Contacts of the strand formed by residues 1641 - 1648 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1600A LEU* 3.5 3.5 - - - -
1601A LEU* 2.9 62.8 + - + +
1602A PRO* 6.0 0.7 - - - -
1640A ARG* 1.3 74.2 - - - +
1642A LEU* 1.3 61.3 + - - +
1643A GLN* 3.5 4.6 + - - +
1662A THR* 3.7 30.1 - - + +
1663A LEU 3.5 7.0 - - - +
1664A PRO* 4.1 12.6 - - + +
1665A LEU* 3.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1565A LEU* 4.8 4.9 - - + -
1567A ILE* 4.4 13.2 - - + -
1574A LEU* 5.5 0.2 - - + -
1576A ILE* 3.9 38.6 - - + -
1598A THR* 3.9 26.2 - - + -
1599A TYR 3.5 14.1 - - - +
1600A LEU* 3.8 14.6 - - + -
1629A TYR* 4.0 12.1 - - + -
1641A GLU* 1.3 69.4 - - - +
1643A GLN* 1.3 60.5 + - - +
1644A LEU* 3.5 6.8 + - + +
1661A VAL 3.6 1.0 - - - +
1662A THR* 3.4 3.3 - - - -
1663A LEU* 2.9 55.2 + - + +
1665A LEU* 3.4 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1597A LYS* 3.7 1.4 - - - +
1598A THR* 3.2 6.5 - - - -
1599A TYR* 2.9 53.8 + - + +
1601A LEU* 3.4 34.3 - - + +
1641A GLU* 3.5 5.3 + - + +
1642A LEU* 1.3 71.0 - - - +
1644A LEU* 1.3 60.4 + - - +
1645A SER* 4.1 16.2 + - - +
1661A VAL 4.0 1.8 - - - -
1662A THR* 3.9 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563A VAL* 4.5 8.7 - - + -
1565A LEU* 3.8 41.1 - - + -
1576A ILE* 5.5 0.4 - - + -
1578A VAL* 5.0 0.9 - - + -
1596A VAL* 3.6 26.9 - - + -
1597A LYS 3.6 2.5 - - - -
1598A THR* 4.1 13.5 - - + -
1642A LEU* 3.5 8.5 + - + +
1643A GLN* 1.3 75.7 - - - +
1645A SER* 1.3 64.2 + - - +
1646A VAL* 3.9 25.8 - - + -
1660A GLY* 3.1 4.7 - - - -
1661A VAL* 2.9 44.9 + - + +
1663A LEU* 6.0 0.4 - - + -
1680A LEU* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595A TYR 3.8 0.3 - - - +
1596A VAL* 3.3 5.2 - - - +
1597A LYS* 2.8 47.7 + - - +
1599A TYR* 6.1 0.2 - - - -
1643A GLN* 4.1 17.7 + - - +
1644A LEU* 1.3 77.3 + - - +
1646A VAL* 1.3 62.8 + - - +
1647A LEU* 3.8 17.7 + - - -
1657A PHE* 3.8 21.4 - - - -
1659A GLY 3.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1581A ILE* 3.7 33.0 - - + -
1584A LEU* 4.2 7.6 - - + -
1594A PRO* 4.0 11.0 - - + -
1595A TYR 3.4 11.2 - - - +
1596A VAL* 4.3 2.0 - - + -
1644A LEU* 3.9 16.6 - - + -
1645A SER* 1.3 76.4 - - - +
1647A LEU* 1.3 58.8 + - - +
1657A PHE* 3.7 2.4 - - - -
1658A LEU* 2.8 52.3 + - + -
1659A GLY 2.7 22.2 + - - +
1680A LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1594A PRO* 3.1 4.5 - - - +
1595A TYR* 2.9 67.1 + - + +
1597A LYS* 3.8 33.7 - - + +
1645A SER* 3.8 21.3 - - - +
1646A VAL* 1.3 76.0 - - - +
1648A SER* 1.3 61.0 + - - +
1655A ASN* 4.6 9.6 - - + +
1656A PHE* 3.1 23.3 - - - +
1657A PHE* 4.2 12.6 - - + +
1658A LEU* 3.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1592A PRO* 3.5 14.8 - - - +
1593A ASN 2.9 24.1 + - - -
1595A TYR* 4.0 2.0 - - - -
1647A LEU* 1.3 71.9 - - - +
1649A ALA* 1.3 59.9 + - - +
1650A GLU* 2.7 24.1 + - - +
1655A ASN* 3.2 26.9 - - - +
1656A PHE* 2.8 40.0 + - - -
1658A LEU* 3.8 3.2 - - - +
----------------------------------------------------------
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