Contacts of the strand formed by residues 1710 - 1719 (chain B) in PDB entry 3SE2
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 ALA1710 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1575B LEU* 5.2 3.6 - - - +
1579B TYR* 4.0 6.5 - - - +
1615B GLY* 4.7 7.3 - - - -
1616B PHE* 3.9 15.4 + - + -
1634B PHE* 3.8 24.0 - - + -
1660B VAL* 3.8 13.5 - - + -
1661B ARG 3.2 11.7 - - - +
1662B VAL* 3.9 7.2 - - + -
1704B ALA* 5.5 1.3 - - + -
1706B TYR 5.1 0.2 + - - -
1708B TYR* 3.3 6.0 + - - -
1709B GLN* 1.3 83.7 + - + +
1711B TYR* 1.3 61.8 + - - +
1712B PRO* 4.1 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1711 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1570B ILE* 2.7 27.0 + - + -
1571B GLN* 3.9 0.5 - - - -
1572B ASN* 2.9 25.6 + - + +
1575B LEU* 3.9 26.0 - - + -
1576B TRP* 3.5 53.8 - + + +
1579B TYR* 3.9 22.4 - - + -
1660B VAL* 3.0 14.0 - - - +
1661B ARG* 2.8 21.7 + - + +
1710B ALA* 1.3 75.1 - - - +
1712B PRO* 1.3 68.2 - - + +
1713B GLU* 2.9 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1712 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1570B ILE* 3.2 28.9 - - + +
1575B LEU* 3.9 14.1 - - + -
1611B VAL* 3.6 44.4 - - + +
1615B GLY* 4.4 4.0 - - - -
1616B PHE* 3.8 11.7 - - + -
1658B TYR* 3.7 19.9 - - + -
1660B VAL* 4.1 5.1 - - + -
1710B ALA 4.1 3.4 - - - +
1711B TYR* 1.3 91.2 - - + +
1713B GLU* 1.3 63.6 + - - +
1714B TYR 3.4 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1569B ARG* 3.5 17.0 - - + +
1570B ILE 2.9 23.6 + - - +
1576B TRP* 4.8 8.2 - - + -
1598B GLN* 4.0 3.1 - - - +
1659B TYR 3.8 8.7 + - - +
1661B ARG* 2.7 50.5 + - + +
1711B TYR* 2.9 32.5 + - + +
1712B PRO* 1.3 72.7 - - - +
1714B TYR* 1.3 96.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1714 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1541B LEU* 3.8 17.7 - - + -
1547B GLU* 2.4 36.9 + - - +
1551B VAL* 3.7 39.0 - - + +
1567B ILE* 4.2 4.5 - - + -
1568B GLU 3.2 13.7 - - - +
1569B ARG* 4.2 12.4 - - + -
1570B ILE* 4.8 0.7 - - - +
1598B GLN* 4.8 6.5 - - - -
1658B TYR* 3.2 13.2 - - - +
1659B TYR* 3.0 50.5 + + + +
1661B ARG* 5.4 1.8 + - - -
1712B PRO 3.4 0.4 + - - -
1713B GLU* 1.3 119.0 + - + +
1715B LEU* 1.3 59.4 + - - +
1716B ILE* 4.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1715 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1538B VAL* 6.2 0.7 - - + -
1566B LYS* 3.6 3.0 - - - +
1567B ILE* 3.4 4.0 - - - -
1568B GLU* 2.9 55.3 + - - +
1570B ILE* 4.5 11.6 - - + +
1608B VAL* 4.0 28.3 - - + -
1612B ASN* 5.4 0.2 - - - +
1656B HIS* 4.3 20.4 - - + -
1657B VAL 3.8 8.1 - - - +
1658B TYR* 3.7 40.8 - - + +
1714B TYR* 1.3 74.5 - - - +
1716B ILE* 1.3 63.9 + - - +
1717B THR* 3.9 12.7 + - - +
1609D PRO* 6.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1716 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551B VAL* 3.9 22.7 - - + -
1555B PHE* 4.0 42.4 - - + -
1564B ILE* 4.2 31.0 - - + -
1566B LYS 3.6 2.2 - - - -
1567B ILE* 4.2 15.0 - - + -
1600B PHE* 4.4 6.5 - - + -
1655B LYS 3.4 1.0 - - - +
1656B HIS* 3.4 4.9 - - - +
1657B VAL 2.7 44.3 + - - +
1659B TYR* 4.2 18.4 - - + +
1715B LEU* 1.3 77.6 - - - +
1717B THR* 1.3 62.8 - - - +
1718B PHE* 3.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1717 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1564B ILE* 3.7 1.9 - - - +
1565B GLU* 2.8 23.7 + - + -
1566B LYS* 2.9 38.0 + - - +
1568B GLU* 4.3 1.4 + - - -
1654B ARG* 3.8 43.5 - - + +
1655B LYS 3.2 8.1 - - - +
1656B HIS* 3.7 24.9 - - - +
1715B LEU* 4.3 9.2 - - - +
1716B ILE* 1.3 72.7 - - - +
1718B PHE* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1718 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1555B PHE* 3.9 22.9 - + + -
1562B PHE* 3.5 38.8 - + + -
1563B ARG 3.1 16.6 - - - +
1564B ILE* 3.8 9.0 - - + -
1565B GLU* 4.0 4.7 - - - +
1642B ALA* 4.2 6.3 - - + -
1647B SER* 4.2 0.7 - - - -
1654B ARG* 3.5 5.4 - - - +
1655B LYS* 2.7 82.7 + - + +
1657B VAL* 3.5 35.4 - - + -
1716B ILE* 3.7 11.2 - - + -
1717B THR* 1.3 76.3 - - - +
1719B ARG* 1.3 73.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1565A GLU* 5.4 1.8 + - - -
1652A ASN* 4.9 3.6 - - - -
1719A ARG* 3.5 53.8 - - - +
1562B PHE* 3.6 7.8 - - - -
1563B ARG* 2.9 40.6 + - + +
1565B GLU* 3.6 26.2 + - + +
1652B ASN* 2.7 33.4 + - - +
1653B GLY* 3.8 18.5 + - - +
1654B ARG* 3.9 17.3 - - - +
1655B LYS* 5.4 1.6 - - - -
1718B PHE* 1.3 82.9 - - - +
1720B LYS* 1.3 70.9 + - - +
----------------------------------------------------------
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