Contacts of the strand formed by residues 44 - 51 (chain O) 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 ALA 44 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363N  SER*     6.5     0.2    -      -       -      -
    366N  VAL*     4.0    22.0    -      -       +      -
     42O  SER*     2.7    26.8    +      -       -      +
     43O  PRO*     1.3    82.2    -      -       -      +
     45O  SER*     1.3    67.6    +      -       -      +
    110O  GLU*     4.9     7.9    -      -       +      +
    111O  CYS      3.7    13.9    -      -       -      +
    112O  LEU*     4.7     4.7    -      -       +      -
    113O  ARG*     4.2     1.3    -      -       -      +
    209O  ILE*     5.2     2.6    -      -       -      +
    210O  GLY*     4.2     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 45 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44O  ALA*     1.3    76.5    -      -       -      +
     46O  ARG*     1.3    66.3    +      -       -      +
     47O  ILE*     4.9     4.7    -      -       -      -
    109O  VAL      4.7     0.4    -      -       -      -
    110O  GLU*     3.7     8.5    -      -       -      +
    111O  CYS*     2.9    31.7    +      -       -      +
    113O  ARG*     3.7    10.4    -      -       -      +
    116O  VAL*     3.2    34.1    -      -       -      +
    209O  ILE*     3.8    11.7    -      -       -      -
    210O  GLY*     3.2    17.1    +      -       -      -
    211O  VAL*     3.9     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 46 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45O  SER*     1.3    80.1    -      -       -      +
     47O  ILE*     1.3    62.4    +      -       -      +
     97O  SER*     5.6     0.8    +      -       -      -
     99O  TYR*     3.9    19.8    +      -       -      -
    108O  CYS*     3.5    28.0    -      -       -      -
    109O  VAL      3.4     9.2    -      -       -      +
    110O  GLU*     3.2    42.2    +      -       +      +
    209O  ILE*     3.4    24.0    +      -       +      +
    375O  ALA*     4.7    16.4    -      -       +      +
    376O  GLN*     3.4    42.9    +      -       -      +
    379O  LEU*     3.4    42.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 47 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45O  SER*     4.9     1.8    -      -       -      -
     46O  ARG*     1.3    77.2    -      -       -      +
     48O  GLY*     1.3    62.0    +      -       -      +
    108O  CYS*     3.2     5.6    -      -       -      +
    109O  VAL*     3.1    38.8    +      -       +      +
    111O  CYS*     6.1     1.1    -      -       -      -
    116O  VAL*     3.2    31.9    -      -       +      +
    119O  VAL*     6.5     0.4    -      -       +      -
    120O  MET*     3.1    52.7    -      -       +      -
    123O  LEU*     4.0    10.7    -      -       +      +
    206O  LEU*     3.9    13.2    -      -       +      -
    207O  VAL      3.5    15.5    -      -       -      +
    208O  GLY*     4.3     6.3    -      -       -      -
    211O  VAL*     4.7    15.0    -      -       +      -
    216O  LEU*     4.0     4.3    -      -       +      -
    379O  LEU*     4.4     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 48 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46O  ARG      4.0     0.8    +      -       -      -
     47O  ILE*     1.3    79.2    -      -       -      +
     49O  VAL*     1.3    64.8    +      -       -      -
     50O  PHE*     4.0    15.9    -      -       -      -
    107O  TYR      3.4     8.7    -      -       -      -
    108O  CYS*     3.8     8.3    -      -       -      -
    123O  LEU*     4.6     0.9    -      -       -      -
    206O  LEU*     3.5     8.9    -      -       -      +
    207O  VAL      3.1    31.2    +      -       -      +
    379O  LEU*     4.3     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 49 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48O  GLY*     1.3    77.2    -      -       -      +
     50O  PHE*     1.3    61.6    +      -       -      +
     51O  ILE*     3.8    15.9    -      -       +      +
    105O  MET      3.5     2.9    -      -       -      +
    106O  THR*     3.3     2.6    -      -       -      -
    107O  TYR*     2.7    45.8    +      -       +      +
    123O  LEU*     3.9    24.2    -      -       +      -
    124O  LEU*     6.2     0.4    -      -       -      -
    127O  THR*     4.2    13.5    -      -       +      +
    204O  MET*     3.7    30.3    -      -       +      -
    205O  ALA      3.4     7.6    -      -       -      +
    206O  LEU*     4.0    16.6    -      -       +      -
    224O  LEU*     6.1     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 50 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48O  GLY      4.0     9.6    -      -       -      -
     49O  VAL*     1.3    74.5    -      -       -      +
     51O  ILE*     1.3    68.9    +      -       -      +
    104O  LYS*     5.5     4.3    -      -       +      -
    105O  MET      3.6     3.8    -      -       -      -
    106O  THR*     3.8    30.7    -      -       +      +
    204O  MET*     3.2     1.2    -      -       -      +
    205O  ALA*     2.8    41.6    +      -       +      +
    207O  VAL*     3.1    35.2    -      -       +      -
    379O  LEU*     3.4    38.6    -      -       +      -
    380O  ASN*     4.0    18.4    -      -       -      -
    383O  GLY*     3.8    19.3    -      -       -      -
    384O  SER*     4.2     3.6    -      -       -      -
    387O  LEU*     3.7    16.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49O  VAL*     3.8    21.8    -      -       +      +
     50O  PHE*     1.3    83.3    -      -       -      +
     52O  LYS*     1.3    72.5    +      -       -      +
     53O  ALA*     3.1     1.9    +      -       +      +
    104O  LYS*     3.2     8.6    -      -       -      +
    105O  MET*     2.8    42.3    +      -       +      +
    107O  TYR*     4.7     7.2    -      -       +      -
    127O  THR*     5.0     2.2    -      -       -      -
    198O  ASN      4.1     8.1    -      -       -      +
    199O  PHE*     3.8    53.2    -      -       +      -
    203O  ARG      3.5     5.4    -      -       -      +
    204O  MET*     3.4    28.9    -      -       +      -
    387O  LEU*     4.0     4.4    -      -       -      +
----------------------------------------------------------
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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