Contacts of the strand formed by residues 1641 - 1648 (chain B) in PDB entry 6BTY
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 GLU1641 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1600B LEU* 3.5 3.3 - - - -
1601B LEU* 2.8 57.9 + - + +
1602B PRO* 5.6 0.9 - - - +
1640B ARG* 1.3 75.9 - - - +
1642B LEU* 1.3 62.0 + - - +
1643B GLN 3.5 1.2 + - - -
1662B THR* 3.6 28.3 - - + +
1663B LEU 3.4 10.5 - - - +
1664B PRO* 4.0 15.7 - - + +
1665B LEU* 3.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1642 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1565B LEU* 4.7 5.2 - - + -
1567B ILE* 4.4 13.2 - - + -
1576B ILE* 3.7 38.6 - - + -
1598B THR* 3.9 26.7 - - + -
1599B TYR 3.5 14.4 - - - +
1600B LEU* 3.9 14.1 - - + -
1629B TYR* 4.0 13.2 - - + -
1641B GLU* 1.3 72.7 - - - +
1643B GLN* 1.3 59.5 + - - +
1644B LEU* 4.9 3.8 - - + +
1661B VAL 3.7 2.1 - - - +
1662B THR* 3.4 2.3 - - - -
1663B LEU* 2.8 55.6 + - + +
1665B LEU* 3.3 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1643 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1597B LYS 3.7 0.7 - - - +
1598B THR* 3.2 5.7 - - - -
1599B TYR* 2.8 56.9 + - + +
1601B LEU* 3.4 33.8 - - + +
1641B GLU* 3.5 1.7 + - + +
1642B LEU* 1.3 70.4 - - - +
1644B LEU* 1.3 61.8 + - - +
1645B SER* 4.1 15.1 + - - +
1661B VAL 3.9 2.5 - - - -
1662B THR* 4.1 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1644 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563B VAL* 4.4 9.0 - - + -
1565B LEU* 3.8 39.3 - - + -
1576B ILE* 5.6 0.4 - - + -
1578B VAL* 4.9 0.9 - - + -
1596B VAL* 3.6 24.5 - - + -
1597B LYS 3.5 2.9 - - - -
1598B THR* 4.0 14.4 - - + -
1642B LEU* 3.8 6.9 + - + -
1643B GLN* 1.3 76.6 - - - +
1645B SER* 1.3 66.0 + - - +
1646B VAL* 3.9 26.2 - - + -
1660B GLY* 3.1 4.2 - - - -
1661B VAL* 2.9 54.8 + - + +
1663B LEU* 6.2 0.9 - - + -
1680B LEU* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1645 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595B TYR 3.9 0.2 - - - +
1596B VAL* 3.4 4.0 - - - +
1597B LYS* 2.8 46.0 + - - +
1643B GLN* 4.5 15.6 + - - +
1644B LEU* 1.3 76.6 + - - +
1646B VAL* 1.3 62.6 - - - +
1647B LEU* 3.7 20.7 + - - -
1657B PHE* 3.8 19.4 - - - -
1659B GLY 3.8 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1646 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563B VAL* 5.4 0.2 - - + -
1581B ILE* 3.8 32.8 - - + -
1584B LEU* 4.0 8.5 - - + -
1594B PRO* 4.1 7.6 - - + -
1595B TYR 3.4 10.3 - - - +
1596B VAL* 4.1 3.4 - - + -
1644B LEU* 3.9 17.9 - - + -
1645B SER* 1.3 76.3 - - - +
1647B LEU* 1.3 58.3 + - - +
1657B PHE* 3.7 2.6 - - - -
1658B LEU* 2.7 54.8 + - + -
1659B GLY 2.7 21.3 + - - +
1680B LEU* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1647 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1594B PRO* 3.2 4.5 - - - +
1595B TYR* 2.9 65.7 + - + +
1597B LYS* 3.8 27.1 - - + +
1645B SER* 3.7 31.0 - - - +
1646B VAL* 1.3 75.6 - - - +
1648B SER* 1.3 62.5 + - - +
1655B ASN* 4.1 22.2 - - + +
1656B PHE 3.2 11.9 - - - +
1657B PHE* 4.3 11.4 - - + +
1658B LEU* 3.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1648 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1592B PRO* 3.4 16.0 - - - +
1593B ASN 2.9 23.0 + - - -
1595B TYR* 4.0 1.6 - - - -
1647B LEU* 1.3 73.2 - - - +
1649B ALA* 1.3 60.5 + - - +
1650B GLU* 2.6 25.8 + - - +
1655B ASN* 3.2 25.5 - - - -
1656B PHE* 2.8 39.6 + - - -
1658B LEU* 3.8 2.6 - - - +
----------------------------------------------------------
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