Contacts of the helix formed by residues 1622 - 1636 (chain B) in PDB entry 3AU5
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 SER1622 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1619B HIS* 3.1 35.4 + - - +
1620B PRO 3.3 1.8 + - - -
1621B GLY* 1.3 84.3 - - - +
1623B VAL* 1.3 69.4 + - - +
1624B GLY* 3.5 5.1 + - - -
1625B ASN* 3.0 14.9 + - - +
1626B LEU* 3.0 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1623 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1621B GLY 4.6 0.2 - - - -
1622B SER* 1.3 71.1 - - - +
1624B GLY* 1.3 65.9 + - - +
1626B LEU* 2.9 23.1 + - - +
1627B TYR* 2.9 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1624 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1579B LEU 5.4 7.0 - - - -
1622B SER* 3.2 5.8 + - - -
1623B VAL* 1.3 81.4 - - - +
1625B ASN* 1.3 61.4 + - - +
1627B TYR* 3.2 12.2 + - - +
1628B SER* 3.1 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1625 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1613B GLN 4.4 1.8 + - - -
1614B THR* 4.4 9.9 + - - +
1617B VAL* 3.7 35.8 - - + +
1619B HIS 3.9 3.1 - - - +
1620B PRO* 3.6 5.4 - - - +
1621B GLY* 3.2 18.9 + - - +
1622B SER* 3.0 20.3 + - - +
1624B GLY* 1.3 74.1 - - - +
1626B LEU* 1.3 62.9 + - - +
1628B SER* 3.2 7.9 + - - -
1629B TRP* 3.2 31.8 + - - +
1665B MET* 3.2 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1626 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1621B GLY* 3.5 17.3 - - - +
1622B SER 3.0 15.0 + - - +
1623B VAL* 2.9 11.7 + - - +
1625B ASN* 1.3 74.8 - - - +
1627B TYR* 1.3 65.3 + - + +
1629B TRP* 3.4 4.9 + - + +
1630B GLN* 3.0 41.3 + - - +
1664B GLU* 3.5 41.5 - - + +
1665B MET* 4.2 17.7 - - + +
1668B TYR* 4.4 8.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1627 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1579B LEU* 4.4 27.8 - - + -
1583B SER* 4.0 22.2 + - - -
1585B PRO* 3.8 41.1 - - + +
1589B ILE* 5.3 1.3 - - + +
1623B VAL* 2.9 39.0 + - + +
1624B GLY* 3.2 11.9 + - - +
1626B LEU* 1.3 77.9 - - + +
1628B SER* 1.3 57.3 + - - +
1630B GLN* 2.9 27.1 + - - +
1631B ILE* 2.8 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1628 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1535B TYR* 6.2 0.2 - - - -
1576B LEU* 5.9 2.8 - - - +
1610B LEU* 3.7 14.9 - - - +
1613B GLN* 4.1 18.6 + - - +
1614B THR* 3.4 24.7 - - - -
1624B GLY 3.1 10.1 + - - -
1625B ASN* 3.2 12.2 + - - -
1627B TYR* 1.3 78.6 - - - +
1629B TRP* 1.3 62.8 + - - -
1631B ILE* 3.1 9.3 + - - +
1632B LEU* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1629 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1614B THR* 4.0 24.7 + - + -
1625B ASN* 3.2 24.5 + - - +
1626B LEU* 3.9 5.4 - - - +
1627B TYR 3.3 0.2 - - - -
1628B SER* 1.3 78.8 - - - +
1630B GLN* 1.3 54.1 + - - +
1632B LEU* 3.4 30.0 - - + +
1633B THR* 2.6 36.9 + - - -
1652B HIS* 4.1 10.5 - + - -
1653B LEU* 3.7 26.5 - - + -
1656B ILE* 3.6 39.1 - - + +
1665B MET* 3.5 43.2 - - + +
1668B TYR* 3.8 23.1 - - + +
1669B ALA* 4.0 22.0 - - + -
1672B THR* 4.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1630 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1585B PRO* 4.9 3.1 - - - +
1589B ILE* 4.7 7.3 - - + +
1626B LEU* 3.0 36.9 + - - +
1627B TYR* 2.9 33.7 + - - +
1629B TRP* 1.3 76.5 - - - +
1631B ILE* 1.3 62.7 + - - +
1633B THR* 3.3 5.5 + - - -
1634B CYS* 3.1 31.7 + - - -
1668B TYR* 3.2 32.6 + - + +
1695B ILE* 3.9 42.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1631 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1576B LEU* 3.3 30.5 - - + -
1588B ILE* 6.4 0.4 - - + -
1589B ILE* 4.0 29.8 - - + -
1592B ILE* 4.2 28.0 - - + -
1593B LEU* 4.6 1.6 - - + +
1610B LEU* 4.0 23.8 - - + -
1627B TYR* 2.8 27.8 + - + +
1628B SER* 3.1 9.4 + - - +
1630B GLN* 1.3 75.7 - - - +
1632B LEU* 1.3 58.0 + - - +
1634B CYS* 3.4 6.3 + - - +
1635B LEU* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1632 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1607B TYR* 3.6 36.1 - - + +
1610B LEU* 4.3 27.6 - - + +
1611B ILE* 5.0 2.5 - - + +
1614B THR* 4.6 9.6 - - + +
1628B SER 3.0 15.5 + - - +
1629B TRP* 3.4 41.1 - - + +
1631B ILE* 1.3 76.8 - - - +
1633B THR* 1.3 59.8 + - - +
1635B LEU* 3.3 5.3 + - + -
1636B SER* 3.0 27.0 + - - -
1649B LEU* 4.2 18.6 - - + -
1652B HIS* 5.4 0.2 - - + -
1653B LEU* 4.8 0.2 - - + -
1672B THR* 4.0 9.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1633 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1629B TRP 2.6 23.4 + - - -
1630B GLN* 3.3 6.3 + - - -
1632B LEU* 1.3 76.3 - - - +
1634B CYS* 1.3 62.7 - - - +
1636B SER* 2.9 17.0 + - - -
1637B CYS* 3.5 12.0 + - - +
1668B TYR* 3.3 22.8 + - + +
1671B PHE* 3.5 37.0 - - + -
1672B THR* 3.3 18.8 + - - +
1694B LEU* 4.2 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1634 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1589B ILE* 4.3 7.4 - - + -
1593B LEU* 4.0 21.3 - - + +
1630B GLN 3.1 22.2 + - - +
1631B ILE 3.8 3.6 - - - +
1633B THR* 1.3 75.3 - - - +
1635B LEU* 1.3 57.7 + - - +
1637B CYS* 3.3 7.6 + - - +
1638B THR* 2.7 27.4 + - - -
1686B PRO* 4.4 2.7 - - + +
1691B ILE* 3.9 28.0 - - + -
1694B LEU* 3.8 37.5 - - + -
1695B ILE* 5.0 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1635 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1592B ILE* 4.7 4.7 - - + -
1593B LEU* 3.3 26.0 - - + -
1606B LEU* 4.0 31.2 - - + -
1607B TYR* 3.4 44.9 - - + +
1610B LEU* 4.5 7.6 - - + -
1631B ILE* 2.9 18.5 + - + +
1632B LEU* 3.4 13.5 - - + +
1634B CYS* 1.3 74.8 - - - +
1636B SER* 1.3 56.2 + - - +
1637B CYS 2.9 9.7 + - - -
1638B THR* 3.0 13.0 + - - -
1639B PHE* 3.2 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1607B TYR* 3.4 11.6 + - - -
1632B LEU 3.0 7.5 + - - -
1633B THR 2.9 15.2 + - - -
1635B LEU* 1.3 73.9 - - - +
1637B CYS* 1.3 51.0 + - - +
1638B THR 3.6 0.7 - - - -
1639B PHE 4.5 1.1 - - - -
1672B THR* 3.4 39.5 - - - +
1675B SER* 3.3 15.8 - - - +
1676B LEU* 3.4 24.9 - - - +
1679B THR* 2.7 26.9 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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