Contacts of the strand formed by residues 137 - 147 (chain M) in PDB entry 3INU


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 137 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131M  THR*     3.3     1.0    -      -       -      -
    132M  SER*     2.7    47.7    +      -       -      +
    134M  GLY*     1.3    85.4    -      -       -      +
    138M  ALA*     1.3    58.2    +      -       -      +
    192M  THR*     4.6    13.4    -      -       -      +
    193M  VAL*     3.1    20.4    -      -       -      +
    194M  PRO*     4.3     5.2    -      -       +      -
    195M  SER*     3.4     5.5    +      -       -      -
    116N  PHE*     4.9     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 138 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126M  PRO*     5.5     0.4    -      -       +      -
    127M  SER      4.6     2.7    -      -       -      +
    130M  SER      2.7    19.5    -      -       -      +
    131M  THR*     3.7     7.4    -      -       -      +
    137M  THR*     1.3    71.4    -      -       -      +
    139M  ALA*     1.3    59.0    +      -       -      +
    191M  VAL      3.7     0.2    -      -       -      +
    192M  THR*     3.0     6.8    -      -       -      -
    193M  VAL*     2.4    50.4    +      -       -      +
    195M  SER*     4.1     1.1    -      -       -      +
    198M  LEU*     3.6    40.2    -      -       +      -
    116N  PHE*     5.2     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 139 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126M  PRO*     3.6    10.1    -      -       -      +
    130M  SER*     3.0    17.4    +      -       -      -
    138M  ALA*     1.3    76.0    -      -       -      +
    140M  LEU*     1.3    61.1    +      -       -      +
    190M  VAL*     5.6     0.7    -      -       +      -
    191M  VAL      3.5     7.0    -      -       -      +
    192M  THR*     4.5     7.0    -      -       +      -
    116N  PHE*     3.8    37.2    -      -       +      -
    118N  PHE*     3.4    18.7    -      -       +      -
    135N  LEU*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 140 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124M  LEU*     3.6     7.2    -      -       -      -
    126M  PRO*     3.4    25.6    -      -       +      -
    139M  ALA*     1.3    73.0    -      -       -      +
    141M  GLY*     1.3    58.8    +      -       -      +
    157M  TRP*     4.4     5.6    -      -       +      -
    190M  VAL*     3.3     6.1    -      -       -      +
    191M  VAL*     2.8    51.2    +      -       +      +
    193M  VAL*     3.2    31.4    -      -       +      -
    206M  TYR*     3.3    42.8    -      -       +      -
    225M  VAL*     3.4    21.3    -      -       +      +
    118N  PHE*     4.4     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 141 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124M  LEU*     2.6    47.8    +      -       -      +
    140M  LEU*     1.3    78.8    -      -       -      +
    142M  CYS*     1.3    57.7    +      -       -      -
    157M  TRP*     3.4    14.7    -      -       -      -
    189M  SER      3.0    13.7    -      -       -      -
    190M  VAL*     4.0     1.6    -      -       -      -
    225M  VAL*     3.1     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 142 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121M  VAL*     3.7    20.4    -      -       +      -
    122M  PHE      3.6     3.6    -      -       -      -
    124M  LEU*     3.8     2.9    -      -       -      +
    141M  GLY*     1.3    76.9    -      -       -      -
    143M  LEU*     1.3    61.1    +      -       -      +
    144M  VAL*     3.5     9.2    +      -       +      +
    157M  TRP*     3.7     2.8    -      -       +      -
    188M  SER*     3.2     4.5    -      -       -      -
    189M  SER*     2.7    37.6    +      -       -      +
    208M  CYS*     2.0    45.8    -      -       +      -
    221M  LYS*     4.2     9.2    -      -       -      -
    225M  VAL*     4.1    14.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 143 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120M  SER      3.4     4.9    -      -       -      +
    122M  PHE*     2.8    49.5    +      -       +      +
    123M  PRO      5.2     0.7    -      -       -      +
    124M  LEU*     3.9    16.2    -      -       +      +
    142M  CYS*     1.3    69.8    -      -       -      +
    144M  VAL*     1.3    60.1    +      -       -      +
    145M  LYS*     3.5    16.1    +      -       +      -
    186M  SER*     5.1     9.0    -      -       -      +
    187M  LEU      4.1     4.5    -      -       -      +
    188M  SER*     4.2    16.4    -      -       -      -
    124N  GLN*     4.1    15.9    -      -       -      +
    131N  SER*     3.8    29.2    -      -       -      +
    133N  VAL*     4.4    19.5    -      -       +      -
    178N  THR*     4.5    11.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119M  PRO*     3.5    26.2    -      -       +      -
    120M  SER      3.6     3.1    -      -       -      +
    121M  VAL*     4.5     5.2    -      -       +      +
    142M  CYS*     4.2    12.6    -      -       +      +
    143M  LEU*     1.3    73.2    -      -       -      +
    145M  LYS*     1.3    57.9    +      -       -      +
    147M  TYR*     4.0     8.5    -      -       +      -
    152M  VAL*     4.2    12.6    -      -       +      -
    154M  VAL*     4.5     3.6    -      -       +      -
    186M  SER*     3.4     3.3    +      -       -      -
    187M  LEU*     2.8    59.9    +      -       +      +
    210M  VAL*     3.5    42.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 145 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119M  PRO*     3.4     1.6    -      -       -      +
    120M  SER*     2.8    42.4    +      -       -      +
    122M  PHE*     4.2    17.9    -      -       +      -
    143M  LEU*     4.3    16.4    -      -       +      +
    144M  VAL*     1.3    76.6    -      -       -      +
    146M  ASP*     1.3    91.4    +      -       -      +
    147M  TYR*     3.6     2.0    -      -       -      -
    179M  GLN*     2.9    24.0    +      -       -      -
    186M  SER*     3.0    15.0    -      -       -      +
    124N  GLN*     4.1    11.9    -      -       -      +
    129N  THR*     4.7     8.0    -      -       +      +
    131N  SER*     3.2    28.0    -      -       -      +
    178N  THR*     5.5     2.0    -      -       -      -
    180N  THR*     4.0    17.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 146 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117M  LYS*     3.5    26.7    -      -       -      +
    118M  GLY      3.8     5.7    -      -       -      +
    120M  SER*     5.4     3.7    +      -       -      +
    145M  LYS*     1.3   103.2    +      -       -      +
    147M  TYR*     1.3    57.7    +      -       -      +
    179M  GLN*     2.9    19.2    +      -       -      -
    182M  SER*     4.0     5.5    +      -       -      -
    184M  LEU*     3.8    28.8    -      -       +      +
    185M  TYR      2.8    16.1    +      -       -      -
    186M  SER*     3.5     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 147 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117M  LYS      3.2    12.8    -      -       -      +
    119M  PRO*     3.6    29.8    -      -       +      -
    144M  VAL*     4.0    22.9    -      -       +      -
    146M  ASP*     1.3    77.7    -      -       -      +
    148M  PHE*     1.3    62.9    +      -       -      +
    149M  PRO      3.5    19.5    -      -       -      -
    150M  GLU*     4.3    13.4    +      -       -      -
    151M  PRO*     5.3     0.2    -      -       -      +
    152M  VAL*     3.8    22.9    +      -       +      +
    176M  ALA*     3.3    26.2    -      -       -      +
    184M  LEU*     3.8     2.4    -      -       -      -
    185M  TYR*     2.9    57.7    +      +       +      +
    186M  SER*     4.0     4.9    -      -       -      -
    187M  LEU*     3.7    15.5    -      -       +      +
    212M  HIS*     3.8     9.6    -      +       -      +
----------------------------------------------------------
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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