Contacts of the strand formed by residues 1712 - 1719 (chain B) in PDB entry 4ASI
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 ARG1712 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1701B MET 3.9 0.3 - - - +
1702B THR* 3.3 3.2 - - - +
1703B PHE* 2.9 69.4 + - + +
1705B SER* 4.0 2.2 - - - -
1707B GLU* 3.1 20.8 + - - +
1708B TYR* 3.5 27.2 - - + -
1711B GLY* 1.3 75.4 - - - +
1713B ASP* 1.3 67.8 + - - +
1714B ILE* 5.0 2.8 - - - +
1749B PRO* 4.4 3.4 - - - +
1936B LEU* 2.8 48.3 + - - +
1939B MET* 3.1 24.1 + - - +
1940B PRO 3.4 15.4 + - - -
1941B LYS* 3.5 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700B LYS* 3.9 21.4 + - - -
1701B MET 3.2 5.2 - - - +
1702B THR* 2.7 43.6 + - - +
1712B ARG* 1.3 75.5 + - - +
1714B ILE* 1.3 72.1 + - - +
1746B GLU* 4.7 2.3 - - - +
1748B ILE* 3.6 27.8 - - + +
1749B PRO* 3.4 15.1 - - - +
1941B LYS* 4.0 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1714 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1642B PHE* 4.0 25.6 - - + -
1700B LYS* 3.6 4.2 - - - +
1701B MET* 2.8 49.6 + - + -
1703B PHE* 3.6 28.7 - - + -
1712B ARG* 5.0 3.1 - - - +
1713B ASP* 1.3 80.4 - - - +
1715B ILE* 1.3 64.7 + - - +
1716B VAL* 4.0 14.1 - - + -
1748B ILE* 3.7 5.4 - - - -
1749B PRO* 3.8 30.3 - - + +
1751B ILE* 4.1 11.7 - - + -
1936B LEU* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1715 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674B LEU* 4.0 11.7 - - + -
1699B TRP 3.5 4.0 - - - +
1700B LYS* 3.7 28.9 - - + -
1714B ILE* 1.3 82.2 - - - +
1716B VAL* 1.3 68.1 + - - +
1717B ILE* 4.3 8.5 - - + -
1739B ALA* 3.9 31.2 - - + +
1742B LEU* 4.2 11.7 - - + -
1743B ALA* 3.8 26.7 - - + +
1748B ILE* 3.7 15.7 - - + -
1749B PRO 3.1 10.3 + - - +
1750B ARG* 3.5 3.3 - - + +
1751B ILE* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1716 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1635B ILE* 6.2 0.2 - - + -
1638B ILE* 4.7 12.8 - - + -
1642B PHE* 4.0 23.8 - - + -
1698B ALA* 3.1 4.7 - - - +
1699B TRP* 2.8 66.3 + - + +
1701B MET* 4.0 15.5 - - + -
1714B ILE* 4.0 15.0 - - + -
1715B ILE* 1.3 77.7 - - - +
1717B ILE* 1.3 70.0 + - - +
1751B ILE* 3.3 15.9 - - + +
1753B VAL* 4.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1717 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1696B MET* 3.6 28.0 - - + -
1697B VAL 3.4 7.6 - - - +
1698B ALA* 4.2 3.4 - - + +
1715B ILE* 4.3 5.4 - - + -
1716B VAL* 1.3 81.6 - - - +
1718B GLY* 1.3 61.9 + - - +
1736B PHE* 3.7 42.4 - - + +
1739B ALA* 3.8 30.7 - - + -
1740B SER 4.2 0.7 - - - +
1750B ARG* 4.1 24.5 - - + -
1751B ILE 2.8 9.9 + - - +
1752B TYR* 3.3 8.2 - - + -
1753B VAL* 2.7 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1718 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1635B ILE* 3.9 17.0 - - - +
1696B MET* 3.4 7.9 - - - +
1697B VAL* 2.7 43.8 + - - +
1699B TRP* 5.1 0.2 - - - -
1717B ILE* 1.3 77.6 - - - +
1719B ASN* 1.3 66.2 + - - -
1752B TYR* 4.5 0.7 - - - -
1753B VAL* 3.3 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1635B ILE* 3.8 14.8 - - - +
1695B GLY 3.5 8.9 + - - +
1696B MET* 3.3 27.6 - - - +
1718B GLY* 1.3 75.7 - - - -
1720B ASP* 1.3 61.1 + - - +
1721B ILE 3.7 2.8 + - - -
1726B GLY 4.2 6.4 + - - +
1727B SER 4.9 2.0 + - - -
1728B PHE* 3.7 14.1 - - - -
1752B TYR* 2.5 31.9 + - - -
1753B VAL* 3.3 7.3 + - - +
1755B ALA* 3.1 30.3 + - - +
1756B ASN* 3.4 19.9 + - + +
----------------------------------------------------------
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