Contacts of the strand formed by residues 133 - 143 (chain L) in PDB entry 3KDM


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 133 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152H  LYS*     4.3    12.1    -      -       -      -
    128L  GLN*     3.1    41.0    -      -       -      +
    129L  LEU*     3.8     7.2    -      -       -      +
    131L  SER*     3.3    11.0    +      -       -      -
    132L  GLY*     1.3    82.4    +      -       -      +
    134L  ALA*     1.3    69.8    +      -       -      +
    184L  THR*     4.1    17.9    -      -       +      +
    185L  LEU      3.5    10.6    +      -       -      +
    186L  SER*     5.0     1.6    -      -       -      -
    187L  LYS*     3.9     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 134 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124L  PRO*     3.8     9.6    -      -       +      -
    128L  GLN*     4.1     0.4    -      -       -      -
    129L  LEU*     3.3    25.1    -      -       +      -
    133L  THR*     1.3    76.4    -      -       -      +
    135L  SER*     1.3    61.0    +      -       -      +
    136L  VAL*     5.0     1.3    -      -       +      +
    183L  LEU      3.5     1.2    -      -       -      +
    184L  THR*     3.5     4.5    -      -       -      -
    185L  LEU*     2.5    41.8    +      -       +      +
    186L  SER      4.6     0.2    -      -       -      +
    187L  LYS      4.2     0.6    -      -       -      +
    190L  TYR*     3.8    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 135 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  LEU*     5.7     1.7    -      -       -      +
    150H  LEU*     3.4    30.8    -      -       -      +
    152H  LYS*     3.7    12.8    -      -       -      +
    123L  PRO      3.9     1.4    -      -       -      +
    124L  PRO*     3.1    24.5    -      -       -      +
    128L  GLN*     2.9    29.3    +      -       -      +
    133L  THR*     4.6     0.7    -      -       -      +
    134L  ALA*     1.3    72.8    +      -       -      +
    136L  VAL*     1.3    62.0    +      -       -      +
    137L  VAL*     4.1     3.8    +      -       -      +
    182L  THR*     4.3    13.2    -      -       -      +
    183L  LEU      3.3     6.3    -      -       -      -
    184L  THR*     4.8     3.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 136 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121L  ILE*     4.1     2.5    -      -       +      -
    122L  PHE      3.5    16.6    -      -       -      +
    124L  PRO*     3.8    16.8    -      -       +      -
    134L  ALA      5.0     1.6    -      -       -      -
    135L  SER*     1.3    77.2    -      -       -      +
    137L  VAL*     1.3    61.8    +      -       -      +
    152L  TRP*     3.6    29.4    -      -       +      -
    182L  THR*     3.5     2.1    -      -       -      +
    183L  LEU*     2.7    49.3    +      -       +      +
    185L  LEU*     5.5     2.5    -      -       +      -
    190L  TYR*     4.2    17.5    -      -       +      -
    196L  TYR*     4.4    13.7    -      -       +      -
    213L  PHE*     3.8    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 137 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133H  LEU*     3.9    31.6    -      -       +      -
    150H  LEU*     4.9     6.3    -      -       +      -
    188H  SER*     4.2    20.6    -      -       -      +
    190H  VAL*     5.9     2.0    -      -       +      -
    121L  ILE*     3.5     4.5    -      -       -      +
    122L  PHE*     2.8    46.5    +      -       +      -
    135L  SER*     4.1     4.9    -      -       -      -
    136L  VAL*     1.3    79.4    -      -       -      +
    138L  CYS*     1.3    72.2    +      -       -      +
    139L  LEU*     4.7     2.5    -      -       +      +
    152L  TRP*     3.8     2.2    -      -       -      -
    180L  SER*     4.8     8.5    -      -       -      -
    181L  SER      3.4     6.3    -      -       -      +
    182L  THR*     3.8    23.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 138 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119L  VAL*     4.0    13.7    -      -       -      -
    120L  PHE      3.3    10.8    -      -       -      -
    121L  ILE*     4.6     0.4    -      -       +      +
    137L  VAL*     1.3    76.1    -      -       -      +
    139L  LEU*     1.3    61.3    +      -       -      +
    140L  LEU*     4.1    10.1    +      -       -      +
    152L  TRP*     3.5    16.8    -      -       +      -
    179L  LEU      3.7     0.9    -      -       -      +
    180L  SER*     3.4     5.2    -      -       -      -
    181L  SER*     2.7    43.2    +      -       -      +
    198L  CYS*     2.0    52.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 139 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146H  ALA*     3.8    28.0    -      -       +      -
    175H  PHE*     3.6    32.1    -      -       +      -
    190H  VAL*     3.7    31.9    -      -       +      -
    192H  THR*     5.0     1.6    -      -       +      -
    118L  SER      3.6     0.3    -      -       -      +
    119L  VAL*     3.2     8.0    -      -       -      +
    120L  PHE*     2.8    51.6    +      -       +      +
    122L  PHE*     4.2    13.4    -      -       +      -
    137L  VAL*     4.2     2.0    -      -       +      -
    138L  CYS*     1.3    71.6    -      -       -      +
    140L  LEU*     1.3    64.5    +      -       -      +
    141L  ASN*     3.8    26.2    -      -       +      +
    179L  LEU      3.6     2.5    -      -       -      +
    180L  SER*     4.8     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117L  PRO*     4.1    13.7    -      -       +      -
    118L  SER      3.7     3.1    -      -       -      -
    119L  VAL*     4.6     1.1    -      -       +      -
    138L  CYS*     4.1    15.7    -      -       -      +
    139L  LEU*     1.3    74.9    -      -       -      +
    141L  ASN*     1.3    58.9    +      -       -      +
    143L  PHE*     3.6    15.8    -      -       +      -
    148L  ALA*     3.9    22.0    -      -       +      -
    149L  LYS      4.6     1.3    -      -       -      +
    150L  VAL*     4.4    13.2    -      -       +      -
    178L  SER*     3.2     6.4    -      -       -      -
    179L  LEU*     2.8    71.5    +      -       +      +
    181L  SER*     5.2     0.9    -      -       -      -
    200L  VAL*     3.5    36.1    -      -       +      -
    201L  THR      5.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 141 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171H  SER      5.4     0.5    -      -       -      +
    173H  HIS*     2.9    21.5    -      -       -      -
    190H  VAL*     4.8     0.6    -      -       -      +
    192H  THR*     3.4    27.6    +      -       -      +
    117L  PRO*     3.5     1.3    -      -       -      +
    118L  SER*     2.7    54.0    +      -       -      +
    120L  PHE*     4.4     4.7    -      -       +      -
    139L  LEU*     3.8    20.6    -      -       +      +
    140L  LEU*     1.3    72.4    -      -       -      +
    142L  ASN*     1.3    85.2    +      -       -      +
    143L  PHE*     3.4     2.6    +      -       -      -
    178L  SER*     2.7    28.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 142 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173H  HIS*     2.8    30.0    +      -       -      -
    192H  THR*     5.6     2.0    +      -       -      -
    115L  ALA*     4.0     7.4    -      -       -      +
    116L  ALA      3.9     7.8    -      -       -      +
    118L  SER*     5.5     0.7    -      -       -      +
    141L  ASN*     1.3    86.2    +      -       -      +
    143L  PHE*     1.3    60.1    +      -       -      +
    174L  ASP*     3.8    14.1    +      -       -      +
    176L  THR*     3.5    28.7    +      -       +      +
    177L  TYR      3.1     7.7    +      -       -      -
    178L  SER*     3.0     8.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 143 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115L  ALA*     3.1    13.2    -      -       -      +
    117L  PRO*     3.6    25.1    -      -       +      -
    140L  LEU*     3.6    39.3    -      -       +      -
    142L  ASN*     1.3    76.6    -      -       -      +
    144L  TYR*     1.3    63.6    +      -       -      +
    145L  PRO      3.3    19.3    -      -       -      -
    146L  ARG*     3.2    26.7    -      -       +      -
    148L  ALA*     4.2    12.6    -      -       +      -
    167L  VAL*     5.0     4.5    -      -       +      -
    176L  THR*     3.4     3.1    -      -       -      -
    177L  TYR*     2.8    59.9    +      -       +      -
    178L  SER      4.2     1.1    -      -       -      -
    179L  LEU*     3.7    23.3    -      -       +      -
    202L  HIS*     3.7     9.9    -      +       -      +
----------------------------------------------------------
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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