Contacts of the strand formed by residues 123 - 135 (chain I) in PDB entry 1FPY


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 THR 123 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112I  GLU*     4.9     4.3    -      -       -      +
    115I  LEU*     3.7     5.3    -      -       -      +
    116I  ARG*     4.7     7.0    -      -       -      +
    121I  ALA      3.7     1.0    -      -       -      -
    122I  ASP*     1.3    97.5    +      -       -      +
    124I  VAL*     1.3    65.3    +      -       -      +
    125I  LEU*     4.2    10.2    +      -       -      +
    227I  THR*     5.0    16.8    -      -       +      -
    274I  LEU*     3.5     5.0    -      -       -      +
    275I  ALA*     3.0    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 124 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112I  GLU*     4.0    20.0    +      -       +      +
    115I  LEU*     3.8    29.4    -      -       +      -
    123I  THR*     1.3    71.8    -      -       -      +
    125I  LEU*     1.3    78.3    +      -       -      +
    126I  PHE*     3.5    23.8    -      -       +      -
    227I  THR*     3.3     2.8    -      -       -      -
    228I  MET*     3.0    32.3    +      -       +      -
    272I  MET*     5.4     1.1    -      -       +      -
    273I  SER      4.3     2.5    -      -       -      +
    274I  LEU*     3.6    16.4    -      -       +      -
    297I  TYR*     4.3     5.8    -      -       +      +
    375I  LEU*     3.8    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 125 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123I  THR*     4.8     9.4    -      -       -      +
    124I  VAL*     1.3    90.5    -      -       -      +
    126I  PHE*     1.3    62.5    +      -       -      +
    225I  PHE*     3.5    29.4    -      -       +      -
    226I  ASN      3.9    11.2    -      -       -      +
    227I  THR*     4.0    10.3    -      -       +      +
    271I  HIS      4.1     0.2    -      -       -      -
    272I  MET*     3.0    33.1    -      -       -      +
    273I  SER*     2.9    34.0    +      -       -      +
    275I  ALA*     4.8    17.9    -      -       +      -
   4479I  ADP      4.0    16.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 126 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124I  VAL*     3.5    19.1    -      -       +      -
    125I  LEU*     1.3    79.4    -      -       -      +
    127I  GLY*     1.3    59.4    +      -       -      +
    128I  PRO*     3.8     2.2    -      -       +      -
    225I  PHE*     3.1    23.1    -      -       -      -
    226I  ASN      3.1    16.2    +      -       -      +
    228I  MET*     3.4    36.1    -      -       +      -
    231I  LYS*     3.5    21.5    -      -       +      +
    270I  CYS*     4.7     7.4    -      -       -      -
    271I  HIS      3.3     3.6    -      -       -      -
    272I  MET*     3.5    33.2    -      -       +      -
    371I  PHE*     3.3    60.8    -      +       +      -
    374I  LEU*     4.0     8.5    -      -       +      -
    375I  LEU*     4.4     3.6    -      -       +      -
   4479I  ADP      4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 127 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126I  PHE*     1.3    75.7    -      -       -      +
    128I  PRO*     1.3    63.2    -      -       -      +
    129I  GLU*     4.7     0.7    -      -       -      +
    225I  PHE*     3.9     9.6    -      -       -      -
    269I  HIS      3.7     1.6    -      -       -      +
    270I  CYS*     4.7     0.4    -      -       -      -
    271I  HIS*     2.9    43.5    +      -       -      +
   4479I  ADP      3.2    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 128 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126I  PHE*     4.5     1.1    -      -       +      -
    127I  GLY*     1.3    90.2    -      -       -      +
    129I  GLU*     1.3    62.2    +      -       -      +
    130I  PRO*     3.2    10.9    -      -       -      +
    222I  ALA*     5.6     0.3    -      -       -      -
    223I  THR*     4.3    12.0    +      -       -      +
    231I  LYS*     3.3    34.3    -      -       +      -
    235I  ILE*     4.2     7.4    -      -       +      -
    268I  MET*     3.8    28.3    -      -       +      -
    269I  HIS      3.1     7.9    -      -       -      +
    270I  CYS*     4.3     8.5    -      -       -      -
    371I  PHE*     3.6    26.9    -      -       +      -
   4479I  ADP      4.3     4.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 129 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127I  GLY      4.7     2.7    -      -       -      +
    128I  PRO*     1.3    73.6    -      -       +      +
    130I  PRO*     1.3    57.9    -      -       -      +
    131I  GLU*     3.4     3.7    +      -       -      +
    220I  GLU*     3.5    20.0    -      -       -      +
    222I  ALA*     5.8     3.1    -      -       +      +
    267I  GLY      2.8    25.8    -      -       -      +
    268I  MET*     3.2     7.5    -      -       -      -
    269I  HIS*     2.9    21.2    +      -       +      +
    271I  HIS*     3.4    13.3    +      -       -      -
    357I  GLU*     2.8     6.8    -      -       -      +
    470I   MN      1.9    33.7    +      -       -      -
   4479I  ADP      2.6    54.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 130 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128I  PRO      3.2    10.8    -      -       -      +
    129I  GLU*     1.3    80.8    -      -       -      +
    131I  GLU*     1.3    64.5    +      -       -      +
    132I  PHE*     3.9     1.2    -      -       -      -
    220I  GLU*     4.0     4.7    -      -       +      +
    221I  VAL      4.1    16.2    -      -       -      +
    223I  THR*     5.0     1.6    -      -       -      +
    235I  ILE*     3.9    15.7    -      -       +      -
    238I  TYR*     2.9    47.8    +      -       +      -
    239I  LYS*     6.2     0.9    -      -       +      -
    255I  PHE*     4.8     6.1    -      -       +      -
    267I  GLY      3.9     2.7    -      -       -      +
    268I  MET*     3.7    35.4    -      -       +      -
    363I  PRO*     4.7     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 131 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129I  GLU      4.4     0.9    -      -       -      +
    130I  PRO*     1.3    71.9    -      -       -      +
    132I  PHE*     1.3    64.5    +      -       -      +
    212I  GLU*     3.1    16.5    -      -       +      +
    218I  GLN*     4.8     2.9    -      -       -      +
    219I  ASN      3.8     5.4    -      -       -      +
    220I  GLU*     3.0    26.7    -      -       +      +
    255I  PHE*     3.4    15.4    -      -       -      -
    266I  SER*     3.7    16.3    -      -       -      -
    267I  GLY      3.0    28.1    +      -       -      +
    269I  HIS*     4.8     1.7    -      -       -      -
    363I  PRO*     3.5    11.3    -      -       -      +
    469I   MN      2.3    30.1    +      -       -      -
   5908I  PPQ      2.4    43.1    +      -       -      +
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Residues in contact with PHE 132 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130I  PRO      3.9     3.6    -      -       -      -
    131I  GLU*     1.3    79.3    -      -       -      +
    133I  PHE*     1.3    74.3    +      -       -      +
    134I  LEU*     3.9    17.5    -      -       +      -
    192I  ARG*     5.5     0.4    -      -       +      -
    195I  MET*     4.0    20.9    -      -       -      -
    218I  GLN*     3.2     6.4    -      -       -      +
    219I  ASN*     2.7    68.4    +      -       +      -
    220I  GLU*     4.2     2.2    -      -       -      -
    221I  VAL*     4.3     8.3    -      -       +      -
    238I  TYR*     3.5    19.3    -      -       -      -
    242I  VAL*     3.9    25.8    -      -       +      -
    253I  ALA*     4.8     0.2    -      -       +      -
    254I  THR      3.5    17.3    -      -       -      +
    255I  PHE*     3.7    26.2    -      +       +      -
    266I  SER*     4.0     6.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 133 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132I  PHE*     1.3    77.4    -      -       -      +
    134I  LEU*     1.3    65.3    +      -       -      +
    135I  PHE*     3.3    22.2    -      +       +      -
    214I  ALA*     3.6     9.9    -      -       +      -
    215I  THR      3.6     2.2    -      -       -      -
    216I  ALA      3.5    17.5    -      -       -      -
    217I  GLY      3.3     3.6    -      -       -      -
    218I  GLN*     3.4    31.6    -      -       +      -
    252I  THR      3.9     0.3    -      -       -      +
    253I  ALA*     3.3     6.8    -      -       -      +
    254I  THR*     3.2    32.9    +      -       +      -
    256I  MET      4.9     0.4    -      -       -      -
    259I  PRO*     3.3    27.1    -      -       +      -
    260I  MET*     3.1    30.1    -      -       +      -
    264I  ASN      3.4    21.8    -      -       -      -
    266I  SER*     3.3    24.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132I  PHE*     3.9    21.5    -      -       +      -
    133I  PHE*     1.3    75.2    -      -       -      +
    135I  PHE*     1.3    63.6    +      -       -      +
    153I  ASP*     3.1    22.6    -      -       -      +
    188I  ALA*     4.9     4.5    -      -       +      -
    191I  ILE*     4.4    27.6    -      -       +      -
    192I  ARG*     5.6     1.8    -      -       +      -
    195I  MET*     4.5     6.5    -      -       +      -
    216I  ALA      3.6     7.1    +      -       -      +
    217I  GLY*     2.8    17.5    +      -       -      +
    219I  ASN*     4.2    14.8    -      -       -      +
    246I  ALA*     3.8    17.5    -      -       +      -
    251I  LYS*     3.9    20.7    +      -       +      -
    252I  THR      3.8     1.3    -      -       -      +
    253I  ALA*     3.5    31.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 135 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462C  PHE*     6.3     0.2    -      +       -      -
    466C  TYR*     3.9    23.3    -      +       -      -
    133I  PHE*     3.3    28.3    -      +       +      -
    134I  LEU*     1.3    71.9    -      -       -      +
    136I  ASP*     1.3    61.1    +      -       -      +
    137I  ASP      4.1     6.3    -      -       -      +
    138I  ILE*     5.0     2.9    -      -       +      -
    151I  ILE*     3.6    32.5    -      -       +      -
    152I  ASP      3.4     8.5    -      -       -      +
    153I  ASP*     3.3    16.6    -      -       +      -
    216I  ALA*     3.2    32.3    -      -       +      -
    251I  LYS*     3.5    10.2    -      -       -      +
    252I  THR*     3.0    39.0    +      -       +      -
    254I  THR*     3.4    24.7    -      -       +      -
    259I  PRO*     4.2    16.4    -      -       +      -
    260I  MET*     4.2     3.1    -      -       +      -
----------------------------------------------------------
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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