Contacts of the strand formed by residues 1686 - 1691 (chain D) in PDB entry 5JH5
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 THR1686 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1650D THR* 3.2 26.5 - - + +
1651D MSE 3.8 13.7 - - - +
1652D PRO* 4.5 5.8 - - + -
1653D LYS* 3.7 8.2 + - - +
1685D GLU* 1.3 87.6 - - - +
1687D VAL* 1.3 68.3 + - - +
1688D GLU* 4.1 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1687 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1624D LEU* 3.7 20.6 - - + -
1649D THR 4.0 0.2 - - - +
1650D THR* 3.1 18.9 - - - +
1651D MSE 3.1 20.9 + - + +
1653D LYS* 4.1 29.6 - - + -
1656D PHE* 3.9 23.3 - - + -
1672D PRO* 6.2 2.7 - - + -
1686D THR* 1.3 80.0 - - - +
1688D GLU* 1.3 65.0 + - - +
1689D LEU* 3.6 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1688 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1624D LEU* 3.8 3.6 - - - +
1625D PHE* 3.0 41.9 + - + -
1626D SER* 5.7 5.9 + - - +
1648D ILE* 5.3 4.5 - - + -
1649D THR 3.6 5.2 - - - +
1650D THR* 4.5 12.6 - - + +
1686D THR* 4.1 16.3 + - - +
1687D VAL* 1.3 83.7 - - - +
1689D LEU* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1689 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1609D TYR* 5.9 1.1 - - + -
1611D LEU* 3.4 28.5 - - + -
1613D VAL* 4.4 0.2 - - + -
1622D TRP* 3.8 22.6 - - + -
1623D PHE 3.3 14.6 - - - +
1624D LEU* 4.1 9.0 - - + -
1625D PHE* 4.0 4.2 - - - +
1647D GLU 3.6 0.3 - - - +
1648D ILE* 3.2 7.1 - - - +
1649D THR* 2.9 47.7 + - + +
1651D MSE 4.0 24.2 - - + -
1656D PHE* 4.1 9.9 - - + -
1687D VAL* 3.6 22.9 - - + +
1688D GLU* 1.3 84.7 - - - +
1690D VAL* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1690 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622D TRP* 3.4 4.8 - - - -
1623D PHE* 2.8 35.6 + - + +
1625D PHE* 4.0 24.0 - - + -
1628D VAL* 3.6 31.9 - - + -
1639D PHE* 4.4 8.3 - - + -
1646D PHE* 4.3 19.5 - - + -
1647D GLU 3.1 12.1 - - - +
1648D ILE* 4.4 4.3 - - + -
1689D LEU* 1.3 74.4 - - - +
1691D ARG* 1.3 64.9 + - - +
1696D LEU* 3.5 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1691 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C TYR* 6.3 0.8 - - - -
1617D ARG* 4.1 14.2 - - - +
1620D CYS* 4.2 15.5 - - + -
1621D ASN 3.7 9.2 - - - +
1622D TRP* 3.5 19.7 - - + -
1645D HIS 5.1 4.0 + - - -
1646D PHE* 5.6 0.2 - - - -
1647D GLU* 2.7 47.2 + - + +
1690D VAL* 1.3 77.9 - - - +
1692D TYR* 1.3 75.4 + - - +
1693D GLU* 3.5 41.5 + - - +
1696D LEU* 3.5 18.4 - - - +
----------------------------------------------------------
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