Contacts of the strand formed by residues 1718 - 1725 (chain B) in PDB entry 3I08
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 LYS1718 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1579A VAL* 3.2 9.5 - - - +
1580A LEU* 3.0 64.4 + - + +
1717B TYR* 1.3 73.3 - - - +
1719B ILE* 1.3 71.7 + - - +
1720B GLU* 3.6 4.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1482A LEU* 3.3 41.4 - - + +
1577A VAL* 3.7 31.6 - - + -
1578A VAL 3.7 3.1 - - - -
1579A VAL* 4.4 5.2 - - + +
1593A PHE* 4.7 4.7 - - + -
1597A LEU* 4.7 11.9 - - + -
1704B LEU* 5.6 4.0 - - + -
1713B LEU* 4.5 14.1 - - + +
1715B ILE* 3.1 36.8 - - + -
1717B TYR* 3.5 12.8 + - + +
1718B LYS* 1.3 86.3 + - - +
1720B GLU* 1.3 61.4 + - - +
1721B ALA 4.1 10.3 - - - +
1722B VAL* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1720 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1462A LYS 5.8 0.2 - - - +
1482A LEU* 4.0 15.0 - - - +
1483A ASN* 3.7 15.2 - - - +
1578A VAL* 2.7 23.1 + - + +
1580A LEU* 3.0 39.5 - - + -
1620A TYR* 4.0 17.3 + - + -
1718B LYS* 4.4 6.7 - - + +
1719B ILE* 1.3 73.9 - - - +
1721B ALA* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1721 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1462A LYS* 6.0 0.7 - - - +
1482A LEU 3.2 10.3 - - - +
1483A ASN* 4.0 15.3 - - + +
1576A VAL 4.0 0.4 - - - +
1577A VAL* 3.6 1.0 - - - -
1578A VAL* 2.9 47.3 + - + +
1620A TYR* 5.9 1.3 - - + +
1719B ILE* 4.1 4.5 - - - +
1720B GLU* 1.3 84.6 - - - +
1722B VAL* 1.3 62.5 + - - +
1723B GLN* 5.9 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1722 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1482A LEU* 2.8 44.9 + - + +
1484A PHE* 3.7 24.6 + - + +
1575A LEU* 3.8 27.1 - - + -
1576A VAL 3.3 15.0 - - - +
1577A VAL* 3.9 6.5 - - + -
1701B ALA* 4.1 20.6 - - + +
1704B LEU* 3.9 14.6 - - + -
1705B GLY 4.4 1.1 - - - +
1719B ILE* 4.6 2.2 - - + -
1721B ALA* 1.3 76.3 - - - +
1723B GLN* 1.3 69.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1723 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483A ASN* 4.5 18.0 + - + +
1484A PHE* 4.8 5.8 - - + -
1575A LEU* 3.7 7.1 - - - +
1576A VAL* 2.9 43.5 + - + +
1701B ALA* 4.3 5.6 - - - -
1721B ALA* 5.9 3.2 - - + +
1722B VAL* 1.3 80.8 - - - +
1724B SER* 1.3 65.6 + - - +
1725B GLU* 4.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1724 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484A PHE* 5.0 4.7 - - - -
1573A GLY* 5.6 0.2 - - - -
1574A THR 3.6 4.5 - - - -
1575A LEU* 5.0 0.2 - - - -
1576A VAL* 5.2 0.4 - - - -
1697B ALA* 3.9 9.0 - - - +
1698B THR* 2.8 49.5 + - - -
1701B ALA* 4.3 5.4 - - - -
1723B GLN* 1.3 80.6 - - - +
1725B GLU* 1.3 72.5 + - - +
1726B THR* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1573A GLY* 3.2 7.6 - - - -
1574A THR* 2.8 41.7 + - - +
1576A VAL* 4.1 18.6 - - + +
1678B TYR* 3.7 25.2 + - - -
1723B GLN* 4.8 10.5 - - + +
1724B SER* 1.3 82.5 + - - +
1726B THR* 1.3 62.0 + - - +
1727B VAL* 4.2 27.7 - - + +
1728B GLU* 5.4 4.4 - - - +
----------------------------------------------------------
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