Contacts of the helix formed by residues 2044 - 2051 (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 SER2044 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2042A THR* 3.0 18.7 + - - -
2043A GLY* 1.3 78.4 - - - +
2045A LEU* 1.3 63.0 + - - +
2047A LEU* 3.1 25.5 + - - +
2048A ASP* 3.1 16.7 + - - -
2260A PHE* 3.3 23.4 - - - -
2268A ILE* 4.0 11.9 - - - +
2270A PHE* 4.3 0.7 - - - -
2273A GLU* 2.5 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2045 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2044A SER* 1.3 71.2 - - - +
2046A SER* 1.3 59.5 + - - +
2048A ASP* 3.1 7.7 + - - +
2049A ILE* 3.0 34.4 + - + +
2270A PHE* 3.5 19.9 - - + +
2273A GLU* 2.9 15.3 + - + +
2274A LEU* 3.7 40.6 - - + +
2277A LEU* 4.3 10.5 - - + -
2320A GLU* 3.6 27.8 - - + +
2323A VAL* 4.2 17.3 - - + -
2324A ARG* 3.8 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2046 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2044A SER* 3.4 0.7 + - - -
2045A LEU* 1.3 76.9 - - - +
2047A LEU* 1.3 58.6 + - - +
2049A ILE* 3.4 12.7 + - - +
2050A ALA* 2.9 27.2 + - - +
2257A GLN 4.8 0.7 - - - +
2258A ALA* 3.3 20.8 - - - +
2259A GLU 3.5 15.5 + - - -
2260A PHE* 4.1 0.7 - - - -
2273A GLU* 2.6 23.8 + - - +
2277A LEU* 4.2 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2047 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2042A THR* 3.5 31.2 - - + +
2044A SER* 3.1 19.1 + - - +
2046A SER* 1.3 74.4 + - - +
2048A ASP* 1.3 54.9 + - - +
2049A ILE 3.1 1.6 - - - -
2050A ALA* 3.0 3.8 + - + -
2051A LEU* 2.7 51.2 + - + +
2075A LEU* 4.0 25.1 - - + -
2223A LEU* 4.5 16.2 - - + -
2244A VAL* 4.3 23.3 - - + +
2246A VAL* 4.3 13.7 - - + -
2258A ALA* 3.5 13.9 - - + +
2260A PHE* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2048 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2041A SER* 3.0 21.9 + - - -
2042A THR* 2.9 31.9 + - - +
2044A SER 3.1 18.0 + - - +
2045A LEU* 3.4 7.5 - - - +
2047A LEU* 1.3 75.6 - - - +
2049A ILE* 1.3 62.3 + - - +
2051A LEU* 3.6 6.5 + - - +
2052A GLY 3.6 0.2 + - - -
2054A GLY* 3.1 47.8 + - - +
2055A GLY* 3.4 7.9 - - - +
2270A PHE* 5.4 0.5 - - - -
2324A ARG* 2.8 28.6 + - - +
2328A LEU* 3.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2049 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2045A LEU* 3.0 42.5 + - + +
2046A SER* 3.6 11.0 - - - +
2048A ASP* 1.3 75.0 - - + +
2050A ALA* 1.3 66.2 + - - +
2052A GLY* 2.9 15.9 + - - -
2256A LYS* 4.2 9.4 + - + +
2277A LEU* 4.2 14.6 - - + -
2323A VAL* 4.1 20.6 - - + -
2324A ARG* 5.3 3.8 - - + -
2327A LEU* 3.8 37.2 - - + +
2328A LEU* 3.6 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2050 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2046A SER 2.9 18.0 + - - +
2047A LEU* 3.5 8.5 - - + +
2049A ILE* 1.3 76.4 - - - +
2051A LEU* 1.3 61.4 + - - +
2052A GLY 3.2 1.4 + - - -
2246A VAL* 4.1 15.3 - - + +
2249A ASN* 4.8 0.2 + - - -
2253A ALA 4.4 5.9 - - - +
2256A LYS* 3.4 38.2 - - + +
2257A GLN 3.9 28.5 - - - +
2258A ALA* 4.2 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2051 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2042A THR* 3.6 31.6 - - + -
2047A LEU* 2.7 34.2 + - + +
2048A ASP* 3.7 7.4 - - - +
2049A ILE 3.1 0.2 - - - -
2050A ALA* 1.3 72.1 - - - +
2052A GLY* 1.3 55.6 + - - +
2053A ALA 2.9 9.8 + - - -
2055A GLY* 3.7 30.5 - - - +
2056A LEU* 4.0 8.5 - - + +
2221A VAL* 3.6 37.9 - - + -
2223A LEU* 4.3 7.9 - - + -
2246A VAL* 4.4 9.2 - - + -
2249A ASN* 3.2 21.9 + - - +
2251A ILE* 4.1 6.6 - - + +
2252A ALA* 3.3 3.6 - - - +
----------------------------------------------------------
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