Contacts of the helix formed by residues 2172 - 2188 (chain D) in PDB entry 6X34
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 GLY2172 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2170D GLN 3.6 1.1 + - - -
2171D MET* 1.3 74.7 - - - +
2173D PRO* 1.3 66.7 - - - +
2174D GLN 3.5 2.2 - - - -
2175D GLU* 3.3 14.0 - - - +
2176D GLU* 2.5 38.8 + - - +
2226D PHE* 4.5 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172D GLY* 1.3 83.0 - - - +
2174D GLN* 1.3 59.8 + - - +
2176D GLU* 3.2 6.1 + - + +
2177D ASN* 2.9 27.7 + - - +
2226D PHE* 5.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680D ARG* 5.4 13.1 + - - +
1794D GLU 4.1 25.0 + - - +
1795D ALA 3.7 19.2 + - - +
1796D PRO* 4.2 10.5 - - - +
1797D ALA* 4.3 9.8 - - - +
2166D LEU* 5.2 2.4 - - - +
2173D PRO* 1.3 80.8 - - - +
2175D GLU* 1.3 62.8 + - - +
2177D ASN* 3.3 8.5 + - + +
2178D LEU* 2.9 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2166D LEU* 4.0 30.0 - - + +
2169D VAL* 5.9 1.8 - - + -
2170D GLN 4.4 5.8 - - - +
2171D MET* 4.2 7.4 - - + -
2172D GLY* 3.3 25.4 + - - +
2173D PRO 3.2 0.4 - - - -
2174D GLN* 1.3 84.7 + - - +
2176D GLU* 1.3 56.6 + - - +
2178D LEU* 3.4 2.7 + - - +
2179D MET* 2.9 29.5 + - - +
2229D MET* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2171D MET* 5.6 1.1 - - + +
2172D GLY 2.5 22.7 + - - +
2173D PRO* 3.6 6.5 - - + +
2175D GLU* 1.3 73.1 - - - +
2177D ASN* 1.3 57.9 + - - +
2179D MET* 3.3 7.5 + - - +
2180D ILE* 2.9 40.2 + - + +
2226D PHE* 5.0 14.4 - - + -
2229D MET* 4.5 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1794D GLU* 4.3 25.9 + - - +
2173D PRO 2.9 15.8 + - - +
2174D GLN* 3.6 10.3 - - + +
2175D GLU 3.3 0.2 - - - -
2176D GLU* 1.3 77.6 - - - +
2178D LEU* 1.3 57.3 + - - +
2180D ILE* 3.2 9.1 + - - +
2181D GLN* 2.9 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1796D PRO* 6.2 5.8 - - + -
1797D ALA 6.3 0.2 - - - +
2162D GLN* 3.4 38.4 - - + +
2166D LEU* 3.7 32.5 - - + -
2174D GLN* 2.9 34.2 + - - +
2175D GLU* 3.8 4.9 - - - +
2177D ASN* 1.3 76.0 - - - +
2179D MET* 1.3 57.2 + - - +
2181D GLN* 3.3 11.0 + - + +
2182D SER* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2163D ILE* 3.7 40.6 - - + +
2166D LEU* 5.6 8.9 - - + +
2167D LEU* 6.1 1.1 - - - -
2175D GLU 2.9 17.8 + - - +
2176D GLU 3.6 5.6 - - - +
2178D LEU* 1.3 78.7 - - - +
2180D ILE* 1.3 56.3 + - + +
2182D SER* 3.3 4.8 + - - -
2183D ILE* 2.9 57.9 + - + +
2208D VAL* 5.7 6.7 - - + -
2211D VAL* 3.8 32.8 - - + -
2229D MET* 3.6 26.5 - - + -
2232D SER* 5.8 1.6 - - - +
2233D CYS* 5.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2176D GLU* 2.9 27.6 + - + +
2177D ASN* 3.6 8.5 - - - +
2179D MET* 1.3 76.8 - - + +
2181D GLN* 1.3 72.1 + - - +
2183D ILE* 3.3 7.0 + - - +
2184D GLY* 2.9 25.6 + - - -
2228D LYS* 3.6 33.9 - - + +
2229D MET* 4.4 4.9 - - - +
2232D SER* 4.0 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2177D ASN* 2.9 42.9 + - - +
2178D LEU* 3.7 13.2 - - + +
2180D ILE* 1.3 89.3 - - - +
2182D SER* 1.3 57.8 + - - +
2184D GLY* 3.3 2.2 + - - +
2185D ASN* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2159D CYS* 4.9 7.0 - - - -
2162D GLN* 5.7 5.4 - - - -
2163D ILE* 3.6 31.9 - - - -
2178D LEU* 2.9 22.7 + - - +
2179D MET* 3.6 6.1 - - - -
2181D GLN* 1.3 77.0 - - - +
2183D ILE* 1.3 57.6 + - - +
2185D ASN* 3.1 6.7 + - - +
2186D ILE* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2163D ILE* 5.0 6.1 - - + -
2179D MET* 2.9 51.5 + - + +
2180D ILE* 3.8 6.1 - - - +
2182D SER* 1.3 76.7 - - - +
2184D GLY* 1.3 61.8 + - - +
2186D ILE* 3.2 32.5 - - + +
2187D MET* 3.3 17.7 - - - +
2208D VAL* 5.3 8.5 - - + -
2232D SER* 3.8 35.9 - - - +
2233D CYS* 5.5 3.8 - - + +
2235D ARG* 5.8 1.8 - - - +
2236D PHE* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2180D ILE 2.9 14.9 + - - -
2181D GLN* 3.7 3.8 - - - -
2182D SER 3.2 0.2 - - - -
2183D ILE* 1.3 78.8 - - - +
2185D ASN* 1.3 59.0 + - - +
2187D MET* 3.7 11.3 + - - +
2188D ASN* 2.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2155D SER* 5.3 5.4 + - - +
2156D LEU* 5.9 0.3 - - - +
2159D CYS* 4.3 20.8 - - + +
2181D GLN 2.9 16.6 + - - +
2182D SER* 3.1 7.4 + - - +
2184D GLY* 1.3 73.7 - - - +
2186D ILE* 1.3 63.0 + - + +
2187D MET 3.1 3.4 + - - -
2188D ASN* 3.4 16.1 + - - +
2189D ASN* 4.0 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2156D LEU* 4.3 15.9 - - + +
2159D CYS* 3.5 29.6 - - - -
2160D LEU* 5.8 0.9 - - + -
2163D ILE* 4.0 16.6 - - + -
2182D SER 2.9 15.9 + - - +
2183D ILE* 3.2 43.3 - - + +
2185D ASN* 1.3 77.6 - - - +
2187D MET* 1.3 59.5 + - - +
2188D ASN 3.4 0.4 + - - -
2189D ASN* 3.8 14.4 - - - +
2192D PHE* 4.4 14.6 - - + +
2208D VAL* 6.0 0.7 - - + -
2236D PHE* 3.5 35.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET2187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2183D ILE* 3.3 28.2 + - - +
2184D GLY* 4.0 9.2 - - - +
2185D ASN 3.1 0.8 - - - -
2186D ILE* 1.3 75.8 - - - +
2188D ASN* 1.3 63.0 + - - +
2189D ASN 3.2 13.5 + - - +
2192D PHE* 5.1 6.4 - - + -
2193D TYR* 4.0 21.9 + - - +
2235D ARG* 4.1 24.7 - - - +
2236D PHE* 4.0 29.4 - - + -
2239D TYR* 3.7 49.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2184D GLY 2.9 19.7 - - - +
2185D ASN* 3.4 11.6 + - - +
2187D MET* 1.3 80.2 + - - +
2189D ASN* 1.3 62.3 + - - +
2190D LYS* 3.7 1.4 + - - +
----------------------------------------------------------
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