Contacts of the strand formed by residues 135 - 145 (chain H) in PDB entry 3MXW


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 135 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131H  THR*     3.1     9.4    +      -       -      -
    132H  SER*     2.6    50.1    +      -       -      +
    133H  GLY      4.1     5.8    -      -       -      +
    134H  GLY*     1.3    83.5    -      -       -      +
    136H  ALA*     1.3    61.7    +      -       -      +
    183H  THR*     4.9    11.6    -      -       -      +
    184H  VAL      3.4    14.1    -      -       -      +
    185H  PRO*     5.3     1.8    -      -       +      -
    186H  SER*     4.3     1.6    -      -       -      -
    116L  PHE*     4.3     7.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 136 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  PRO*     4.2    11.9    -      -       +      -
    127H  SER      5.7     1.6    -      -       -      +
    130H  SER      3.2     9.6    -      -       -      +
    131H  THR*     5.1     2.7    -      -       -      -
    135H  THR*     1.3    75.2    -      -       -      +
    137H  ALA*     1.3    61.1    +      -       -      +
    183H  THR*     3.3     3.8    -      -       -      -
    184H  VAL*     2.8    43.6    +      -       +      +
    186H  SER*     4.1     8.3    -      -       -      +
    189H  LEU*     3.9    27.4    -      -       +      -
    116L  PHE*     4.5     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 137 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  PRO*     3.4     6.6    -      -       -      +
    130H  SER*     3.0    26.3    +      -       -      -
    136H  ALA*     1.3    75.0    -      -       -      +
    138H  LEU*     1.3    63.5    +      -       -      +
    182H  VAL      3.3     8.3    -      -       -      +
    183H  THR*     4.0    10.5    -      -       +      +
    116L  PHE*     3.6    35.8    -      -       +      -
    118L  PHE*     3.4    16.7    -      -       +      -
    135L  LEU*     4.0     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 138 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  LEU*     3.3    15.5    -      -       -      +
    126H  PRO*     3.6    29.2    -      -       +      -
    137H  ALA*     1.3    75.5    -      -       -      +
    139H  GLY*     1.3    60.0    +      -       -      +
    154H  TRP*     3.6    23.6    -      -       +      -
    181H  VAL*     3.2     6.7    -      -       -      +
    182H  VAL*     2.8    51.7    +      -       +      +
    184H  VAL*     3.8    22.9    -      -       +      -
    189H  LEU*     4.4     0.9    -      -       +      -
    194H  TYR*     3.6    37.2    -      -       +      -
    211H  VAL*     4.0     8.5    -      -       +      +
    118L  PHE*     4.1     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 139 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  LEU*     2.8    43.1    +      -       -      +
    138H  LEU*     1.3    79.5    -      -       -      +
    140H  CYS*     1.3    63.7    +      -       -      -
    154H  TRP*     3.5    15.7    -      -       -      -
    180H  SER      3.1    12.3    -      -       -      -
    181H  VAL*     4.0     1.1    -      -       -      -
    211H  VAL*     3.5     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 140 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121H  VAL*     4.1    12.1    -      -       +      -
    122H  PHE      3.3     8.3    -      -       -      +
    124H  LEU*     3.9     4.4    -      -       -      +
    139H  GLY*     1.3    79.9    -      -       -      -
    141H  LEU*     1.3    59.6    +      -       -      +
    142H  VAL*     3.9     8.4    +      -       +      +
    152H  VAL*     5.6     0.2    -      -       +      -
    154H  TRP*     3.9     1.5    -      -       +      -
    179H  SER*     3.4     4.0    -      -       -      -
    180H  SER*     2.8    34.4    +      -       -      +
    196H  CYS*     2.1    52.9    -      -       +      -
    198H  VAL*     5.1     0.4    -      -       +      -
    209H  LYS*     4.3     4.3    -      -       -      -
    211H  VAL*     3.6    16.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 141 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120H  SER      3.5     1.4    -      -       -      +
    121H  VAL*     3.4     5.2    -      -       -      +
    122H  PHE*     2.8    61.7    +      -       +      +
    124H  LEU*     4.1    15.9    -      -       +      +
    140H  CYS*     1.3    71.9    -      -       -      +
    142H  VAL*     1.3    60.1    +      -       -      +
    143H  LYS*     3.8    10.5    +      -       +      -
    177H  SER*     3.9    14.4    -      -       -      +
    178H  LEU      3.7    17.7    -      -       -      +
    179H  SER*     4.5     8.7    -      -       -      +
    124L  GLN*     4.4     4.0    -      -       -      +
    131L  SER*     3.6    32.8    -      -       -      +
    133L  VAL*     4.7    15.5    -      -       +      -
    178L  THR*     4.7    11.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 142 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119H  PRO*     3.5    26.5    -      -       +      -
    120H  SER      3.5     3.1    -      -       -      +
    121H  VAL*     4.5     5.6    -      -       +      -
    140H  CYS*     4.4     8.3    -      -       +      +
    141H  LEU*     1.3    74.5    -      -       -      +
    143H  LYS*     1.3    60.0    +      -       -      +
    145H  TYR*     3.7     4.7    -      -       +      -
    150H  VAL*     3.9    16.6    -      -       +      -
    152H  VAL*     4.3     5.8    -      -       +      -
    177H  SER*     3.3     4.4    +      -       -      -
    178H  LEU*     2.7    60.4    +      -       +      +
    198H  VAL*     3.9    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 143 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119H  PRO*     3.4     2.2    -      -       -      +
    120H  SER*     2.9    42.6    +      -       -      +
    122H  PHE*     4.4    15.5    -      -       +      -
    141H  LEU*     4.5    10.1    -      -       +      -
    142H  VAL*     1.3    73.8    -      -       -      +
    144H  ASP*     1.3   102.8    +      -       -      +
    145H  TYR*     3.7     1.3    -      -       -      -
    171H  GLN*     3.5    15.6    +      -       -      +
    177H  SER*     3.6    15.7    -      -       -      +
    124L  GLN*     3.7    22.4    -      -       -      +
    129L  THR*     4.5    12.1    +      -       -      +
    131L  SER*     3.9    15.7    -      -       -      +
    180L  THR*     4.4    15.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 144 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117H  LYS*     2.9    35.5    +      -       -      +
    118H  GLY      3.3     6.9    -      -       -      +
    120H  SER*     5.4     2.4    +      -       -      +
    143H  LYS*     1.3   106.7    +      -       -      +
    145H  TYR*     1.3    57.5    +      -       -      +
    171H  GLN*     2.7    31.1    +      -       -      +
    173H  SER*     4.8     1.6    +      -       -      -
    175H  LEU*     3.8    22.0    -      -       +      +
    176H  TYR      2.9    14.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 145 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117H  LYS*     3.3    13.7    -      -       -      +
    119H  PRO*     3.8    24.9    -      -       +      -
    142H  VAL*     3.7    22.7    -      -       +      -
    144H  ASP*     1.3    77.2    -      -       -      +
    146H  PHE*     1.3    62.9    +      -       -      +
    147H  PRO      3.5    20.4    -      -       -      -
    148H  GLU*     4.2     9.5    +      -       +      -
    150H  VAL*     3.6    40.6    +      -       +      +
    168H  ALA*     3.3    17.2    -      -       -      +
    175H  LEU*     3.6     3.6    -      -       -      -
    176H  TYR*     2.8    66.4    +      +       +      -
    177H  SER*     4.0     1.8    -      -       -      -
    178H  LEU*     3.2    25.9    -      -       +      +
    200H  HIS*     3.7     3.8    -      +       +      -
----------------------------------------------------------
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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