Contacts of the strand formed by residues 127 - 137 (chain H) in PDB entry 4BEI


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 GLY 127 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83H  PRO*     4.2     5.6    -      -       -      -
    125H  ALA      3.7     1.4    +      -       -      -
    126H  ASP*     1.3    74.5    -      -       -      +
    128H  LYS*     1.3    62.4    +      -       -      -
    129H  TYR*     3.5     8.0    -      -       -      -
    150H  VAL*     3.4     3.3    -      -       -      -
    151H  LYS      2.8    36.4    +      -       -      -
    153H  VAL*     4.3    18.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 128 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81H  LYS      4.4     0.3    -      -       -      +
     82H  GLY*     3.9     2.6    -      -       -      -
     83H  PRO*     3.5    23.1    -      -       -      +
    127H  GLY*     1.3    71.2    -      -       -      -
    129H  TYR*     1.3    61.8    +      -       -      +
    130H  THR*     5.6     0.2    -      -       -      -
    148H  GLU*     6.2     4.9    -      -       +      +
    149H  PHE      3.9     4.0    -      -       -      +
    150H  VAL*     4.3    11.9    -      -       +      -
    153H  VAL*     4.9     1.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 129 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80H  ILE*     3.8    13.0    -      -       +      -
     81H  LYS      3.4     3.8    -      -       -      -
     82H  GLY*     3.6    20.0    -      -       -      -
     83H  PRO*     3.6    14.5    -      -       +      +
     86H  ILE*     4.0     6.6    -      -       +      +
     88H  PHE*     4.1    18.6    -      +       -      -
    120H  VAL*     4.8     4.3    -      -       +      -
    124H  MET*     3.4    11.5    -      -       +      +
    125H  ALA*     2.5    42.5    +      -       -      -
    127H  GLY      3.5    16.2    -      -       -      -
    128H  LYS*     1.3    75.2    -      -       -      +
    130H  THR*     1.3    63.0    +      -       -      +
    148H  GLU*     3.3     8.7    -      -       -      +
    149H  PHE*     2.8    74.8    +      +       +      +
    151H  LYS*     4.0    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 130 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79H  SER      3.9     0.5    -      -       -      +
     80H  ILE*     3.5     3.4    -      -       -      -
     81H  LYS*     2.7    50.2    +      -       +      +
    128H  LYS      5.6     0.2    -      -       -      -
    129H  TYR*     1.3    75.3    +      -       -      +
    131H  VAL*     1.3    70.3    +      -       -      +
    132H  SER*     4.0     4.1    +      -       -      +
    146H  ASN*     3.8    27.4    -      -       +      +
    147H  GLN      3.6     8.1    -      -       -      +
    148H  GLU*     4.5    13.8    +      -       +      +
   1272H  O4B      4.1    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 131 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44H  LEU*     3.7    20.0    -      -       +      +
     46H  LEU*     4.3    13.7    -      -       +      -
     60H  SER*     5.7     0.2    -      -       -      -
     78H  LEU*     3.8    17.3    -      -       +      -
     79H  SER      3.6     2.5    -      -       -      -
     80H  ILE*     3.7    17.7    -      -       +      -
    118H  PHE*     3.6    22.0    -      -       +      -
    129H  TYR      4.1     0.2    -      -       -      -
    130H  THR*     1.3    73.9    -      -       -      +
    132H  SER*     1.3    62.1    +      -       -      +
    146H  ASN*     3.2     5.9    -      -       -      +
    147H  GLN      2.7    39.5    +      -       -      +
    149H  PHE*     3.3    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 132 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213G  ILE*     5.3     5.6    -      -       -      -
     78H  LEU*     3.7     4.1    -      -       -      -
     79H  SER*     2.8    39.6    +      -       -      -
    130H  THR*     5.0     4.5    -      -       -      -
    131H  VAL*     1.3    74.8    -      -       -      +
    133H  LEU*     1.3    61.5    +      -       -      +
    134H  GLN*     2.8    39.5    +      -       -      +
    144H  LYS*     4.4     2.6    -      -       -      +
    146H  ASN*     3.0    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 133 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42H  ALA*     4.2    15.3    -      -       +      -
     43H  ASN      3.2    28.9    -      -       -      +
     44H  LEU*     3.7     9.9    -      -       +      +
     62H  LEU*     4.0    25.8    -      -       +      -
     63H  GLY      3.9    13.0    -      -       -      +
     64H  ILE*     4.2     9.9    -      -       +      -
     76H  TYR*     3.9    23.1    -      -       +      -
     77H  TRP      3.8     9.9    -      -       -      +
     78H  LEU*     3.7    14.0    -      -       +      +
    132H  SER*     1.3    71.3    +      -       -      +
    134H  GLN*     1.3    69.3    +      -       -      +
    135H  VAL*     4.6     1.1    -      -       +      -
    144H  LYS*     3.2     7.6    -      -       -      +
    145H  ALA      2.8    40.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 134 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211G  GLY      3.0    23.9    +      -       -      -
    212G  LEU*     3.4    19.1    -      -       +      +
    213G  ILE*     2.9    33.0    +      -       -      +
     76H  TYR*     3.2     5.4    -      -       -      +
     77H  TRP*     3.0    60.9    +      -       +      +
     79H  SER*     5.0     1.3    -      -       -      -
    132H  SER*     2.8    39.3    +      -       -      +
    133H  LEU*     1.3    74.3    -      -       -      +
    135H  VAL*     1.3    64.0    +      -       -      +
    143H  PHE      3.6     3.8    -      -       -      -
    144H  LYS*     4.0    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 135 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40H  ILE*     4.2    20.4    -      -       +      -
     42H  ALA*     4.2    14.8    -      -       +      -
     64H  ILE*     3.9    31.4    -      -       +      -
     74H  PHE*     3.8    35.2    -      -       +      -
     75H  LYS      3.5     3.6    -      -       -      +
     76H  TYR*     4.1     0.7    -      -       +      -
    133H  LEU*     4.6     3.6    -      -       +      -
    134H  GLN*     1.3    78.1    -      -       -      +
    136H  VAL*     1.3    66.5    +      -       -      +
    137H  ALA      4.5     0.9    -      -       -      +
    141H  LYS      3.8     1.0    -      -       -      +
    142H  VAL*     3.5     5.8    -      -       -      +
    143H  PHE*     2.8    49.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 136 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212G  LEU*     4.0    27.6    -      -       +      -
    241G  SER*     4.0    28.9    +      -       -      +
    242G  TYR*     4.3    13.5    -      -       +      -
    243G  PRO*     4.9     0.7    -      -       +      -
     74H  PHE*     3.4     2.0    -      -       -      -
     75H  LYS*     2.7    44.1    +      -       +      +
     77H  TRP*     3.7    27.8    -      -       +      -
    135H  VAL*     1.3    75.5    -      -       -      +
    137H  ALA*     1.3    69.7    +      -       -      +
    140H  GLY      4.7     5.6    -      -       -      +
    141H  LYS      3.8     5.6    -      -       -      +
    142H  VAL*     4.4     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 137 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241G  SER*     3.9     6.0    -      -       -      -
     38H  PRO      5.4     2.0    -      -       -      +
     40H  ILE*     4.5     8.7    -      -       +      -
     72H  VAL*     4.7     7.9    -      -       +      -
     73H  LYS      4.2     4.3    -      -       -      +
     74H  PHE*     3.8    12.6    -      -       +      -
    135H  VAL*     4.0     1.8    -      -       -      +
    136H  VAL*     1.3    75.6    -      -       -      +
    138H  GLU*     1.3    56.4    +      -       -      +
    139H  ASN*     3.0    20.9    -      -       -      +
    140H  GLY*     2.8    27.9    +      -       -      -
    141H  LYS      3.1    14.5    +      -       -      +
    143H  PHE*     4.1    15.5    -      -       +      -
----------------------------------------------------------
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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