607A LYS* 3.9 7.0 - - - +
1609A LEU* 1.3 72.9 - - - +
1611A MET* 1.3 53.1 + - - +
1614A GLU* 2.5 73.7 + - - +
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Residues in contact with MET1611 (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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1607A LYS 3.2 13.0 + - - +
1608A ASN* 3.7 12.3 - - - +
1609A LEU 3.2 0.2 - - - -
1610A LYS* 1.3 78.1 - - - +
1612A LYS* 1.3 101.1 + - + +
1614A GLU* 4.2 3.8 - - - +
1615A LYS* 3.3 24.3 + - - +
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Residues in contact with LYS1612 (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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1608A ASN* 2.8 54.4 + - - +
1609A LEU* 4.1 10.5 - - + +
1611A MET* 1.3 94.5 - - + +
1613A VAL* 1.3 60.6 + - + +
1615A LYS* 3.9 3.3 + - - +
1616A GLU* 3.4 22.7 + - - +
131D GLU* 4.8 6.9 + - - -
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Residues in contact with VAL1613 (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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1543A PHE* 3.5 33.2 - - + -
1547A GLU* 5.5 0.4 - - - +
1573A ILE* 3.9 17.5 - - + +
1574A ALA* 4.3 10.1 - - - +
1577A ILE* 3.6 33.2 - - + -
1609A LEU* 2.9 24.5 + - + +
1610A LYS 4.6 0.2 - - - +
1612A LYS* 1.3 78.1 - - + +
1614A GLU* 1.3 66.0 + - + +
1615A LYS 3.2 0.9 - - - -
1617A TYR* 2.9 32.4 + - + +
1618A GLY 3.3 3.7 - - - +
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Residues in contact with GLU1614 (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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1577A ILE* 4.4 6.5 - - + +
1610A LYS* 2.5 76.7 + - + +
1611A MET* 4.2 4.0 - - - +
1613A VAL* 1.3 74.7 - - + +
1615A LYS* 1.3 56.9 + - - +
1618A GLY* 2.4 45.0 + - - +
1619A VAL* 3.9 27.7 - - + +
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Residues in contact with LYS1615 (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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1611A MET 3.3 15.7 + - - +
1612A LYS* 4.1 3.8 - - - +
1613A VAL 3.2 0.2 - - - -
1614A GLU* 1.3 81.7 - - - +
1616A GLU* 1.3 64.4 + - - +
1618A GLY* 3.8 3.1 + - - -
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Residues in contact with GLU1616 (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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1547A GLU* 5.6 0.4 - - - +
1612A LYS 3.4 15.5 + - - +
1614A GLU 3.4 0.2 - - - -
1615A LYS* 1.3 83.7 - - - +
1617A TYR* 1.3 100.0 + - + +
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Residues in contact with TYR1617 (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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1547A GLU* 3.3 28.2 + - - +
1551A PHE* 3.3 31.4 - + - -
1570A LYS* 3.9 35.4 - - + +
1573A ILE* 4.0 26.7 - - + -
1574A ALA* 4.1 23.8 - - + +
1613A VAL* 2.9 23.1 + - + +
1616A GLU* 1.3 110.1 - - + +
1618A GLY* 1.3 65.2 + - - +
1619A VAL 3.7 1.6 + - - +
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Residues in contact with GLY1618 (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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1574A ALA* 4.5 3.8 - - - +
1613A VAL* 3.3 3.6 - - - +
1614A GLU* 2.4 41.6 + - - +
1615A LYS 3.8 3.4 + - - -
1616A GLU 3.4 2.2 + - - -
1617A TYR* 1.3 80.2 - - - +
1619A VAL* 1.3 62.6 + - - -
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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
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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