Contacts of the strand formed by residues 75 - 86 (chain A) in PDB entry 3DM6


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 LYS 75 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  TYR*     3.6    20.6    -      -       +      +
     69A  VAL      3.4    13.2    -      -       -      +
     70A  PRO*     4.2     9.6    -      -       +      -
     71A  TYR*     4.5     2.2    -      -       -      -
     74A  GLY*     1.3    77.5    -      -       -      +
     76A  TRP*     1.3    65.2    -      -       -      +
    105A  SER*     3.4     1.7    -      -       -      -
    106A  ASP*     2.7    70.4    +      -       +      +
    107A  LYS*     5.2     3.0    -      -       -      +
    108A  PHE*     3.9     4.3    -      -       -      +
   1000A  757      4.1     0.2    -      -       -      -
      1B  GLU*     4.3    15.0    +      -       -      +
      3B  VAL      5.5     1.8    -      -       -      -
     48B  VAL*     3.4    26.9    -      -       +      +
     89B  HIS*     5.6     5.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ASN*     4.4     8.1    -      -       +      -
     39A  ALA*     3.3    29.8    -      -       +      +
     67A  VAL*     3.8    25.6    -      -       +      -
     68A  TYR*     3.5     7.1    -      -       -      -
     69A  VAL*     2.6    63.5    +      -       +      +
     71A  TYR*     3.0    34.4    +      +       -      -
     75A  LYS*     1.3    75.3    -      -       -      +
     77A  GLU*     1.3    71.0    +      -       -      +
     78A  GLY*     4.2     0.7    -      -       -      -
    100A  ALA*     3.6    15.3    -      -       +      -
    102A  ILE*     3.8    24.0    -      -       +      +
    104A  GLU      3.5    14.1    -      -       -      +
    105A  SER*     3.8     5.2    -      -       -      +
    108A  PHE*     3.6    39.8    -      +       -      -
     48B  VAL*     4.7     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  VAL      2.9    15.0    -      -       -      +
     68A  TYR*     4.0     9.4    -      -       +      -
     76A  TRP*     1.3    85.9    -      -       -      +
     78A  GLY*     1.3    62.0    +      -       -      +
    102A  ILE*     3.8     1.6    -      -       -      -
    103A  THR*     3.3    17.6    +      -       -      +
    104A  GLU*     3.1    27.9    +      -       +      +
      3B  VAL*     3.7     7.3    -      -       -      +
     47B  PHE*     5.2     1.0    -      -       -      +
     48B  VAL*     3.1    26.5    -      -       +      +
    180B  ASP*     2.6    44.0    -      -       -      +
    181B  HIS*     4.6     4.3    +      -       -      +
    182B  SER*     3.7     8.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  GLY*     3.3     4.9    -      -       -      -
     67A  VAL*     2.7    41.9    +      -       -      +
     76A  TRP*     4.9     0.4    -      -       -      -
     77A  GLU*     1.3    79.8    -      -       -      +
     79A  GLU*     1.3    65.7    +      -       -      +
    101A  ALA      3.0    12.8    -      -       -      -
    103A  THR*     3.7    12.3    -      -       -      -
    182B  SER*     5.2     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  ARG*     2.5    49.9    +      -       -      +
     60A  TYR*     5.0     1.6    +      -       -      +
     62A  ASP*     5.5     7.9    -      -       -      +
     65A  LYS      3.8     6.3    -      -       -      +
     66A  GLY*     5.7     1.6    -      -       -      -
     78A  GLY*     1.3    76.2    -      -       -      +
     80A  LEU*     1.3    64.9    -      -       -      +
     99A  ILE      3.7     0.3    -      -       -      +
    100A  ALA*     3.6     1.1    -      -       -      -
    101A  ALA*     2.7    40.7    +      -       +      +
    103A  THR*     3.8    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     4.2     4.5    +      -       -      -
     62A  ASP*     3.7     8.8    -      -       -      +
     63A  LEU*     3.2    26.6    +      -       +      +
     64A  ARG      4.0     1.7    +      -       -      -
     65A  LYS*     3.0    44.3    +      -       +      +
     66A  GLY      4.0     7.9    -      -       -      +
     67A  VAL*     3.5    29.4    -      -       +      -
     79A  GLU*     1.3    75.4    -      -       -      +
     81A  GLY*     1.3    58.9    +      -       -      +
     99A  ILE      3.6     4.0    -      -       -      +
    100A  ALA*     3.9    16.4    -      -       +      +
    129A  PRO*     4.0    22.4    -      -       +      -
    133A  LEU*     4.0    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     4.2    13.7    -      -       -      -
     61A  ARG      3.5    13.0    -      -       -      -
     63A  LEU*     3.7    10.3    -      -       -      +
     80A  LEU*     1.3    77.6    -      -       -      +
     82A  THR*     1.3    59.5    +      -       -      -
     98A  ASN*     3.4     4.7    -      -       -      +
     99A  ILE*     2.6    39.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     3.6     7.7    -      -       -      -
     61A  ARG*     3.3    36.1    +      -       +      +
     63A  LEU*     4.0    18.2    -      -       +      -
     81A  GLY*     1.3    76.9    -      -       -      -
     83A  ASP*     1.3    66.0    +      -       -      +
     96A  ARG*     2.2    43.7    +      -       +      -
     97A  ALA      3.3    12.3    -      -       -      +
     98A  ASN*     3.7    20.4    -      -       -      +
     99A  ILE*     4.2     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  GLY*     3.4    17.9    -      -       -      -
     52A  TYR*     2.4    23.4    +      -       -      +
     57A  SER*     3.1    17.5    +      -       -      -
     59A  THR*     3.1    25.8    +      -       -      -
     60A  TYR*     3.9     5.4    -      -       -      +
     82A  THR*     1.3    78.8    -      -       -      +
     84A  LEU*     1.3    76.8    +      -       -      +
     85A  VAL*     3.9     2.7    +      -       -      +
     95A  VAL      3.5     0.5    -      -       -      +
     96A  ARG*     3.1    16.2    -      -       -      +
     97A  ALA      2.9    30.7    +      -       -      +
     99A  ILE*     3.4    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  THR*     3.5     0.9    +      -       -      +
     20A  VAL*     3.3     6.4    -      -       -      -
     21A  GLY*     3.0    27.3    +      -       -      +
     22A  SER*     3.4    12.3    -      -       -      +
     59A  THR*     3.3    31.2    -      -       +      -
     83A  ASP*     1.3    84.1    +      -       -      +
     85A  VAL*     1.3    60.8    +      -       -      +
     94A  THR*     4.0    22.2    -      -       +      +
     95A  VAL      3.4     0.9    -      -       -      -
     96A  ARG*     4.1    38.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  MET*     3.4    33.7    -      -       +      -
     19A  THR      3.2    10.5    -      -       -      +
     20A  VAL*     3.8     5.2    -      -       +      -
     38A  PHE*     3.8    15.7    -      -       +      -
     83A  ASP      4.1     6.1    -      -       -      +
     84A  LEU*     1.3    81.1    -      -       -      +
     86A  SER*     1.3    65.2    +      -       -      +
     93A  VAL      4.2     0.2    -      -       -      +
     94A  THR*     3.3     3.3    -      -       -      -
     95A  VAL*     2.7    46.2    +      -       +      +
     97A  ALA*     4.5     9.4    -      -       +      -
     99A  ILE*     3.8    26.9    -      -       +      -
    136A  PHE*     4.0    13.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  MET*     3.6     4.3    -      -       -      +
     19A  THR*     3.0    48.9    +      -       -      +
     85A  VAL*     1.3    70.9    -      -       -      +
     87A  ILE*     1.3    69.3    +      -       -      +
     88A  PRO*     3.5     3.7    -      -       -      +
     91A  PRO      5.8     0.2    -      -       -      -
     93A  VAL      3.1    22.9    -      -       -      -
     94A  THR*     3.2    18.4    +      -       -      -
    136A  PHE*     6.1     0.4    -      -       -      -
----------------------------------------------------------
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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