Contacts of the strand formed by residues 1591 - 1599 (chain B) in PDB entry 2VK7
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 SER1591 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467B ARG* 5.2 0.5 - - - -
1541B GLN* 4.4 6.6 + - - -
1589B GLN* 4.8 0.7 - - - -
1590B LEU* 1.3 77.4 - - - +
1592B VAL* 1.3 64.7 + - - +
1593B ILE* 4.6 1.4 - - - +
1607B PHE* 3.3 5.5 - - - -
1608B SER* 2.8 34.0 + - - +
1656B SER* 3.5 26.8 + - - -
1657B CYS* 3.5 11.5 - - - -
1658B LEU* 3.0 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467B ARG* 5.2 1.7 - - - +
1541B GLN* 3.9 33.5 - - + +
1542B VAL 4.4 3.5 - - - +
1543B VAL* 3.9 23.2 - - + +
1553B PHE* 3.8 44.0 - - + -
1590B LEU* 4.5 0.2 - - + -
1591B SER* 1.3 77.1 + - - +
1593B ILE* 1.3 72.2 + - - +
1605B VAL* 4.1 16.8 - - + -
1606B ILE 3.2 13.2 - - - +
1607B PHE* 4.0 11.9 - - + -
1658B LEU* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467B ARG* 3.7 38.8 - - + +
1543B VAL* 3.6 9.2 - - - -
1591B SER* 4.6 1.6 - - - +
1592B VAL* 1.3 80.4 - - - +
1594B ASN* 1.3 71.0 + - - +
1595B TYR* 5.7 0.2 - - - -
1605B VAL* 3.2 5.9 - - - +
1606B ILE* 2.9 57.1 + - + +
1658B LEU* 3.8 21.8 - - + +
1659B THR* 3.7 9.2 - - - -
1660B GLU* 3.5 31.4 - - + +
1666B ILE* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1594 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1469B ILE* 5.0 6.8 - - - +
1543B VAL* 3.5 8.9 - - - +
1544B GLU* 2.8 51.4 + - - +
1545B MET* 5.0 0.4 - - - +
1593B ILE* 1.3 88.4 - - - +
1595B TYR* 1.3 62.7 + - - +
1604B ALA 4.1 5.0 + - - -
1605B VAL* 4.0 14.9 - - - +
1625B ILE* 5.0 3.2 - - - +
1660B GLU* 4.1 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1593B ILE 3.7 0.6 + - - -
1594B ASN* 1.3 77.8 + - - +
1596B SER* 1.3 61.6 + - - +
1597B GLN* 3.2 49.7 + - + +
1598B LYS 5.1 0.2 - - - -
1599B VAL* 4.1 11.0 - - + -
1603B ASP* 5.9 0.2 - - - -
1604B ALA* 3.1 27.9 + - + +
1606B ILE* 4.0 21.1 - - + -
1660B GLU* 3.3 25.8 - - + -
1664B GLY* 2.6 33.2 + - - -
1666B ILE* 3.8 24.9 - - + -
1685B LEU* 3.5 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595B TYR* 1.3 73.5 - - - +
1597B GLN* 1.3 80.7 + - - +
1660B GLU* 2.6 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595B TYR* 3.2 42.0 - - + +
1596B SER* 1.3 105.9 + - - +
1598B LYS* 1.3 71.9 + - - +
1599B VAL* 3.6 1.9 + - - +
1602B LYS 4.4 1.2 - - - +
1603B ASP* 5.7 1.1 - - - -
1604B ALA* 4.5 5.1 + - - +
1660B GLU* 4.7 1.3 - - - +
1664B GLY* 6.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595B TYR* 5.1 0.2 - - - -
1597B GLN* 1.3 83.0 - - - +
1599B VAL* 1.3 63.2 + - - +
1601B GLY* 4.0 19.5 + - - +
1602B LYS 3.2 24.0 - - - +
1603B ASP* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595B TYR* 4.1 2.9 - - + -
1597B GLN 3.9 8.3 - - - +
1598B LYS* 1.3 77.9 - - - +
1600B ASP* 1.3 76.4 + - - +
1601B GLY 3.0 0.7 - - - -
1602B LYS* 2.8 23.5 + - - +
1604B ALA* 3.9 13.9 - - + -
1622B ILE* 4.4 8.3 - - + -
1624B LEU* 3.7 23.8 - - + +
1644B TYR* 4.2 15.5 - - + -
1685B LEU* 3.6 26.7 - - + -
1689B GLU* 3.8 21.1 - - - +
----------------------------------------------------------
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