Contacts of the strand formed by residues 1594 - 1601 (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 PRO1594 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1584A LEU* 3.8 20.4 - - + -
1592A PRO* 3.3 11.4 - - + +
1593A ASN* 1.3 88.6 - - - +
1595A TYR* 1.3 61.0 + - - +
1615A SER 2.9 39.4 + - - +
1618A THR* 3.4 19.1 - - + +
1621A PRO* 3.6 30.1 - - + -
1623A PHE* 3.6 6.2 - - + -
1646A VAL* 4.0 11.2 - - + -
1647A LEU 3.1 8.7 - - - +
1658A LEU* 4.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1593A ASN 4.0 0.4 - - - -
1594A PRO* 1.3 74.9 - - - +
1596A VAL* 1.3 73.8 + - - +
1597A LYS* 4.4 8.7 + - + -
1611A LYS* 4.1 33.4 + - + -
1612A THR* 3.6 13.0 - - - +
1613A LYS 3.5 15.9 - - - +
1614A ILE* 4.1 10.3 - - + -
1623A PHE* 4.1 2.2 - - - -
1645A SER 3.8 0.2 - - - +
1646A VAL* 3.4 5.0 - - - +
1647A LEU* 2.9 73.0 + - + +
1649A ALA* 3.7 28.9 - - + -
1655A ASN* 3.0 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1563A VAL* 5.3 0.7 - - + -
1578A VAL* 3.9 22.4 - - + -
1581A ILE* 3.8 29.4 - - + -
1595A TYR* 1.3 78.7 - - - +
1597A LYS* 1.3 61.2 + - - +
1598A THR* 4.2 8.1 - - + -
1610A ARG 4.0 0.2 - - - +
1611A LYS* 3.2 5.2 - - - +
1612A THR* 2.9 42.3 + - + +
1623A PHE* 3.9 13.2 - - + -
1627A LEU* 4.8 1.4 - - + +
1644A LEU* 3.6 34.5 - - + -
1645A SER 3.3 3.1 - - - +
1646A VAL* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595A TYR* 4.1 6.7 + - + -
1596A VAL* 1.3 74.1 - - - +
1598A THR* 1.3 64.6 + - - +
1599A TYR* 3.9 31.4 + - + -
1609A LYS* 4.0 20.2 - - + +
1610A ARG 3.2 10.1 - - - +
1611A LYS* 4.2 17.8 - - + +
1643A GLN 3.7 0.9 - - - +
1644A LEU* 3.6 1.7 - - - -
1645A SER* 2.8 45.1 + - - +
1647A LEU* 3.8 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1576A ILE* 5.3 3.1 - - + -
1596A VAL* 4.2 3.6 - - + -
1597A LYS* 1.3 79.4 - - - +
1599A TYR* 1.3 65.2 + - - +
1608A SER 3.2 2.8 - - - +
1609A LYS* 3.4 4.0 - - - -
1610A ARG* 2.8 44.4 + - - +
1627A LEU* 3.6 22.6 - - + +
1629A TYR* 2.8 24.0 + - - -
1642A LEU* 3.9 17.5 - - + -
1643A GLN 3.2 6.1 - - - -
1644A LEU* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1597A LYS* 3.9 31.0 + - + +
1598A THR* 1.3 75.2 - - - +
1600A LEU* 1.3 59.8 + - - +
1601A LEU* 3.8 28.0 - - + -
1603A ASP* 4.2 7.4 - - - -
1608A SER* 3.4 17.3 - - - +
1609A LYS* 3.2 43.3 - - + +
1629A TYR* 3.7 5.8 - - - -
1642A LEU* 3.5 8.3 - - - +
1643A GLN* 2.9 49.5 + - - +
1645A SER* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1574A LEU* 4.2 7.6 - - + -
1599A TYR* 1.3 72.3 - - - +
1601A LEU* 1.3 58.6 - - - +
1602A PRO 3.4 5.1 - - - +
1603A ASP* 3.4 20.4 - - - +
1608A SER* 2.9 19.1 + - - -
1629A TYR* 3.6 30.5 - - + -
1632A TYR* 3.7 26.2 + - + +
1637A LEU* 3.8 18.6 - - + -
1640A ARG* 4.1 16.5 + - + -
1641A GLU 3.5 8.7 - - - +
1642A LEU* 3.8 25.1 - - + -
1665A LEU* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1599A TYR* 3.8 25.8 - - + -
1600A LEU* 1.3 78.2 - - - +
1602A PRO* 1.3 69.0 - - + +
1603A ASP* 3.8 19.3 - - + +
1640A ARG* 3.2 6.4 - - - -
1641A GLU* 2.9 55.7 + - + +
1643A GLN* 3.4 43.7 - - + +
----------------------------------------------------------
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