Contacts of the strand formed by residues 239 - 245 (chain N) in PDB entry 3L73


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 SER 239 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156N  THR*     3.0    26.1    +      -       -      +
    159N  GLN*     3.5     8.6    +      -       -      -
    237N  THR*     3.1    14.2    +      -       -      +
    238N  GLY*     1.3    75.7    -      -       -      -
    240N  GLU*     1.3    54.7    +      -       -      +
    420N  PRO      3.0     6.2    +      -       -      +
    421N  ALA*     3.1     3.3    -      -       -      +
    422N  LEU      2.6    32.1    +      -       -      -
    434N  TYR*     3.9    11.4    -      -       -      -
     17T  SER      2.9    19.1    -      -       -      -
     18T  LEU*     3.5    16.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 240 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156N  THR*     4.1     6.8    +      -       -      -
    239N  SER*     1.3    76.8    -      -       -      +
    241N  ILE*     1.3    63.5    -      -       -      +
    242N  ARG*     2.8    43.4    +      -       +      +
    422N  LEU*     3.0    27.8    -      -       +      +
    433N  ASP*     5.6     0.2    -      -       -      -
    434N  TYR*     3.1    42.4    +      -       +      +
    229Q  VAL*     5.9     0.2    -      -       -      +
     15T  THR*     5.1     2.4    +      -       -      +
     16T  TYR*     3.5     5.2    -      -       -      +
     17T  SER*     3.1    46.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 241 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152N  TYR*     3.8    47.0    -      -       +      +
    155N  ALA*     5.3     2.2    -      -       +      -
    156N  THR*     3.6    24.5    -      -       +      -
    240N  GLU*     1.3    74.9    -      -       -      +
    242N  ARG*     1.3    66.3    +      -       -      +
    243N  ALA      4.0     1.6    -      -       -      +
    422N  LEU*     3.0    11.3    +      -       -      +
    423N  ALA*     3.6     9.4    -      -       +      -
    424N  ALA      3.0    24.8    +      -       -      +
      5R  VAL*     4.5     5.2    -      -       +      -
      7R  VAL*     5.1     6.1    -      -       +      -
     14T  ILE*     4.0    18.6    -      -       +      -
     15T  THR      3.1     7.4    -      -       -      +
     16T  TYR*     4.1    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 242 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240N  GLU*     2.8    41.8    +      -       +      +
    241N  ILE*     1.3    77.2    -      -       -      +
    243N  ALA*     1.3    60.4    +      -       -      +
    244N  ARG*     3.5     2.3    +      -       +      +
    422N  LEU*     3.9    14.7    -      -       +      +
    424N  ALA*     3.4     7.6    -      -       +      -
    428N  ILE*     3.7    21.8    +      -       +      +
    431N  LEU*     2.7    37.6    +      -       -      +
    432N  LEU*     3.4    40.8    +      -       -      +
    433N  ASP      3.5     3.8    -      -       -      +
    437N  ILE*     4.0     4.6    -      -       -      +
     13T  ILE      3.2     5.0    -      -       -      +
     14T  ILE*     3.2    25.0    -      -       -      -
     15T  THR*     3.0    29.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 243 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152N  TYR*     3.6    35.0    -      -       +      +
    241N  ILE*     4.0     1.4    -      -       +      -
    242N  ARG*     1.3    69.8    -      -       -      +
    244N  ARG*     1.3    60.9    +      -       -      +
    245N  ASP*     5.1     1.1    -      -       -      +
    424N  ALA      2.7    12.6    +      -       -      +
    425N  VAL*     3.1    13.6    -      -       +      +
    426N  GLY      3.1    22.9    +      -       -      +
    428N  ILE*     4.2     0.9    -      -       -      -
     13T  ILE      4.1     2.0    -      -       -      -
     14T  ILE*     4.5    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 244 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242N  ARG*     3.5     2.2    +      -       +      +
    243N  ALA*     1.3    74.1    -      -       -      +
    245N  ASP*     1.3    65.7    +      -       -      +
    246N  ASP*     2.6    36.7    +      -       -      +
    426N  GLY      3.4    12.6    -      -       -      +
    428N  ILE*     4.0    19.5    -      -       +      -
    429N  GLU*     3.2    43.8    +      -       -      +
    432N  LEU*     6.1     1.0    -      -       -      +
    215P  ASP      5.3     1.8    +      -       -      -
    216P  SER      4.9     8.1    +      -       -      -
      8T  ALA      2.9    17.8    +      -       -      -
     10T  VAL*     3.5    34.9    -      -       +      +
     11T  ARG      3.8     0.3    -      -       -      -
     12T  HIS*     2.9    28.4    +      -       -      -
     13T  ILE*     3.2    18.3    +      -       +      +
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Residues in contact with ASP 245 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243N  ALA      3.9     0.6    +      -       -      +
    244N  ARG*     1.3    77.4    -      -       -      +
    246N  ASP*     1.3    62.7    +      -       -      +
    247N  ALA*     3.0     9.1    +      -       -      +
    248N  LEU*     3.2    43.0    +      -       +      +
    425N  VAL*     6.1     1.1    -      -       +      -
    426N  GLY*     3.1    12.3    +      -       -      +
    427N  PRO      3.2    12.6    -      -       -      -
     10T  VAL      3.8     3.6    -      -       -      -
     11T  ARG*     2.4    50.6    +      -       -      +
     12T  HIS*     4.4     9.7    +      -       +      +
----------------------------------------------------------
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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