Contacts of the strand formed by residues 1655 - 1663 (chain B) in PDB entry 3SMJ
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 LYS1655 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1562B PHE* 4.1 15.5 - - + -
1642B ALA 2.8 26.5 + - - -
1644B ASP* 2.6 32.0 + - - +
1647B SER* 2.7 35.8 + - - +
1648B ARG 4.6 0.7 - - - -
1649B PRO* 4.0 15.5 - - + -
1653B GLY 4.2 4.3 - - - +
1654B ARG* 1.3 74.7 - - - +
1656B HIS* 1.3 65.2 + - - +
1717B THR* 3.3 7.1 - - - +
1718B PHE* 2.8 70.0 + - + +
1719B ARG* 5.1 1.1 - - - -
1720B LYS* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1603B THR* 3.0 40.0 + - + +
1605B ALA* 3.6 34.4 + - + +
1608B VAL* 4.3 21.5 - - + +
1647B SER* 3.4 9.7 - - - -
1648B ARG 4.8 1.6 + - - -
1650B ASP* 3.6 16.3 + - - -
1654B ARG* 3.6 21.0 + - + +
1655B LYS* 1.3 75.5 - - - +
1657B VAL* 1.3 62.6 + - - +
1658B TYR 4.3 0.2 - - - -
1715B LEU* 4.1 16.6 - - + -
1716B ILE 3.5 3.8 - - - -
1717B THR* 3.7 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1555B PHE* 4.6 9.0 - - + -
1600B PHE* 3.6 29.4 - - + -
1601B HIS 3.5 5.8 - - - +
1602B GLY* 3.9 3.4 - - - -
1638B ALA* 5.2 1.6 - - + +
1641B SER* 3.8 28.9 - - - +
1642B ALA* 4.3 1.3 - - + +
1647B SER* 4.0 1.6 - - - -
1656B HIS* 1.3 77.5 - - - +
1658B TYR* 1.3 75.5 + - - +
1715B LEU* 4.1 3.5 - - - +
1716B ILE* 2.8 43.3 + - + +
1718B PHE* 3.5 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1570B ILE* 4.4 4.5 - - + -
1599B LEU 3.8 0.2 - - - +
1600B PHE* 3.2 7.1 - - - -
1601B HIS 2.8 39.7 + - - +
1603B THR* 3.8 26.9 - - + -
1608B VAL* 3.3 26.1 + - + +
1611B VAL* 3.5 23.2 - - + +
1612B ASN* 2.7 28.1 + - - -
1616B PHE* 4.2 13.9 - + + -
1657B VAL* 1.3 78.1 - - - +
1659B TYR* 1.3 58.6 + - - +
1660B VAL* 3.5 19.0 - - + +
1712B PRO* 3.8 17.5 - - + -
1714B TYR 3.2 18.2 - - - -
1715B LEU* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1550B THR* 5.2 7.1 - - + +
1551B VAL* 3.9 31.2 - - + -
1554B LYS* 3.4 33.3 + - + +
1598B GLN* 3.5 59.1 + - + +
1599B LEU 3.5 9.9 - - - -
1600B PHE* 3.4 36.8 - + + -
1657B VAL 3.9 1.0 + - - -
1658B TYR* 1.3 70.9 - - - +
1660B VAL* 1.3 61.4 + - - +
1713B GLU* 3.6 9.0 + - - +
1714B TYR* 2.8 52.5 + + + +
1716B ILE* 4.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1597B LYS 3.5 0.5 - - - +
1598B GLN* 3.3 6.5 - - - -
1599B LEU 2.7 37.5 + - - +
1601B HIS* 4.2 4.3 - - + -
1616B PHE* 3.9 16.6 - - + -
1634B PHE* 3.8 13.5 - - + -
1658B TYR* 3.5 33.0 - - + +
1659B TYR* 1.3 72.6 - - - +
1661B ARG* 1.3 72.4 + - - +
1662B VAL* 3.6 17.3 + - + +
1710B ALA* 3.7 13.0 - - + -
1711B TYR 3.3 23.8 - - - +
1712B PRO* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1661 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1576B TRP* 4.4 20.2 - - + -
1579B TYR* 3.3 22.9 - - + +
1580B GLN* 5.5 0.2 - - - +
1596B GLU* 2.7 41.8 + - - +
1597B LYS 3.6 4.9 - - - -
1598B GLN* 3.4 38.3 + - + +
1659B TYR 4.3 0.4 + - - -
1660B VAL* 1.3 71.8 - - - +
1662B VAL* 1.4 57.0 + - - +
1710B ALA* 3.2 4.5 - - - -
1711B TYR* 2.8 45.4 + - + +
1713B GLU* 2.8 33.8 + - + +
1714B TYR* 5.8 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1579B TYR* 3.6 4.0 + - - -
1596B GLU* 3.3 1.2 - - - -
1597B LYS 2.8 35.9 + - - +
1599B LEU* 3.8 20.0 - - + -
1634B PHE* 3.9 32.3 - - + -
1660B VAL* 3.6 25.6 - - + +
1661B ARG* 1.4 78.9 - - - +
1663B LEU* 1.3 64.8 + - - +
1664B THR* 3.1 22.8 + - + +
1691B THR* 5.0 1.8 - - + -
1702B PHE* 5.4 1.8 - - + -
1704B ALA* 4.7 12.8 - - + -
1709B GLN 3.4 9.2 - - - +
1710B ALA* 4.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1579B TYR* 3.6 42.0 - - + +
1582B LYS* 3.7 17.0 - - + -
1583B LYS* 3.7 53.8 - - + +
1586B MET* 3.6 18.6 - - + +
1595B ASN* 3.2 15.3 - - + +
1596B GLU* 4.3 5.6 - - + -
1662B VAL* 1.3 70.9 - - - +
1664B THR* 1.3 63.8 + - - +
1665B GLY 3.4 1.0 + - - -
1691B THR* 3.5 0.7 - - - +
1708B TYR 4.1 3.6 - - - +
1709B GLN* 2.8 44.8 + - + +
----------------------------------------------------------
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