Contacts of the helix formed by residues 2130 - 2147 (chain D) in PDB entry 3O2X
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 THR2130 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SO4 3.3 22.2 - - - +
2131B HIS* 4.3 2.5 - - + +
2129D MET* 1.3 75.5 - - - +
2131D HIS* 1.3 65.3 + - - +
2132D SER* 3.7 8.9 + - - -
2133D GLU* 3.0 44.2 + - - +
2134D VAL* 2.9 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SO4 2.7 33.7 + - - +
2125B TYR* 4.8 0.4 - - - +
2126B THR 3.7 13.3 + - - -
2127B PRO* 3.5 25.3 + - + +
2129B MET 3.3 24.7 + - - -
2130B THR* 4.6 0.6 - - - +
2131B HIS* 3.6 26.2 + - - -
2125D TYR* 3.7 28.3 - + + +
2130D THR* 1.3 70.4 - - - +
2132D SER* 1.3 58.3 + - - +
2134D VAL* 3.3 2.1 + - - +
2135D GLU* 2.8 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SO4 5.4 0.4 + - - -
2130D THR* 3.7 8.9 + - - -
2131D HIS* 1.3 79.5 - - - +
2133D GLU* 1.3 52.3 + - - +
2135D GLU* 3.2 11.8 + - - +
2136D LYS* 2.7 72.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2128D ASP 4.9 0.2 - - - +
2129D MET* 3.5 27.8 - - + +
2130D THR* 3.0 46.9 + - - +
2132D SER* 1.3 75.5 - - - +
2134D VAL* 1.3 57.6 + - - +
2136D LYS* 3.5 6.9 + - - +
2137D ALA* 3.0 29.6 + - - +
2209D SER* 4.2 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2122D ILE* 4.5 0.4 - - + -
2125D TYR* 3.7 28.7 - - + -
2126D THR* 4.0 18.8 - - + +
2129D MET* 3.7 27.1 - - + +
2130D THR 2.9 18.1 + - - +
2131D HIS 3.6 6.5 - - - +
2133D GLU* 1.3 73.9 - - - +
2135D GLU* 1.3 64.0 + - - +
2137D ALA* 3.3 3.5 + - - +
2138D PHE* 3.1 51.0 + - + -
2167D PHE* 4.4 7.2 - - + -
2216D LEU* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D SO4 4.1 17.4 + - - +
2120D TYR* 4.9 2.1 + - - -
2122D ILE* 3.7 17.9 - - + +
2125D TYR* 2.6 33.0 + - + +
2131D HIS* 2.8 30.4 + - - +
2132D SER* 3.5 12.9 + - - +
2134D VAL* 1.3 75.9 - - - +
2136D LYS* 1.3 61.4 + - + +
2138D PHE* 3.5 1.7 + - - +
2139D LYS* 3.0 31.0 + - - +
2155D ARG* 3.7 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D SO4 5.3 3.4 - - - +
2132D SER* 2.7 53.6 + - - +
2133D GLU* 3.8 7.2 - - - +
2135D GLU* 1.3 76.9 + - + +
2137D ALA* 1.3 62.8 + - - +
2139D LYS* 3.8 8.3 - - + +
2140D LYS* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2129D MET* 4.3 4.5 - - + -
2133D GLU 3.0 18.3 + - - +
2134D VAL 3.3 5.8 + - - +
2136D LYS* 1.3 76.6 - - - +
2138D PHE* 1.3 57.6 + - - +
2140D LYS* 4.7 1.3 - - - -
2141D ALA* 3.0 27.9 + - - +
2209D SER* 5.9 0.2 - - - +
2216D LEU* 4.1 17.7 - - + -
2217D PHE* 3.7 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2120D TYR* 4.5 13.5 - - + -
2122D ILE* 3.7 27.6 - - + -
2134D VAL* 3.1 34.0 + - + +
2135D GLU 4.1 2.9 - - - +
2137D ALA* 1.3 77.3 - - - +
2139D LYS* 1.3 60.6 + - - +
2141D ALA* 3.2 4.4 + - - +
2142D PHE* 2.9 36.3 + - - -
2165D ILE* 3.6 28.0 - - + -
2167D PHE* 3.9 20.2 - + - -
2201D PHE* 3.8 26.7 - + - -
2216D LEU* 4.0 13.7 - - + -
2220D ALA* 3.6 17.9 - - + -
2224D PHE* 3.6 14.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D SO4 3.6 30.5 - - - +
2120D TYR* 4.0 17.8 + - - +
2135D GLU 3.0 18.4 + - - +
2136D LYS* 3.8 9.0 - - + +
2138D PHE* 1.3 77.6 - - - +
2140D LYS* 1.3 57.4 + - - +
2142D PHE* 3.4 5.7 + - - +
2143D LYS* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2136D LYS 3.0 18.6 + - - +
2137D ALA* 3.7 4.9 - - - +
2139D LYS* 1.3 75.6 - - - +
2141D ALA* 1.3 62.6 + - - +
2143D LYS* 3.3 12.3 + - + +
2144D VAL* 3.2 22.9 + - + +
2217D PHE* 3.5 39.7 - - + -
2251D HIS* 6.2 1.4 - - - +
2252D PHE* 5.2 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2137D ALA 3.0 15.4 + - - +
2138D PHE 3.2 8.5 + - - +
2140D LYS* 1.3 77.0 - - - +
2142D PHE* 1.3 61.6 + - - +
2144D VAL* 3.3 18.2 - - - +
2145D TRP* 3.4 12.1 + - - -
2217D PHE* 3.6 13.6 - - - +
2220D ALA* 3.8 5.6 - - + -
2221D ALA* 3.6 22.5 - - - +
2224D PHE* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2120D TYR* 3.4 58.8 - + + -
2138D PHE* 2.9 25.4 + - + +
2139D LYS* 3.4 4.9 + - - +
2141D ALA* 1.3 73.3 - - - +
2143D LYS* 1.3 60.5 + - - +
2145D TRP* 2.9 23.2 + + - +
2146D SER* 3.0 14.6 + - - -
2153D PHE* 3.5 52.1 - + + -
2163D ILE* 3.8 15.9 - - + -
2165D ILE* 4.2 0.2 - - + -
2224D PHE* 3.4 49.4 - + + -
2228D LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2139D LYS* 3.0 24.0 + - + +
2140D LYS* 3.3 13.0 + - + +
2142D PHE* 1.3 76.0 - - - +
2144D VAL* 1.3 61.3 + - - +
2146D SER* 3.3 11.2 - - - +
2147D ASP* 2.8 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2140D LYS* 3.2 15.4 + - + +
2141D ALA* 3.3 13.0 - - - +
2142D PHE 3.1 0.6 - - - -
2143D LYS* 1.3 78.3 - - - +
2145D TRP* 1.3 71.6 + - + +
2147D ASP* 4.0 5.8 + - - +
2148D VAL* 3.5 18.0 - - - +
2217D PHE* 3.9 17.0 - - + -
2221D ALA* 4.4 4.3 - - + -
2239D LEU* 4.5 4.3 - - + -
2252D PHE* 3.8 26.2 - - + -
2254D LEU* 3.7 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP2145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2141D ALA 3.4 21.8 + - - -
2142D PHE* 2.9 8.2 + + - +
2144D VAL* 1.3 80.9 - - + +
2146D SER* 1.3 59.5 + - - +
2147D ASP 3.2 2.0 - - - -
2148D VAL* 3.2 8.8 + - + +
2149D THR* 2.8 34.3 + - + +
2153D PHE* 4.5 4.5 - - + -
2221D ALA* 2.9 31.1 + - - +
2224D PHE* 3.8 14.8 - - + +
2225D GLY* 3.5 18.5 - - - +
2228D LEU* 3.6 24.9 - - + -
2230D LEU* 3.4 30.7 - - + -
2239D LEU* 3.7 20.4 - - + -
2240D MET* 4.3 3.8 - - - -
2254D LEU* 4.1 17.9 - - + -
2258D ASP* 4.2 7.4 - - + -
2262D ILE* 3.7 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2142D PHE 3.0 10.1 + - - -
2143D LYS* 3.3 22.9 - - - +
2145D TRP* 1.3 76.3 - - - +
2147D ASP* 1.3 61.1 + - - +
2148D VAL 3.2 0.2 - - - -
2149D THR* 3.0 21.0 - - - +
2151D LEU 3.2 24.9 - - - +
2152D ASN* 4.8 4.9 - - - -
2153D PHE* 4.1 15.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2143D LYS* 2.8 62.0 + - - +
2144D VAL* 4.1 6.2 - - - +
2145D TRP 3.2 0.2 - - - -
2146D SER* 1.3 81.6 + - - +
2148D VAL* 1.3 63.9 + - + +
2149D THR 3.7 0.7 - - - -
----------------------------------------------------------
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