Contacts of the strand formed by residues 123 - 135 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112B  GLU*     5.1     3.4    -      -       -      +
    115B  LEU*     3.9     4.7    -      -       -      +
    116B  ARG*     5.0     4.9    -      -       -      +
    121B  ALA      3.8     0.4    -      -       -      -
    122B  ASP*     1.3    97.9    +      -       +      +
    124B  VAL*     1.3    61.9    +      -       -      +
    125B  LEU*     4.6    13.7    -      -       -      +
    227B  THR*     4.7    15.3    -      -       +      -
    274B  LEU*     3.7     6.1    -      -       -      +
    275B  ALA*     3.1    39.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112B  GLU*     3.4    23.7    +      -       +      +
    115B  LEU*     3.7    20.6    -      -       +      -
    123B  THR*     1.3    73.7    -      -       -      +
    125B  LEU*     1.3    64.6    +      -       -      +
    126B  PHE*     3.9    14.6    -      -       +      -
    227B  THR*     3.2     8.1    -      -       -      -
    228B  MET*     3.0    32.2    +      -       +      -
    272B  MET*     6.0     1.1    -      -       +      -
    273B  SER      3.9     3.8    -      -       -      +
    274B  LEU*     3.3    21.1    -      -       +      -
    297B  TYR*     4.7     3.4    -      -       -      +
    375B  LEU*     3.7    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  THR*     4.2     9.8    +      -       -      +
    124B  VAL*     1.3    84.5    -      -       -      +
    126B  PHE*     1.3    65.8    +      -       -      +
    225B  PHE*     3.6    33.9    -      -       +      -
    226B  ASN      3.7     1.8    -      -       -      +
    227B  THR*     4.2    22.2    -      -       +      +
    271B  HIS      4.4     0.2    -      -       -      -
    272B  MET*     3.2    25.6    -      -       -      +
    273B  SER*     2.9    35.1    +      -       -      +
    275B  ALA*     5.0    14.6    -      -       +      -
   1472B  ADP      4.1    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  VAL*     3.9    17.5    -      -       +      -
    125B  LEU*     1.3    79.5    -      -       -      +
    127B  GLY*     1.3    59.3    +      -       -      +
    128B  PRO*     3.9     2.0    -      -       +      -
    225B  PHE*     3.1     5.4    -      -       -      -
    226B  ASN      2.9    36.5    +      -       -      +
    228B  MET*     3.5    36.1    -      -       +      -
    231B  LYS*     3.4    20.9    -      -       +      +
    270B  CYS*     4.7     7.2    -      -       +      -
    271B  HIS      3.5     2.2    -      -       -      -
    272B  MET*     3.5    35.7    -      -       +      -
    297B  TYR*     4.8     0.2    -      -       -      -
    371B  PHE*     3.3    60.6    -      +       +      -
    374B  LEU*     4.1     8.3    -      -       +      -
    375B  LEU*     4.6     3.4    -      -       +      -
   1472B  ADP      4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  PHE*     1.3    76.4    -      -       -      +
    128B  PRO*     1.3    66.2    -      -       -      +
    225B  PHE*     3.9     3.8    -      -       -      -
    269B  HIS      3.7     0.3    -      -       -      +
    270B  CYS*     4.6     0.4    -      -       -      -
    271B  HIS*     2.9    47.9    +      -       -      -
   1472B  ADP      3.9    27.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  PHE*     5.1     0.2    -      -       +      -
    127B  GLY*     1.3    88.4    -      -       -      +
    129B  GLU*     1.3    60.3    +      -       -      +
    130B  PRO*     3.2     8.5    -      -       -      +
    222B  ALA*     5.9     0.7    -      -       -      -
    223B  THR*     4.7     9.9    +      -       -      +
    231B  LYS*     3.3    29.4    -      -       +      -
    235B  ILE*     3.9    16.2    -      -       +      -
    268B  MET*     3.8    26.5    -      -       +      -
    269B  HIS      3.1     8.7    -      -       -      +
    270B  CYS*     4.4     5.2    -      -       -      -
    371B  PHE*     3.4    30.3    -      -       +      -
   1472B  ADP      4.4     5.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  PRO*     1.3    76.1    -      -       -      +
    130B  PRO*     1.3    62.2    -      -       -      +
    131B  GLU*     3.5     5.1    +      -       -      +
    220B  GLU*     3.6    10.2    -      -       -      +
    221B  VAL      5.9     0.7    -      -       -      -
    222B  ALA*     5.9     4.0    -      -       +      +
    267B  GLY      3.2    13.7    -      -       -      +
    268B  MET*     3.4     6.7    -      -       -      +
    269B  HIS*     2.7    29.7    +      -       +      +
    271B  HIS*     3.1    16.5    +      -       +      -
    357B  GLU*     2.5    10.6    -      -       -      +
    470B   MN      2.0    36.6    +      -       -      -
   1472B  ADP      2.6    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  PRO*     3.2    19.1    -      -       +      +
    129B  GLU*     1.3    83.7    -      -       -      +
    131B  GLU*     1.3    60.0    +      -       -      +
    132B  PHE*     4.3     0.2    -      -       -      -
    220B  GLU*     3.7     8.3    -      -       -      +
    221B  VAL      4.9     3.8    -      -       -      +
    223B  THR*     5.4     2.9    -      -       -      +
    235B  ILE*     3.8    18.2    -      -       +      -
    238B  TYR*     2.9    57.6    +      -       +      +
    239B  LYS*     6.5     0.2    -      -       +      -
    255B  PHE*     4.8     3.6    -      -       +      -
    267B  GLY      3.7     5.8    -      -       -      +
    268B  MET*     3.8    21.7    -      -       +      -
    363B  PRO*     4.4    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129B  GLU      4.2     3.1    -      -       -      +
    130B  PRO*     1.3    73.7    -      -       -      +
    132B  PHE*     1.3    64.2    +      -       -      +
    212B  GLU*     2.9    18.0    -      -       +      +
    218B  GLN*     4.5     3.6    -      -       -      +
    219B  ASN      3.8     4.9    -      -       -      +
    220B  GLU*     3.3    22.0    -      -       +      +
    255B  PHE*     3.5     6.5    -      -       -      -
    266B  SER*     3.5    16.2    -      -       -      +
    267B  GLY*     2.9    28.3    +      -       -      +
    269B  HIS*     5.7     3.3    +      -       -      -
    363B  PRO*     3.4    18.9    -      -       -      +
    469B   MN      2.0    35.1    +      -       -      -
    474B   TL      2.7    30.5    -      -       -      -
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Residues in contact with PHE 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130B  PRO      4.3     0.2    -      -       -      -
    131B  GLU*     1.3    79.5    -      -       -      +
    133B  PHE*     1.3    66.3    +      -       -      +
    134B  LEU*     3.9    24.7    -      -       +      -
    192B  ARG*     5.4     1.1    -      -       +      -
    195B  MET*     3.8    24.2    -      -       +      -
    218B  GLN*     3.2     7.1    -      -       -      +
    219B  ASN*     2.8    65.9    +      -       +      -
    220B  GLU*     4.0     6.3    -      -       -      -
    221B  VAL*     4.2     7.9    -      -       +      -
    238B  TYR*     3.6    23.6    -      +       -      -
    242B  VAL*     3.8    27.6    -      -       +      -
    254B  THR      3.4    16.4    -      -       -      +
    255B  PHE*     3.6    23.1    -      +       +      -
    266B  SER*     3.8     5.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  PHE*     1.3    76.5    -      -       -      +
    134B  LEU*     1.3    63.4    +      -       -      +
    135B  PHE*     3.7    23.6    -      +       +      -
    214B  ALA*     3.5    14.8    -      -       +      -
    215B  THR      3.7     3.4    -      -       -      -
    216B  ALA      3.7    12.1    -      -       -      -
    217B  GLY      3.3     2.9    -      -       -      -
    218B  GLN*     3.5    32.1    -      -       +      -
    252B  THR      3.8     0.7    -      -       -      +
    253B  ALA*     3.2     8.0    -      -       -      +
    254B  THR*     3.0    38.3    +      -       +      +
    256B  MET      4.8     2.7    -      -       -      -
    259B  PRO*     3.5    28.9    -      -       +      -
    260B  MET*     3.4    23.6    -      -       +      -
    264B  ASN      3.5    21.1    -      -       -      -
    266B  SER*     3.4    27.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  PHE*     3.9    20.0    -      -       +      -
    133B  PHE*     1.3    73.2    -      -       -      +
    135B  PHE*     1.3    61.2    +      -       -      +
    153B  ASP*     3.4    13.3    -      -       -      +
    188B  ALA*     4.5    10.1    -      -       +      -
    191B  ILE*     4.0    30.1    -      -       +      -
    192B  ARG*     5.7     1.6    -      -       +      -
    195B  MET*     4.1     8.7    -      -       +      -
    216B  ALA      3.5    13.5    -      -       -      +
    217B  GLY*     2.8    17.1    +      -       -      +
    219B  ASN*     3.9    18.2    -      -       -      +
    246B  ALA*     3.8    17.3    -      -       +      -
    251B  LYS*     4.0    15.8    +      -       +      -
    252B  THR      3.6     2.2    -      -       -      +
    253B  ALA*     3.6    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  PHE*     3.7    25.8    -      +       +      -
    134B  LEU*     1.3    72.8    -      -       -      +
    136B  ASP*     1.3    60.5    +      -       -      +
    137B  ASP      4.2     4.5    -      -       -      +
    138B  ILE*     4.8     5.4    -      -       +      -
    151B  ILE*     3.6    39.9    -      -       +      -
    152B  ASP      3.6     7.6    -      -       -      +
    153B  ASP*     3.4    14.4    -      -       +      -
    216B  ALA*     3.1    33.0    -      -       +      -
    251B  LYS*     3.3     9.7    -      -       -      +
    252B  THR*     2.9    40.3    +      -       +      +
    254B  THR*     3.9    20.9    -      -       +      -
    259B  PRO*     4.2    15.5    -      -       +      -
    260B  MET*     4.6     2.5    -      -       +      -
    462H  PHE*     5.9     0.2    -      +       -      -
    466H  TYR*     3.9    23.1    -      +       -      -
----------------------------------------------------------
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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