Contacts of the strand formed by residues 129 - 139 (chain L) 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 129 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145H  LYS*     4.8     8.1    -      -       +      +
    124L  GLN*     3.1    50.4    +      -       -      +
    125L  LEU*     3.6     9.0    +      -       -      +
    127L  SER*     3.3     9.1    +      -       -      -
    128L  GLY*     1.3    81.5    +      -       -      +
    130L  ALA*     1.3    65.0    +      -       -      +
    180L  THR*     3.7    24.5    -      -       +      -
    181L  LEU      3.6     4.5    -      -       -      +
    182L  SER*     4.6     0.7    -      -       -      +
    183L  LYS      4.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 130 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120L  PRO*     4.1     7.4    -      -       +      -
    124L  GLN*     3.9     1.8    -      -       -      -
    125L  LEU*     3.9    11.7    -      -       +      -
    129L  THR*     1.3    76.4    -      -       -      +
    131L  SER*     1.3    61.2    +      -       -      +
    132L  VAL*     4.0     2.0    +      -       -      +
    179L  LEU      3.5     1.7    -      -       -      +
    180L  THR*     3.5     1.2    -      -       -      -
    181L  LEU*     2.7    42.7    +      -       +      +
    183L  LYS*     4.6     1.3    -      -       -      -
    186L  TYR*     3.6    43.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 131 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  LEU*     6.0     1.0    -      -       -      +
    143H  LEU*     3.5    23.1    -      -       -      +
    145H  LYS*     3.4    22.9    -      -       -      -
    118L  PHE      4.2     0.2    -      -       -      +
    119L  PRO      4.1     0.5    -      -       -      -
    120L  PRO*     3.3    24.3    -      -       -      +
    124L  GLN*     3.0    28.3    +      -       -      +
    130L  ALA*     1.3    71.3    -      -       -      +
    132L  VAL*     1.3    62.4    +      -       -      +
    133L  VAL*     4.1     2.5    +      -       -      +
    178L  THR*     4.0     8.8    -      -       -      +
    179L  LEU      3.2     4.3    -      -       -      -
    180L  THR*     3.4     9.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 132 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117L  ILE*     4.1     3.8    -      -       +      -
    118L  PHE      3.4    15.7    -      -       -      +
    120L  PRO*     3.8    15.7    -      -       +      -
    130L  ALA      4.9     2.2    -      -       -      +
    131L  SER*     1.3    76.4    -      -       -      +
    133L  VAL*     1.3    60.4    +      -       -      +
    148L  TRP*     3.4    30.7    -      -       +      -
    178L  THR*     3.5     1.4    -      -       -      -
    179L  LEU*     2.7    49.8    +      -       +      +
    181L  LEU*     6.1     1.3    -      -       +      -
    186L  TYR*     4.3    17.3    -      -       +      -
    192L  TYR*     4.4    15.5    -      -       +      -
    209L  PHE*     3.7    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  LEU*     3.8    37.7    -      -       +      -
    143H  LEU*     4.4    19.5    -      -       +      -
    188H  SER*     5.3     2.0    -      -       -      +
    117L  ILE*     3.5     2.8    -      -       -      +
    118L  PHE*     2.7    54.2    +      -       +      -
    131L  SER      4.1     2.0    +      -       -      +
    132L  VAL*     1.3    75.0    -      -       -      +
    134L  CYS*     1.3    73.0    +      -       -      +
    135L  LEU*     5.1     2.5    -      -       +      -
    148L  TRP*     4.0     2.2    -      -       -      -
    176L  SER*     4.1    15.5    -      -       -      +
    177L  SER      3.5     3.8    -      -       -      +
    178L  THR*     3.6    19.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 134 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115L  VAL*     4.1    13.0    -      -       -      -
    116L  PHE      3.4     9.4    -      -       -      -
    117L  ILE*     4.6     2.0    -      -       +      +
    133L  VAL*     1.3    76.0    -      -       -      +
    135L  LEU*     1.3    62.7    +      -       -      +
    136L  LEU*     4.2     8.8    -      -       -      +
    148L  TRP*     3.4    19.0    -      -       +      -
    175L  LEU      3.8     0.5    -      -       -      +
    176L  SER*     3.5     4.2    -      -       -      -
    177L  SER*     2.8    41.3    +      -       -      +
    194L  CYS*     2.0    50.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139H  ALA*     4.0    16.4    -      -       +      -
    174H  PHE*     3.6    25.8    -      -       +      -
    190H  VAL*     4.1    27.4    -      -       +      -
    192H  THR*     5.3     0.9    -      -       +      -
    114L  SER      3.2     4.9    -      -       -      +
    115L  VAL*     3.3     3.6    -      -       -      +
    116L  PHE*     2.8    67.8    +      -       +      +
    118L  PHE*     4.1    13.2    -      -       +      -
    133L  VAL*     5.1     2.9    -      -       +      -
    134L  CYS*     1.3    73.6    -      -       -      +
    136L  LEU*     1.3    72.2    +      -       -      +
    137L  ASN*     4.4    13.0    -      -       +      +
    175L  LEU      3.5    14.4    -      -       -      +
    176L  SER*     4.8     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 136 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113L  PRO*     4.1     9.4    -      -       +      -
    114L  SER      3.3     4.5    -      -       -      -
    115L  VAL*     4.5     3.1    -      -       +      -
    134L  CYS*     4.2    11.7    -      -       -      -
    135L  LEU*     1.3    81.2    -      -       -      +
    137L  ASN*     1.3    60.3    +      -       -      +
    139L  PHE*     3.5    19.0    -      -       +      -
    144L  ALA*     3.9    20.2    -      -       +      -
    146L  VAL*     3.6    29.2    -      -       +      -
    174L  SER*     3.2     7.6    -      -       -      -
    175L  LEU*     2.8    50.4    +      -       +      +
    196L  VAL*     3.5    42.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 137 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172H  HIS*     3.2    16.9    -      -       -      -
    190H  VAL*     5.2     0.7    -      -       -      +
    192H  THR*     3.4    32.9    +      -       -      +
    113L  PRO*     3.5     1.2    -      -       -      +
    114L  SER*     2.8    45.6    +      -       -      +
    116L  PHE*     4.1    11.5    -      -       +      -
    135L  LEU*     4.4    12.4    -      -       +      +
    136L  LEU*     1.3    72.6    -      -       -      +
    138L  ASN*     1.3    93.4    +      -       -      +
    139L  PHE*     3.6     1.1    -      -       -      -
    174L  SER*     2.9    20.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 138 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172H  HIS*     3.3    25.5    +      -       -      -
    192H  THR*     5.6     0.6    +      -       -      -
    111L  ALA*     4.5     3.8    -      -       -      +
    112L  ALA      3.5    11.6    -      -       -      +
    114L  SER*     5.8     1.0    +      -       -      -
    137L  ASN*     1.3    96.1    +      -       -      +
    139L  PHE*     1.3    58.3    +      -       -      +
    167L  ASP*     5.9     0.7    -      -       -      -
    170L  ASP*     4.4    11.5    +      -       -      +
    172L  THR*     3.4    27.0    +      -       +      +
    173L  TYR      3.1     9.5    +      -       -      -
    174L  SER*     3.0     8.5    +      -       -      -
    229M  SO4      5.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 139 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111L  ALA      3.3    14.1    -      -       -      +
    113L  PRO*     3.6    33.4    -      -       +      -
    136L  LEU*     3.5    33.0    -      -       +      -
    138L  ASN*     1.3    74.6    -      -       -      +
    140L  TYR*     1.3    61.4    +      -       -      +
    141L  PRO      3.1    20.2    -      -       -      -
    142L  ARG*     3.1    30.3    -      -       -      -
    144L  ALA*     4.0    12.8    -      -       +      -
    163L  VAL*     5.1     2.0    -      -       +      -
    172L  THR*     3.1     9.2    -      -       -      -
    173L  TYR*     2.8    49.1    +      -       +      +
    174L  SER      4.2     2.9    -      -       -      -
    175L  LEU*     3.7    24.9    -      -       +      -
    198L  HIS*     3.6    11.2    -      +       -      +
----------------------------------------------------------
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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