Contacts of the helix formed by residues 2165 - 2186 (chain A) in PDB entry 3CMT
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 GLY2165 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199A ILE* 4.2 9.7 - - - +
2163A HIS 3.2 2.2 + - - -
2164A MET* 1.3 70.7 - - - +
2166A LEU* 1.3 58.1 + - - +
2167A ALA 3.5 1.8 - - - -
2168A ALA* 3.4 14.8 + - - +
2169A ARG* 2.9 38.4 + - - +
1006B C 4.4 10.2 + - - +
1007B A 4.5 15.6 + - - -
1008B C 5.7 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2123A GLU* 4.7 8.3 - - - +
2151A PRO* 3.8 28.0 - - + -
2153A ALA* 3.8 25.6 - - + +
2154A GLU 4.7 0.4 - - - +
2163A HIS* 3.1 37.0 + - + +
2164A MET 3.0 3.0 + - - -
2165A GLY* 1.3 73.1 - - - +
2167A ALA* 1.3 60.9 + - - +
2169A ARG* 3.3 24.7 + - + +
2170A MET* 2.9 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2149A LEU 4.7 2.9 - - - +
2151A PRO* 3.8 26.7 - - + +
2163A HIS 4.9 0.2 + - - -
2166A LEU* 1.3 79.0 - - - +
2168A ALA* 1.3 57.4 + - - +
2170A MET* 3.4 11.0 + - + +
2171A MET* 2.9 34.2 + - + +
2210A THR* 6.4 1.6 - - + -
2211A GLY* 4.7 6.5 - - - -
3176A ARG* 5.0 11.0 - - - +
1008B C 4.3 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2165A GLY* 3.4 9.3 + - - +
2166A LEU 3.2 0.4 - - - -
2167A ALA* 1.3 80.7 - - - +
2169A ARG* 1.3 56.7 + - - +
2171A MET* 3.4 3.5 + - - +
2172A SER* 2.9 29.7 + - - -
2211A GLY 4.0 12.2 - - - +
2212A GLY* 3.8 5.6 - - - -
2214A ALA* 5.1 1.0 - - - +
1006B C 3.3 25.5 - - - +
1007B A 3.6 32.9 + - - +
1008B C 4.2 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2164A MET 3.5 3.8 + - - -
2165A GLY 2.9 30.5 + - - +
2166A LEU* 3.7 30.4 - - + +
2168A ALA* 1.3 75.7 - - - +
2170A MET* 1.3 59.5 + - - +
2172A SER* 3.5 1.9 + - - -
2173A GLN* 3.0 27.9 + - - +
2176A ARG* 4.5 1.9 + - - +
1005B C 3.4 29.6 - - - +
1006B C 2.8 55.1 + - - +
2010C G 3.3 13.1 - - - +
2011C G 3.1 23.7 + - - +
2012C G 5.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159A ILE* 4.5 6.5 - - + +
1160A GLY* 5.7 1.6 - - - +
2122A GLY* 4.1 2.7 - - - -
2123A GLU* 3.7 49.8 - - + +
2126A LEU* 3.9 12.7 - - + +
2149A LEU* 3.7 26.5 - - + +
2151A PRO* 4.4 8.7 - - + -
2166A LEU* 2.9 22.4 + - + +
2167A ALA* 3.6 15.5 - - + +
2169A ARG* 1.3 73.4 - - - +
2171A MET* 1.3 86.3 + - + +
2173A GLN* 3.3 14.0 + - - +
2174A ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2126A LEU* 3.5 32.8 - - + -
2146A VAL* 4.5 16.6 - - + -
2149A LEU* 3.4 32.3 - - + -
2167A ALA 2.9 21.0 + - - +
2168A ALA 3.5 2.0 - - - +
2170A MET* 1.3 80.8 - - + +
2172A SER* 1.3 66.6 + - - +
2174A ALA* 3.2 3.0 + - + +
2175A MET* 3.0 43.8 + - + +
2191A PHE* 4.8 4.9 - - + -
2211A GLY* 3.5 31.6 - - - +
2214A ALA* 4.2 6.5 - - + -
2215A LEU* 5.6 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196A ARG* 3.3 28.2 + - - -
2168A ALA 2.9 17.1 + - - -
2169A ARG 3.6 2.2 - - - -
2170A MET 3.3 0.2 - - - -
2171A MET* 1.3 77.4 - - - +
2173A GLN* 1.3 61.8 + - - +
2175A MET* 3.6 3.1 + - - +
2176A ARG* 3.4 26.9 + - - +
2214A ALA* 3.5 14.2 - - - +
2218A TYR* 5.1 1.7 + - - -
1006B C 3.0 34.2 + - - -
1007B A 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154A GLU* 3.2 31.1 - - + +
1158A GLU 4.0 5.1 - - - +
1159A ILE* 3.9 10.6 - - - +
1160A GLY* 2.9 35.4 - - - +
1161A ASP 2.9 22.4 + - - +
1163A HIS* 3.9 5.5 - - - -
2169A ARG 3.0 12.7 + - - +
2170A MET* 3.5 11.7 + - - +
2171A MET 3.2 0.2 - - - -
2172A SER* 1.3 75.8 - - - +
2174A ALA* 1.3 65.3 + - - +
2176A ARG* 3.2 21.3 + - - +
2177A LYS* 3.2 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159A ILE* 4.2 17.2 - - + +
2126A LEU* 3.8 29.8 - - + -
2170A MET 2.9 13.8 + - - +
2171A MET* 3.2 9.8 + - - +
2173A GLN* 1.3 76.3 - - - +
2175A MET* 1.3 65.1 + - + +
2177A LYS* 3.1 3.7 + - - +
2178A LEU* 2.8 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2061A ILE* 4.1 17.7 - - - -
2171A MET* 3.0 36.2 + - - +
2172A SER 3.9 2.9 - - - +
2173A GLN 3.3 0.2 - - - -
2174A ALA* 1.3 86.4 - - + +
2176A ARG* 1.3 63.6 + - - +
2178A LEU* 4.4 5.8 - - + +
2179A ALA* 3.0 30.0 + - - +
2191A PHE* 3.8 28.9 - - + -
2214A ALA* 3.8 14.4 - - + -
2215A LEU* 3.9 25.1 - - + +
2218A TYR* 3.3 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A ALA 3.4 26.2 - - - +
1148A ALA* 4.6 3.4 - - - +
1149A LEU 5.3 1.1 - - - -
1150A THR* 3.1 36.5 + - + +
1151A PRO* 5.3 0.7 - - - -
1154A GLU* 2.8 33.9 + - - +
1155A ILE* 5.4 1.2 - - - +
1167A ALA* 4.9 14.3 - - - +
2169A ARG* 4.5 2.0 + - - +
2172A SER* 3.4 13.6 + - - +
2173A GLN* 3.2 35.8 + - - +
2175A MET* 1.3 80.1 - - - +
2177A LYS* 1.3 61.8 - - + +
2179A ALA* 4.2 6.8 + - - +
2180A GLY* 4.5 3.6 + - - -
2218A TYR* 3.6 11.8 + - - +
1005B C 5.2 3.8 + - - -
1006B C 3.8 17.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150A THR* 4.6 6.5 - - + -
1154A GLU* 3.3 40.2 - - + +
1155A ILE* 3.3 24.8 + - + +
1157A GLY 2.7 23.2 + - - +
1158A GLU* 4.0 3.5 - - - +
1159A ILE* 3.8 22.2 - - + +
2127A GLU* 3.5 17.0 + - - -
2130A ASP* 3.4 26.6 + - - +
2134A ARG* 5.1 0.8 - - - +
2173A GLN* 3.2 13.4 + - + +
2174A ALA 3.1 7.6 + - - +
2176A ARG* 1.3 78.2 - - - +
2178A LEU* 1.3 64.1 + - - +
2180A GLY* 4.2 1.4 + - - -
2181A ASN* 3.7 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159A ILE* 5.0 3.4 - - + -
2061A ILE* 4.9 2.5 - - + -
2126A LEU* 4.5 9.6 - - + +
2129A CYS* 4.1 11.0 - - + +
2130A ASP* 3.6 43.1 - - + +
2133A ALA* 4.8 4.7 - - + -
2174A ALA* 2.8 37.8 + - + +
2175A MET* 4.1 6.5 - - + +
2177A LYS* 1.3 70.6 - - - +
2179A ALA* 1.3 67.2 + - - +
2180A GLY 3.2 2.2 - - - -
2181A ASN* 3.0 4.0 + - - +
2182A LEU* 2.8 37.7 + - + +
2189A LEU* 3.8 24.9 - - + -
2191A PHE* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A ALA 5.2 2.0 - - - +
1096A GLU 4.4 14.1 - - - +
1097A HIS* 4.2 9.4 - - + +
1148A ALA* 6.0 0.2 - - + -
2059A GLY 4.6 1.9 - - - +
2061A ILE* 4.4 14.0 - - + +
2175A MET 3.0 18.8 + - - +
2176A ARG 4.5 3.6 - - - +
2177A LYS 3.6 0.4 - - - -
2178A LEU* 1.3 77.0 - - - +
2180A GLY* 1.3 60.8 + - - +
2182A LEU* 3.5 4.2 + - - +
2183A LYS* 3.2 22.7 + - - +
2218A TYR* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A HIS* 3.8 25.0 - - - -
1120A ASP* 6.0 2.7 - - - -
2176A ARG 4.5 4.4 + - - -
2177A LYS 4.2 3.3 + - - -
2178A LEU 3.2 0.8 - - - -
2179A ALA* 1.3 75.7 - - - +
2181A ASN* 1.3 66.9 + - - +
2183A LYS* 3.3 3.5 + - - +
2184A GLN* 3.1 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1155A ILE* 5.9 5.0 - - - +
2130A ASP* 2.8 26.9 - - - +
2133A ALA* 4.0 19.5 - - + +
2134A ARG* 3.2 30.8 + - + +
2177A LYS* 3.7 9.4 + - - +
2178A LEU* 3.0 8.0 + - - +
2180A GLY* 1.3 76.8 - - - +
2182A LEU* 1.3 60.7 + - - +
2184A GLN* 3.7 6.9 + - - +
2185A SER* 3.0 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2059A GLY* 3.4 9.5 - - - +
2060A ARG 4.9 0.9 - - - +
2061A ILE* 3.7 29.6 - - + -
2133A ALA* 4.0 15.9 - - + -
2141A ILE* 4.8 3.1 - - + -
2178A LEU* 2.8 30.4 + - + +
2179A ALA* 3.8 4.0 - - - +
2181A ASN* 1.3 75.6 - - - +
2183A LYS* 1.3 59.7 + - - +
2185A SER 3.4 0.3 + - - -
2186A ASN 3.0 7.4 + - - -
2187A THR* 2.9 68.3 + - + +
2189A LEU* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A HIS* 3.5 48.9 + - + +
1098A ALA* 4.9 0.4 - - - +
1099A LEU 5.1 3.6 + - - -
1118A GLN* 3.7 21.8 + - - +
2034A SER* 3.9 23.8 + - - +
2035A MET* 5.1 8.3 + - - +
2058A MET 4.6 5.8 - - - -
2059A GLY* 3.6 19.5 + - - +
2060A ARG* 3.5 28.4 - - - +
2179A ALA 3.2 11.7 + - - +
2180A GLY 3.3 1.1 + - - +
2182A LEU* 1.3 79.4 - - - +
2184A GLN* 1.3 64.0 + - + +
2186A ASN* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A HIS* 3.9 25.7 - - - -
1118A GLN* 4.1 8.5 + - - +
1119A PRO 4.9 0.4 + - - -
1120A ASP* 3.0 29.5 + - - +
2180A GLY* 3.1 17.5 + - - +
2181A ASN* 4.3 8.3 + - - +
2183A LYS* 1.3 77.7 - - + +
2185A SER* 1.3 59.4 + - - +
2186A ASN 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2133A ALA 2.5 30.1 + - - -
2134A ARG* 4.2 5.2 + - - -
2136A GLY* 4.0 21.9 + - - +
2138A VAL 4.9 2.1 - - - +
2139A ASP* 5.6 1.7 - - - +
2181A ASN 3.0 14.7 + - - -
2183A LYS 3.1 0.8 - - - -
2184A GLN* 1.3 77.8 - - - +
2186A ASN* 1.3 70.5 + - - +
2187A THR* 3.1 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2034A SER 5.6 1.2 - - - +
2036A ASP 5.5 2.6 - - - +
2038A GLU* 3.2 28.8 + - - +
2058A MET* 3.4 51.1 - - - +
2059A GLY* 3.6 7.7 + - - -
2139A ASP* 4.1 3.5 - - - +
2182A LEU 3.0 6.5 + - - -
2183A LYS* 3.1 15.2 + - - +
2184A GLN 3.4 0.4 - - - -
2185A SER* 1.3 81.2 - - - +
2187A THR* 1.3 58.3 + - - +
----------------------------------------------------------
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