Contacts of the strand formed by residues 2188 - 2193 (chain D) 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.
For CSU analysis of other PDB entry

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 LEU2188 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2040D  ILE*     4.9     9.4    -      -       +      -
   2056D  LEU*     4.0    19.3    -      -       +      -
   2057D  PRO      3.3    24.9    -      -       -      +
   2058D  MET*     4.0    16.4    -      -       -      -
   2059D  GLY      3.7     3.6    -      -       -      +
   2060D  ARG      3.5    11.2    -      -       -      +
   2062D  VAL*     3.8    24.2    -      -       +      -
   2079D  VAL*     4.9     3.4    -      -       +      -
   2139D  ASP      2.9    12.3    +      -       -      +
   2140D  VAL*     3.3    14.2    -      -       +      -
   2141D  ILE      2.9    26.5    +      -       -      +
   2186D  ASN      3.9     1.2    +      -       -      -
   2187D  THR*     1.3    74.0    -      -       -      +
   2189D  LEU*     1.3    67.1    +      -       -      +
   2190D  ILE*     3.9    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU2189 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2060D  ARG      3.0    10.1    +      -       -      +
   2061D  ILE*     3.4     6.5    -      -       +      +
   2062D  VAL*     2.9    26.7    +      -       -      +
   2129D  CYS*     4.8     7.9    -      -       +      -
   2141D  ILE*     3.2    20.9    -      -       +      +
   2143D  VAL*     3.9    17.3    -      -       +      -
   2178D  LEU*     3.8    17.3    -      -       +      -
   2182D  LEU*     3.7    37.5    -      -       +      -
   2187D  THR      3.8     0.4    +      -       -      -
   2188D  LEU*     1.3    73.1    -      -       -      +
   2190D  ILE*     1.3    76.5    +      -       -      +
   2191D  PHE*     3.6    34.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE2190 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2056D  LEU*     3.8    23.3    -      -       +      -
   2062D  VAL*     3.4    18.8    -      -       +      +
   2064D  ILE*     3.6    28.9    -      -       +      -
   2076D  THR*     4.0    12.8    -      -       -      +
   2079D  VAL*     3.9    25.8    -      -       +      -
   2140D  VAL*     4.8     7.0    -      -       +      -
   2141D  ILE      2.8    10.5    +      -       -      +
   2142D  VAL*     3.2    13.9    -      -       +      +
   2143D  VAL      2.8    27.9    +      -       -      +
   2188D  LEU*     3.9    17.7    -      -       +      -
   2189D  LEU*     1.3    78.0    -      -       -      +
   2191D  PHE*     1.3    67.0    +      -       -      +
   2192D  ILE*     4.0     1.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE2191 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2061D  ILE*     3.7    16.6    -      -       +      -
   2062D  VAL      2.7    12.0    +      -       -      +
   2063D  GLU*     3.3     3.5    -      -       +      +
   2064D  ILE      2.9    25.8    +      -       -      +
   2126D  LEU*     4.1    21.1    -      -       +      -
   2143D  VAL*     3.8    31.4    -      -       +      -
   2146D  VAL*     3.8    18.4    -      -       +      -
   2149D  LEU*     4.5     4.5    -      -       +      -
   2171D  MET*     4.8     3.6    -      -       +      -
   2175D  MET*     3.8    30.7    -      -       +      -
   2178D  LEU*     4.4     1.8    -      -       +      -
   2189D  LEU*     3.6    33.9    -      -       +      -
   2190D  ILE*     1.3    73.9    -      -       -      +
   2192D  ILE*     1.3    62.0    +      -       -      +
   2215D  LEU*     3.7    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE2192 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2064D  ILE*     3.4     7.0    -      -       +      +
   2072D  LYS*     3.6    54.5    -      -       +      +
   2073D  THR*     3.9     2.7    -      -       -      -
   2076D  THR*     3.4    33.2    -      -       +      +
   2142D  VAL*     4.4     3.8    -      -       +      -
   2143D  VAL      2.9    11.2    +      -       -      +
   2144D  ASP*     3.4    36.6    -      -       +      +
   2145D  SER*     3.0    17.3    -      -       -      +
   2146D  VAL*     2.8    27.8    +      -       -      +
   2190D  ILE*     4.8     3.6    -      -       +      -
   2191D  PHE*     1.3    73.9    -      -       -      +
   2193D  ASN*     1.3    62.4    +      -       -      +
   2501D  ALF      5.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN2193 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2063D  GLU*     3.1    20.6    -      -       +      +
   2064D  ILE      2.8     8.2    +      -       -      +
   2065D  TYR*     3.3    28.6    -      -       +      -
   2066D  GLY      3.7     0.7    +      -       -      -
   2072D  LYS*     3.4    13.7    -      -       -      +
   2145D  SER*     4.9     0.4    -      -       -      +
   2146D  VAL*     3.3    21.0    -      -       +      +
   2147D  ALA      3.9     2.8    -      -       -      +
   2191D  PHE      3.8     0.2    +      -       -      -
   2192D  ILE*     1.3    76.1    -      -       -      +
   2194D  GLN*     1.3    80.5    +      -       -      +
   2209D  THR*     3.0    13.6    -      -       -      +
   2210D  THR*     2.9    53.2    +      -       -      +
   2215D  LEU*     4.5     1.7    -      -       -      +
----------------------------------------------------------
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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