Contacts of the strand formed by residues 123 - 135 (chain L) 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 L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112L  GLU*     4.9     4.7    -      -       -      +
    115L  LEU*     3.7     4.7    -      -       -      +
    116L  ARG*     4.7     7.6    -      -       -      +
    121L  ALA      3.7     1.4    -      -       -      -
    122L  ASP*     1.3    98.6    +      -       -      +
    124L  VAL*     1.3    65.8    +      -       -      +
    125L  LEU*     4.8    10.0    -      -       -      +
    227L  THR*     5.0    15.7    -      -       +      -
    274L  LEU*     3.5     5.4    -      -       -      +
    275L  ALA*     3.0    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 124 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112L  GLU*     4.0    19.5    +      -       +      +
    115L  LEU*     3.8    29.6    -      -       +      -
    123L  THR*     1.3    71.6    -      -       -      +
    125L  LEU*     1.3    76.1    +      -       -      +
    126L  PHE*     3.5    24.2    -      -       +      -
    227L  THR*     3.3     2.9    -      -       -      -
    228L  MET*     3.0    32.0    +      -       +      -
    272L  MET*     5.4     0.9    -      -       +      -
    273L  SER      4.3     2.9    -      -       -      +
    274L  LEU*     3.6    15.3    -      -       +      -
    297L  TYR*     4.3     5.6    -      -       +      +
    375L  LEU*     3.8    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 125 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123L  THR*     4.8     9.9    -      -       -      +
    124L  VAL*     1.3    90.2    -      -       -      +
    126L  PHE*     1.3    61.9    +      -       -      +
    225L  PHE*     3.5    30.7    -      -       +      -
    226L  ASN      3.9    10.5    -      -       -      +
    227L  THR*     4.0    11.0    -      -       +      +
    271L  HIS      4.1     0.4    -      -       -      -
    272L  MET*     3.0    32.9    -      -       -      +
    273L  SER*     2.9    35.3    +      -       -      +
    275L  ALA*     4.8    17.0    -      -       +      -
   4482L  ADP      4.0    14.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 126 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124L  VAL*     3.5    18.8    -      -       +      -
    125L  LEU*     1.3    78.1    -      -       -      +
    127L  GLY*     1.3    57.7    +      -       -      +
    128L  PRO*     3.8     2.7    -      -       +      -
    225L  PHE*     3.1    23.7    -      -       -      -
    226L  ASN      3.1    16.3    +      -       -      +
    228L  MET*     3.4    36.3    -      -       +      -
    231L  LYS*     3.5    22.0    -      -       +      +
    270L  CYS*     4.7     8.1    -      -       +      -
    271L  HIS      3.3     3.6    -      -       -      -
    272L  MET*     3.5    33.9    -      -       +      -
    371L  PHE*     3.3    61.2    -      +       +      -
    374L  LEU*     4.0     8.3    -      -       +      -
    375L  LEU*     4.4     3.6    -      -       +      -
   4482L  ADP      4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 127 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126L  PHE*     1.3    74.9    -      -       -      +
    128L  PRO*     1.3    64.4    -      -       -      +
    129L  GLU*     4.1     0.7    +      -       -      +
    225L  PHE*     3.9     9.0    -      -       -      -
    269L  HIS      3.7     1.2    -      -       -      +
    270L  CYS*     4.7     0.2    -      -       -      -
    271L  HIS*     2.9    44.2    +      -       -      +
   4482L  ADP      3.2    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 128 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126L  PHE*     4.5     1.8    -      -       +      -
    127L  GLY*     1.3    90.1    -      -       -      +
    129L  GLU*     1.3    62.6    +      -       -      +
    130L  PRO*     3.2    10.7    -      -       -      +
    222L  ALA*     5.6     0.2    -      -       -      -
    223L  THR*     4.3    12.6    +      -       -      +
    231L  LYS*     3.3    33.9    -      -       +      -
    235L  ILE*     4.1     8.2    -      -       +      +
    268L  MET*     3.8    27.8    -      -       +      -
    269L  HIS      3.1     8.3    -      -       -      +
    270L  CYS*     4.3     8.1    -      -       -      -
    371L  PHE*     3.6    26.7    -      -       +      -
   4482L  ADP      4.3     4.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 129 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127L  GLY      4.7     2.5    -      -       -      +
    128L  PRO*     1.3    73.2    -      -       +      +
    130L  PRO*     1.3    58.3    -      -       -      +
    131L  GLU*     3.4     3.3    +      -       -      +
    220L  GLU*     3.5    20.0    -      -       -      +
    222L  ALA*     5.8     3.4    -      -       +      +
    267L  GLY      2.8    25.8    -      -       -      +
    268L  MET*     3.2     8.0    -      -       -      +
    269L  HIS*     2.9    22.0    +      -       +      +
    271L  HIS*     3.4    13.7    +      -       -      -
    357L  GLU*     2.8     6.6    -      -       -      +
    470L   MN      1.9    33.3    +      -       -      -
   4482L  ADP      2.6    55.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 130 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128L  PRO      3.2    11.2    -      -       -      +
    129L  GLU*     1.3    80.5    -      -       -      +
    131L  GLU*     1.3    64.4    +      -       -      +
    132L  PHE*     3.9     1.4    -      -       -      -
    220L  GLU*     4.0     4.8    -      -       +      +
    221L  VAL      4.1    15.5    -      -       -      +
    222L  ALA*     5.7     0.2    -      -       -      -
    223L  THR*     5.0     1.8    -      -       -      +
    235L  ILE*     3.9    15.5    -      -       +      -
    238L  TYR*     2.9    47.0    +      -       +      -
    239L  LYS*     6.2     0.9    -      -       +      -
    255L  PHE*     4.8     6.3    -      -       +      -
    267L  GLY      3.9     2.5    -      -       -      +
    268L  MET*     3.7    35.9    -      -       +      -
    363L  PRO*     4.7     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 131 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129L  GLU*     4.4     0.9    -      -       -      +
    130L  PRO*     1.3    72.8    -      -       -      +
    132L  PHE*     1.3    65.0    +      -       -      +
    212L  GLU*     3.1    16.5    -      -       +      +
    218L  GLN*     4.6     3.3    -      -       -      +
    219L  ASN      3.8     5.6    -      -       -      +
    220L  GLU*     3.0    25.8    -      -       +      +
    255L  PHE*     3.4    15.1    -      -       -      -
    266L  SER*     3.7    16.0    -      -       -      -
    267L  GLY      3.0    28.4    +      -       -      +
    269L  HIS*     4.8     1.5    -      -       -      -
    363L  PRO*     3.5    11.7    -      -       -      +
    469L   MN      2.3    30.2    +      -       -      -
   5911L  PPQ      2.4    43.3    +      -       -      +
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Residues in contact with PHE 132 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130L  PRO      3.9     3.8    -      -       -      -
    131L  GLU*     1.3    79.3    -      -       -      +
    133L  PHE*     1.3    76.6    +      -       -      +
    134L  LEU*     3.9    17.7    -      -       +      -
    192L  ARG*     5.5     0.4    -      -       +      -
    195L  MET*     4.0    21.1    -      -       -      -
    218L  GLN*     3.2     5.4    -      -       -      +
    219L  ASN*     2.7    67.2    +      -       +      -
    220L  GLU*     4.2     2.5    -      -       -      -
    221L  VAL*     4.3     8.1    -      -       +      -
    238L  TYR*     3.5    19.1    -      -       -      -
    242L  VAL*     3.9    24.9    -      -       +      -
    254L  THR      3.5    16.2    -      -       -      +
    255L  PHE*     3.7    25.8    -      +       +      -
    266L  SER*     4.0     6.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 133 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132L  PHE*     1.3    77.8    -      -       -      +
    134L  LEU*     1.3    64.5    +      -       -      +
    135L  PHE*     3.3    21.5    -      +       +      -
    214L  ALA*     3.6     9.0    -      -       +      -
    215L  THR      3.6     2.9    -      -       -      -
    216L  ALA      3.5    17.3    -      -       -      -
    217L  GLY      3.3     4.7    -      -       -      -
    218L  GLN*     3.4    32.3    -      -       +      -
    252L  THR      3.9     0.2    -      -       -      +
    253L  ALA*     3.3     6.8    -      -       -      +
    254L  THR*     3.2    31.8    +      -       +      +
    256L  MET      4.9     0.9    -      -       -      -
    259L  PRO*     3.3    27.1    -      -       +      -
    260L  MET*     3.1    31.9    -      -       +      -
    264L  ASN      3.4    21.8    -      -       -      -
    266L  SER*     3.3    25.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132L  PHE*     3.9    21.3    -      -       +      -
    133L  PHE*     1.3    75.9    -      -       -      +
    135L  PHE*     1.3    63.6    +      -       -      +
    153L  ASP*     3.1    22.6    -      -       -      +
    188L  ALA*     4.9     4.5    -      -       +      -
    191L  ILE*     4.4    27.6    -      -       +      -
    192L  ARG*     5.6     1.8    -      -       +      -
    195L  MET*     4.5     6.7    -      -       +      -
    216L  ALA      3.6     6.9    -      -       -      +
    217L  GLY*     2.8    17.3    +      -       -      +
    219L  ASN*     4.2    15.0    -      -       -      +
    246L  ALA*     3.8    17.5    -      -       +      -
    251L  LYS*     4.0    21.0    +      -       +      -
    252L  THR      3.8     1.3    -      -       -      +
    253L  ALA*     3.5    31.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 135 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462F  PHE*     6.3     0.2    -      +       -      -
    466F  TYR*     3.9    24.2    -      +       -      -
    133L  PHE*     3.3    29.4    -      +       +      -
    134L  LEU*     1.3    72.5    -      -       -      +
    136L  ASP*     1.3    61.7    +      -       -      +
    137L  ASP      4.1     6.3    -      -       -      +
    138L  ILE*     5.0     3.6    -      -       +      -
    151L  ILE*     3.6    31.0    -      -       +      -
    152L  ASP      3.4     8.1    -      -       -      +
    153L  ASP*     3.3    16.2    -      -       +      -
    216L  ALA*     3.2    32.3    -      -       +      -
    251L  LYS*     3.4     9.5    -      -       -      +
    252L  THR*     3.0    39.2    +      -       +      -
    254L  THR*     3.4    24.9    -      -       +      -
    259L  PRO*     4.2    16.6    -      -       +      -
    260L  MET*     4.2     3.8    -      -       +      -
----------------------------------------------------------
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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