Contacts of the strand formed by residues 123 - 135 (chain H) in PDB entry 1F1H


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 H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112H  GLU*     5.1     3.4    -      -       -      +
    115H  LEU*     3.9     3.9    -      -       -      +
    116H  ARG*     5.0     4.7    -      -       -      +
    121H  ALA      3.8     0.6    -      -       -      -
    122H  ASP*     1.3    98.5    +      -       +      +
    124H  VAL*     1.3    62.8    +      -       -      +
    125H  LEU*     4.2    13.7    +      -       -      +
    227H  THR*     4.7    15.3    -      -       +      -
    274H  LEU*     3.7     5.9    -      -       -      +
    275H  ALA*     3.1    40.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 124 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112H  GLU*     3.4    24.1    +      -       +      +
    115H  LEU*     3.7    19.7    -      -       +      -
    123H  THR*     1.3    73.6    -      -       -      +
    125H  LEU*     1.3    65.0    +      -       -      +
    126H  PHE*     3.9    14.8    -      -       +      -
    227H  THR*     3.2     8.3    -      -       -      -
    228H  MET*     3.0    31.2    +      -       +      -
    272H  MET*     6.0     1.1    -      -       +      -
    273H  SER      3.9     2.9    -      -       -      +
    274H  LEU*     3.3    21.3    -      -       +      -
    297H  TYR*     4.7     3.6    -      -       +      +
    375H  LEU*     3.7    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 125 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123H  THR*     4.2     8.9    -      -       -      +
    124H  VAL*     1.3    85.5    -      -       -      +
    126H  PHE*     1.3    65.2    +      -       -      +
    225H  PHE*     3.6    33.2    -      -       +      -
    226H  ASN      3.7     1.6    -      -       -      +
    227H  THR*     4.2    21.8    -      -       +      +
    271H  HIS      4.4     0.4    -      -       -      -
    272H  MET*     3.2    25.8    -      -       -      +
    273H  SER*     2.9    35.9    +      -       -      +
    275H  ALA*     5.0    14.6    -      -       +      -
   1478H  ADP      4.1    13.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 126 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  VAL*     3.9    17.5    -      -       +      -
    125H  LEU*     1.3    78.6    -      -       -      +
    127H  GLY*     1.3    59.3    +      -       -      +
    128H  PRO*     3.9     1.8    -      -       +      -
    225H  PHE*     3.1     6.1    -      -       -      -
    226H  ASN      2.9    37.6    +      -       -      +
    228H  MET*     3.5    36.3    -      -       +      -
    231H  LYS*     3.4    21.2    -      -       +      +
    270H  CYS*     4.7     6.7    -      -       +      -
    271H  HIS      3.5     2.2    -      -       -      -
    272H  MET*     3.5    35.7    -      -       +      -
    297H  TYR*     4.8     0.2    -      -       -      -
    371H  PHE*     3.3    59.7    -      +       +      -
    374H  LEU*     4.1     8.7    -      -       +      -
    375H  LEU*     4.6     2.9    -      -       +      -
   1478H  ADP      4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 127 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  PHE*     1.3    75.1    -      -       -      +
    128H  PRO*     1.3    67.4    -      -       -      +
    225H  PHE*     3.9     2.9    -      -       -      -
    269H  HIS      3.7     0.5    -      -       -      +
    270H  CYS*     4.6     0.4    -      -       -      -
    271H  HIS*     2.9    46.9    +      -       -      -
   1478H  ADP      3.9    28.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 128 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  PHE*     4.8     0.9    -      -       +      -
    127H  GLY*     1.3    88.4    -      -       -      +
    129H  GLU*     1.3    60.4    +      -       -      +
    130H  PRO*     3.2     9.4    -      -       -      +
    222H  ALA*     5.9     0.2    -      -       -      -
    223H  THR*     4.7    10.0    +      -       -      +
    231H  LYS*     3.3    29.2    -      -       +      -
    235H  ILE*     3.9    16.8    -      -       +      -
    268H  MET*     3.8    26.2    -      -       +      -
    269H  HIS      3.1     8.7    -      -       -      +
    270H  CYS*     4.4     5.4    -      -       -      -
    371H  PHE*     3.4    30.1    -      -       +      -
   1478H  ADP      4.4     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 129 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  PRO*     1.3    75.6    -      -       -      +
    130H  PRO*     1.3    62.7    -      -       -      +
    131H  GLU*     3.5     5.2    +      -       -      +
    220H  GLU*     3.6    10.4    -      -       -      +
    221H  VAL      5.9     0.2    -      -       -      -
    222H  ALA*     5.9     4.3    -      -       +      +
    267H  GLY      3.2    14.4    -      -       -      +
    268H  MET*     3.4     7.0    -      -       -      +
    269H  HIS*     2.7    29.7    +      -       +      +
    271H  HIS*     3.1    16.3    +      -       +      -
    357H  GLU*     2.5     9.9    -      -       -      +
    470H   MN      2.0    37.2    +      -       -      -
   1478H  ADP      2.6    61.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 130 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  PRO*     3.2    17.7    -      -       +      +
    129H  GLU*     1.3    83.5    -      -       -      +
    131H  GLU*     1.3    61.1    +      -       -      +
    132H  PHE*     4.3     0.2    -      -       -      -
    220H  GLU*     3.7     8.0    -      -       -      +
    221H  VAL      4.9     3.6    -      -       -      +
    222H  ALA*     6.2     0.2    -      -       -      -
    223H  THR*     5.4     3.1    -      -       -      +
    235H  ILE*     3.8    17.7    -      -       +      -
    238H  TYR*     2.9    58.5    +      -       +      -
    239H  LYS*     6.5     0.2    -      -       +      -
    255H  PHE*     4.8     3.8    -      -       +      -
    267H  GLY      3.7     4.9    -      -       -      +
    268H  MET*     3.8    21.8    -      -       +      -
    363H  PRO*     4.4    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 131 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  GLU      4.2     2.7    -      -       -      +
    130H  PRO*     1.3    73.9    -      -       -      +
    132H  PHE*     1.3    64.9    +      -       -      +
    212H  GLU*     2.9    19.2    -      -       +      +
    218H  GLN*     4.5     3.8    -      -       -      +
    219H  ASN      3.8     5.6    -      -       -      +
    220H  GLU*     3.3    22.2    -      -       +      +
    255H  PHE*     3.5     6.1    -      -       -      -
    266H  SER*     3.5    16.8    -      -       -      +
    267H  GLY*     2.9    27.2    +      -       -      +
    269H  HIS*     5.7     3.8    +      -       -      -
    363H  PRO*     3.4    18.8    -      -       -      +
    469H   MN      2.0    34.3    +      -       -      -
    474H   TL      2.7    30.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 132 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130H  PRO      4.3     0.4    -      -       -      -
    131H  GLU*     1.3    79.7    -      -       -      +
    133H  PHE*     1.3    65.4    +      -       -      +
    134H  LEU*     3.9    25.1    -      -       +      -
    192H  ARG*     5.4     1.3    -      -       +      -
    195H  MET*     3.8    23.3    -      -       +      -
    218H  GLN*     3.2     7.6    -      -       -      +
    219H  ASN*     2.8    65.7    +      -       +      -
    220H  GLU*     4.0     6.5    -      -       -      -
    221H  VAL*     4.2     7.6    -      -       +      -
    238H  TYR*     3.6    24.2    -      +       -      -
    242H  VAL*     3.8    26.9    -      -       +      -
    253H  ALA*     4.7     0.2    -      -       +      -
    254H  THR      3.4    15.3    -      -       -      +
    255H  PHE*     3.6    22.9    -      +       +      -
    266H  SER*     3.8     4.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 133 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132H  PHE*     1.3    75.4    -      -       -      +
    134H  LEU*     1.3    62.4    +      -       -      +
    135H  PHE*     3.7    23.3    -      +       +      -
    214H  ALA*     3.5    15.3    -      -       +      -
    215H  THR      3.7     4.0    -      -       -      -
    216H  ALA      3.7    11.7    -      -       -      -
    217H  GLY      3.3     3.4    -      -       -      -
    218H  GLN*     3.5    32.3    -      -       +      -
    252H  THR      3.8     0.9    -      -       -      +
    253H  ALA*     3.2     7.8    -      -       -      +
    254H  THR*     3.0    38.8    +      -       +      +
    256H  MET      4.8     2.5    -      -       -      -
    259H  PRO*     3.5    27.4    -      -       +      -
    260H  MET*     3.4    23.8    -      -       +      -
    264H  ASN      3.5    21.5    -      -       -      -
    266H  SER*     3.4    27.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132H  PHE*     3.9    20.2    -      -       +      -
    133H  PHE*     1.3    74.2    -      -       -      +
    135H  PHE*     1.3    61.8    +      -       -      +
    153H  ASP*     3.4    12.9    -      -       -      +
    188H  ALA*     4.6    10.3    -      -       +      -
    191H  ILE*     4.0    30.5    -      -       +      -
    192H  ARG*     5.7     1.3    -      -       +      -
    195H  MET*     4.1     8.3    -      -       +      -
    216H  ALA      3.5    13.3    -      -       -      +
    217H  GLY*     2.8    16.3    +      -       -      +
    219H  ASN*     3.9    17.5    -      -       -      +
    246H  ALA*     3.8    17.7    -      -       +      -
    251H  LYS*     4.0    15.6    +      -       +      -
    252H  THR      3.6     1.6    -      -       -      +
    253H  ALA*     3.6    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 135 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462B  PHE*     5.9     0.2    -      +       -      -
    466B  TYR*     3.8    23.8    -      +       -      -
    133H  PHE*     3.7    25.6    -      +       +      -
    134H  LEU*     1.3    72.8    -      -       -      +
    136H  ASP*     1.3    61.0    +      -       -      +
    137H  ASP      4.2     4.9    -      -       -      +
    138H  ILE*     4.8     5.2    -      -       +      -
    151H  ILE*     3.6    40.8    -      -       +      -
    152H  ASP      3.6     6.7    -      -       -      +
    153H  ASP*     3.4    14.4    -      -       +      -
    216H  ALA*     3.1    32.8    -      -       +      -
    251H  LYS*     3.3     9.9    -      -       -      +
    252H  THR*     2.9    40.9    +      -       +      -
    254H  THR*     3.9    20.6    -      -       +      -
    259H  PRO*     4.2    15.9    -      -       +      -
    260H  MET*     4.6     2.9    -      -       +      -
----------------------------------------------------------
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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