Contacts of the helix formed by residues 2151 - 2163 (chain C) in PDB entry 1G24
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 ASN2151 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2142C THR* 3.6 20.4 + - - +
2143C LEU 2.6 18.1 + - - +
2144C LEU 5.2 0.2 - - - -
2145C ASN* 4.6 14.9 - - + +
2149C THR 3.6 2.4 + - - -
2150C ILE* 1.3 71.2 - - - +
2152C LYS* 1.3 60.9 + - - +
2153C THR* 3.2 18.7 + - - +
2154C ALA* 2.7 33.6 - - + +
2155C PHE* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2150C ILE 3.0 7.7 + - - +
2151C ASN* 1.3 73.2 + - - +
2153C THR* 1.3 57.6 + - - +
2155C PHE* 3.7 16.0 - - + +
2156C GLU* 2.9 28.4 + - + +
2230C LEU* 5.2 6.3 - - + -
2235C LYS* 4.7 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2151C ASN* 3.1 16.8 + - - +
2152C LYS* 1.3 76.1 - - - +
2154C ALA* 1.3 64.9 + - - +
2156C GLU* 3.4 17.0 + - - +
2157C LYS* 3.1 45.3 + - - +
3153D THR* 4.2 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2139C PHE* 3.4 11.7 - - + -
2142C THR* 3.8 22.4 - - + +
2143C LEU* 3.9 18.2 - - + +
2151C ASN* 2.7 30.6 - - + +
2153C THR* 1.3 74.7 - - - +
2155C PHE* 1.3 59.8 + - - +
2157C LYS* 2.9 14.6 + - - +
2158C ALA* 2.8 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2143C LEU* 4.5 0.6 - - - +
2150C ILE* 4.0 11.9 - - + -
2151C ASN 2.8 16.6 + - - +
2152C LYS* 3.7 13.2 - - + +
2154C ALA* 1.3 76.7 - - - +
2156C GLU* 1.3 58.1 + - - +
2158C ALA* 3.1 7.8 + - + +
2159C LYS* 2.9 69.5 + - + +
2228C MET* 3.4 23.1 - - + -
2229C ARG* 3.6 13.2 - - - -
2230C LEU* 3.7 30.5 - - + -
2237C ILE* 3.8 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2152C LYS* 2.9 19.4 + - + +
2153C THR* 3.4 18.2 + - - +
2154C ALA 3.1 0.2 - - - -
2155C PHE* 1.3 78.9 - - + +
2157C LYS* 1.3 63.7 + - + +
2159C LYS* 3.5 11.6 + - - +
2160C ALA* 3.2 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2139C PHE* 4.0 15.8 - - + -
2142C THR* 5.8 6.9 - - + +
2153C THR* 3.1 33.6 + - + +
2154C ALA* 2.9 12.9 + - - +
2156C GLU* 1.3 77.9 - - + +
2158C ALA* 1.3 64.0 + - - +
2160C ALA* 3.6 6.9 + - - +
2161C LYS* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2135C LEU* 4.0 22.7 - - + -
2139C PHE* 3.7 18.6 - - + -
2143C LEU* 5.3 0.2 - - + -
2154C ALA 2.8 12.3 + - - +
2155C PHE* 3.4 15.5 - - + +
2157C LYS* 1.3 75.4 - - - +
2159C LYS* 1.3 59.3 + - - +
2161C LYS* 3.2 3.3 + - - -
2162C PHE* 3.0 36.0 + - - +
2228C MET* 4.0 13.3 - - + +
2237C ILE* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2155C PHE* 2.9 58.9 + - + +
2156C GLU* 3.8 8.7 - - - +
2157C LYS 3.3 0.2 - - - -
2158C ALA* 1.3 73.7 - - - +
2160C ALA* 1.3 61.3 + - - +
2163C LEU* 2.8 54.9 + - + +
2228C MET* 3.8 32.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2156C GLU* 3.2 14.6 + - + +
2157C LYS* 3.9 8.1 - - - +
2159C LYS* 1.3 78.4 - - - +
2161C LYS* 1.3 59.6 + - - +
2163C LEU 5.1 0.9 + - - +
2165C LYS* 3.9 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2135C LEU 3.0 18.7 + - - +
2136C GLY* 4.2 5.7 - - - -
2138C GLU* 2.7 27.5 + - - +
2139C PHE* 4.1 11.0 - - + -
2157C LYS 3.2 16.8 + - - +
2158C ALA* 3.5 4.9 - - - +
2159C LYS 3.1 0.6 - - - -
2160C ALA* 1.3 80.0 - - - +
2162C PHE* 1.3 90.8 + - + +
2165C LYS* 3.5 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2134C TYR* 4.5 0.4 - + - -
2135C LEU* 3.4 47.6 - - + -
2158C ALA* 3.0 19.8 + - - +
2161C LYS* 1.3 114.3 - - + +
2163C LEU* 1.3 67.9 + - - +
2164C ASN 3.4 0.3 + - - -
2165C LYS* 3.3 21.0 + - + +
2167C ARG* 3.2 47.1 - - + -
2225C ILE* 3.5 29.4 - - + +
2228C MET* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2159C LYS* 2.8 53.0 + - + +
2160C ALA 5.3 1.0 - - - +
2162C PHE* 1.3 73.6 - - - +
2164C ASN* 1.3 93.5 + - - +
2165C LYS* 3.4 11.3 + - - +
2225C ILE* 4.0 2.9 - - - +
2226C ASP 3.6 24.9 - - - +
2227C ASP* 3.8 16.4 - - - +
2228C MET* 3.9 16.8 - - + +
----------------------------------------------------------
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