Contacts of the strand formed by residues 1748 - 1754 (chain X) in PDB entry 3HM6
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 PRO1748 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1746X TYR* 4.1 16.8 - - + +
1747X ARG* 1.3 100.9 - - + +
1749X LEU* 1.3 61.0 - - - +
1771X VAL 4.7 0.7 - - - +
1772X LEU* 3.7 19.1 - - + -
1843X ASP* 4.8 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1749 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1747X ARG* 3.6 26.2 + - - +
1748X PRO* 1.3 81.9 - - - +
1750X THR* 1.3 66.5 + - - +
1751X LEU* 4.9 7.4 - - + -
1770X LYS* 3.7 1.4 - - - +
1771X VAL* 2.7 48.6 + - + +
1772X LEU 4.0 2.0 - - - -
1773X ASP* 3.3 34.5 - - + +
1836X LEU* 4.3 15.7 - - + -
1841X VAL 4.0 17.3 - - - +
1842X PRO* 5.2 0.2 - - + -
1843X ASP* 3.6 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1750 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1749X LEU* 1.3 77.5 + - - +
1751X LEU* 1.3 64.5 + - - +
1768X PRO* 4.4 10.3 - - + -
1769X VAL 3.2 19.5 - - - +
1770X LYS* 4.2 9.9 - - + +
1843X ASP* 2.7 13.4 + - - +
1844X GLY* 2.7 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1751 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1749X LEU* 4.9 7.6 - - + -
1750X THR* 1.3 78.4 - - - +
1752X ASN* 1.3 63.5 + - - +
1753X ALA* 3.7 1.8 - - + +
1768X PRO* 3.2 6.9 - - - +
1769X VAL* 2.8 37.8 + - + +
1771X VAL* 3.5 36.8 - - + -
1780X ALA* 5.3 1.6 - - + -
1784X MET* 4.5 14.6 - - + -
1836X LEU* 4.5 15.5 - - + -
1841X VAL* 4.3 23.3 - - + -
1842X PRO 4.3 10.3 - - - +
1844X GLY* 4.8 1.1 - - - +
1845X ALA* 3.6 12.6 - - + +
1847X VAL* 4.3 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1752 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1751X LEU* 1.3 69.6 - - - +
1753X ALA* 1.3 60.0 + - - +
1754X LEU* 3.9 1.3 + - - +
1766X GLY* 3.3 33.5 - - - +
1767X VAL 3.9 1.7 - - - -
1768X PRO* 4.5 2.5 - - - -
1844X GLY* 4.3 11.2 - - - +
1845X ALA 2.8 13.6 + - - +
1846X THR* 3.1 31.2 + - - +
1847X VAL 3.2 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1753 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1751X LEU* 3.7 2.8 + - + +
1752X ASN* 1.3 71.8 + - - +
1754X LEU* 1.3 60.9 + - - +
1765X GLN 4.3 0.3 - - - +
1766X GLY* 3.3 2.3 - - - -
1767X VAL* 2.5 56.0 + - + +
1769X VAL* 3.4 27.1 - - + -
1784X MET* 3.9 22.0 - - + +
1788X LEU* 5.9 5.2 - - + +
1847X VAL 3.5 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1754 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1752X ASN* 3.9 1.1 + - - +
1753X ALA* 1.3 74.9 - - - +
1755X LEU* 1.3 68.4 + - - +
1756X ALA* 3.8 5.6 - - + +
1764X ALA* 3.3 33.4 - - + +
1765X GLN* 3.2 31.9 - - - +
1766X GLY* 4.1 2.9 - - - +
1784X MET* 4.4 1.7 - - - +
1788X LEU* 5.7 2.7 - - - +
1808X ARG* 3.4 28.9 - - - +
1846X THR* 5.0 11.4 - - + -
1847X VAL 3.2 7.7 + - - +
1848X ALA* 3.5 12.0 - - + +
1849X LEU* 3.1 25.4 + - - +
----------------------------------------------------------
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