Contacts of the helix formed by residues 1595 - 1617 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1524B ILE* 5.3 4.5 - - + -
1525B ASN* 4.3 12.3 - - - +
1528B SER* 5.1 8.5 - - - +
1591B VAL* 4.0 13.5 - - + -
1592B SER* 3.3 15.6 + - - +
1593B ASP 3.1 0.4 - - - -
1594B ASN* 1.3 81.1 - - - +
1596B ARG* 1.3 62.9 + - - +
1597B PRO* 3.3 3.6 - - - -
1598B PHE* 3.1 22.0 + - + +
1599B HIS* 2.9 22.0 + - - +
5D LYS* 4.4 9.6 - - - +
70D LEU 3.8 7.2 - - - +
71D SER* 4.5 1.1 - - - -
73D PRO* 2.9 43.1 - - + +
74D GLN* 3.4 32.3 - - + +
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Residues in contact with ARG1596 (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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1588B GLU* 3.6 42.0 + - - +
1591B VAL* 4.2 14.1 + - - +
1592B SER 3.7 3.5 + - - -
1593B ASP* 3.4 30.6 + - + +
1595B LEU* 1.3 77.1 - - - +
1597B PRO* 1.3 70.6 - - + +
1599B HIS* 3.1 18.7 + - - +
1600B ASP* 2.8 52.6 + - - +
1603B GLU* 5.1 2.2 + - - -
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Residues in contact with PRO1597 (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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1593B ASP 4.2 3.8 - - - +
1594B ASN 4.0 12.1 - - - +
1595B LEU 3.4 3.6 - - - -
1596B ARG* 1.3 96.1 - - + +
1598B PHE* 1.3 60.9 - - - +
1600B ASP* 3.2 10.7 + - + +
1601B ARG* 3.1 22.2 + - - +
70D LEU* 4.2 20.8 - - + +
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Residues in contact with PHE1598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1528B SER* 4.0 11.2 - - - -
1532B ASN* 3.8 32.8 - - + -
1587B HIS* 4.0 12.1 - - - -
1595B LEU* 3.1 28.0 + - + +
1597B PRO* 1.3 76.7 - - - +
1599B HIS* 1.3 69.7 + - - +
1601B ARG* 3.5 4.2 + - - +
1602B MET* 2.9 53.3 + - + +
56D TRP* 3.9 13.7 - + - -
70D LEU* 3.4 33.7 + - + +
71D SER* 3.7 32.5 - - - -
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Residues in contact with HIS1599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584B ILE* 3.6 16.0 + - + +
1587B HIS* 2.9 40.8 - + + +
1588B GLU* 3.3 37.7 + - + +
1591B VAL* 4.4 12.1 - - + -
1595B LEU 2.9 11.8 + - - +
1596B ARG* 3.1 20.3 + - - +
1598B PHE* 1.3 81.7 - - - +
1600B ASP* 1.3 67.1 + - - +
1602B MET* 3.2 9.8 + - + +
1603B GLU* 3.1 52.8 + - + +
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Residues in contact with ASP1600 (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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1596B ARG* 2.8 54.9 + - - +
1597B PRO* 3.2 11.3 + - + +
1599B HIS* 1.3 79.5 + - - +
1601B ARG* 1.3 62.2 + - - +
1603B GLU* 3.3 11.5 + - - +
1604B GLU* 3.2 30.9 + - - +
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Residues in contact with ARG1601 (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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1597B PRO 3.1 7.9 + - - +
1598B PHE 3.8 5.4 - - - +
1599B HIS 3.4 0.2 - - - -
1600B ASP* 1.3 73.9 - - - +
1602B MET* 1.3 60.3 + - - +
1604B GLU* 2.9 29.8 + - - +
1605B CYS* 3.0 20.7 + - - -
133C LYS* 5.2 11.0 - - - +
67D LEU* 5.3 4.7 - - + -
70D LEU* 3.8 29.4 - - + -
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Residues in contact with MET1602 (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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1528B SER 4.4 3.4 - - - +
1531B LEU* 4.0 28.7 - - - -
1532B ASN* 3.7 24.7 - - + +
1535B VAL* 3.5 24.1 - - + +
1584B ILE* 4.4 13.9 - - + +
1587B HIS* 4.0 23.1 - - + +
1598B PHE* 2.9 51.4 + - + +
1599B HIS* 3.2 13.6 + - + +
1601B ARG* 1.3 79.0 - - - +
1603B GLU* 1.3 58.6 + - - +
1605B CYS* 4.7 3.1 - - - -
1606B PHE* 3.0 26.7 + - - +
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Residues in contact with GLU1603 (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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1584B ILE* 3.8 19.1 - - + +
1588B GLU* 4.6 12.7 - - - +
1596B ARG* 5.1 3.1 + - - -
1599B HIS* 3.1 46.0 + - + +
1600B ASP* 3.4 13.6 - - - +
1602B MET* 1.3 74.1 - - - +
1604B GLU* 1.3 54.4 + - + +
1606B PHE* 3.0 11.7 + - - +
1607B LYS* 2.6 62.5 + - - +
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Residues in contact with GLU1604 (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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1600B ASP* 3.2 18.6 + - - +
1601B ARG* 2.9 13.5 + - - +
1603B GLU* 1.3 78.8 - - + +
1605B CYS* 1.3 57.9 + - - +
1607B LYS* 3.3 10.8 + - + +
1608B ASN* 2.9 33.9 + - - +
133C LYS* 3.1 35.1 + - - -
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Residues in contact with CYS1605 (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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1535B VAL* 3.7 24.5 - - + +
1536B ASP* 4.2 26.5 - - + -
1601B ARG* 3.0 22.3 + - - -
1602B MET* 3.8 2.9 - - - +
1604B GLU* 1.3 75.4 - - - +
1606B PHE* 1.3 53.0 + - - +
1608B ASN* 3.2 8.0 - - - +
1609B LEU* 2.6 37.7 + - - +
131C GLU 5.7 4.5 - - - -
67D LEU* 6.4 2.5 - - - -
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Residues in contact with PHE1606 (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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1535B VAL* 4.4 10.3 - - + -
1577B ILE* 3.4 49.4 - - + -
1578B PRO* 5.7 0.2 - - + -
1580B LEU* 3.6 19.3 - - + -
1581B GLY* 3.4 20.2 - - - -
1584B ILE* 3.5 29.2 - - + -
1602B MET 3.0 13.4 + - - +
1603B GLU* 3.3 12.1 - - - +
1605B CYS* 1.3 79.7 - - - +
1607B LYS* 1.3 59.6 + - + +
1609B LEU* 2.9 8.4 + - + +
1610B LYS* 2.5 51.4 + - + +
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Residues in contact with LYS1607 (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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1603B GLU* 2.6 53.9 + - - +
1604B GLU* 3.4 11.0 - - + +
1606B PHE* 1.3 78.2 - - + +
1608B ASN* 1.3 63.8 + - - +
1610B LYS* 3.2 7.8 + - - +
1611B MET* 2.9 27.2 + - - +
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Residues in contact with ASN1608 (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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1604B GLU 2.9 18.1 + - - +
1605B CYS* 3.2 12.8 - - - +
1607B LYS* 1.3 72.7 - - - +
1609B LEU* 1.3 63.3 + - - +
1611B MET* 3.2 19.1 - - - +
1612B LYS* 3.1 32.5 + - - +
130C LYS* 4.5 16.2 + - - +
131C GLU* 4.2 23.8 - - - +
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Residues in contact with LEU1609 (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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1534B ILE 4.9 4.3 - - - +
1535B VAL* 3.8 28.3 - - + +
1543B PHE* 3.9 24.0 - - + -
1577B ILE* 4.2 12.1 - - + -
1580B LEU* 5.3 6.3 - - + -
1605B CYS 2.6 19.0 + - - +
1606B PHE* 2.9 12.9 + - + +
1608B ASN* 1.3 70.3 - - - +
1610B LYS* 1.3 68.8 + - - +
1611B MET 3.0 2.0 + - - -
1612B LYS* 3.2 5.8 + - + -
1613B VAL* 3.0 41.0 + - + +
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Residues in contact with LYS1610 (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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1577B ILE* 3.8 33.7 - - + +
1606B PHE* 2.5 35.0 + - + +
1607B LYS* 3.4 9.2 - - - +
1609B LEU* 1.3 71.4 - - - +
1611B MET* 1.3 53.8 + - + +
1613B VAL* 3.3 1.9 + - - +
1614B GLU* 2.5 72.2 + - + +
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Residues in contact with MET1611 (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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1607B LYS 2.9 12.4 + - - +
1608B ASN* 3.2 22.7 - - - +
1609B LEU 3.0 0.6 + - - -
1610B LYS* 1.3 76.3 - - + +
1612B LYS* 1.3 72.4 + - - +
1614B GLU* 3.2 17.7 + - - +
1615B LYS* 3.4 13.0 + - - +
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Residues in contact with LYS1612 (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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1608B ASN* 3.1 20.6 + - - +
1609B LEU* 4.1 5.4 - - + +
1611B MET* 1.3 86.9 - - - +
1613B VAL* 1.3 64.1 + - + +
1615B LYS* 3.8 4.6 + - - +
1616B GLU* 3.4 23.9 + - - +
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Residues in contact with VAL1613 (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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1543B PHE* 4.0 16.2 - - + -
1547B GLU* 5.8 0.4 - - - +
1573B ILE* 4.0 12.6 - - + +
1574B ALA* 4.2 9.4 - - - -
1577B ILE* 3.8 24.7 - - + -
1609B LEU* 3.0 37.8 + - + +
1610B LYS 3.7 2.9 - - - +
1612B LYS* 1.3 78.1 - - + +
1614B GLU* 1.3 61.5 + - + +
1615B LYS 3.2 0.2 - - - -
1616B GLU* 4.6 0.4 - - - -
1617B TYR* 2.7 54.8 + - + +
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Residues in contact with GLU1614 (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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1577B ILE* 5.0 5.8 - - + +
1610B LYS* 2.5 68.8 + - + +
1611B MET* 3.2 6.7 + - - +
1613B VAL* 1.3 75.4 - - + +
1615B LYS* 1.3 61.7 + - - +
1617B TYR 2.3 25.3 - - - +
1618B GLY* 3.7 6.1 + - - -
1619B VAL* 2.6 39.5 + - + +
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Residues in contact with LYS1615 (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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1611B MET 3.4 11.8 + - - +
1612B LYS* 4.0 5.2 - - - +
1613B VAL 3.2 0.2 - - - -
1614B GLU* 1.3 79.7 - - - +
1616B GLU* 1.3 64.9 + - - +
1617B TYR* 4.2 1.2 - - - -
1618B GLY* 4.8 0.7 + - - -
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Residues in contact with GLU1616 (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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1547B GLU* 5.7 2.5 - - - +
1612B LYS 3.4 15.5 + - - +
1613B VAL* 4.6 0.2 - - - -
1615B LYS* 1.3 82.3 - - - +
1617B TYR* 1.3 92.6 + - + +
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Residues in contact with TYR1617 (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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1547B GLU* 3.5 23.0 + - - +
1551B PHE* 3.6 24.5 - + - -
1570B LYS* 4.3 28.0 - - + +
1573B ILE* 3.9 29.7 - - + +
1574B ALA* 4.2 17.7 - - + -
1613B VAL* 2.7 44.6 + - + +
1614B GLU* 2.3 24.7 - - - +
1615B LYS 4.3 0.4 - - - -
1616B GLU* 1.3 103.3 - - + +
1618B GLY* 1.3 63.9 + - - +
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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