Contacts of the strand formed by residues 66 - 72 (chain D) in PDB entry 3P1M


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 66 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65D  ASP*     1.3    79.6    -      -       -      +
     67D  ILE*     1.3    64.4    +      -       -      +
     68D  THR*     4.4     0.7    +      -       -      -
     82D  LYS*     4.7    23.1    -      -       +      +
     83D  GLY      3.4    18.2    -      -       -      +
     84D  LYS*     4.8     9.0    -      -       +      +
     85D  VAL      5.2     0.2    -      -       -      +
    161D  ASP*     4.5     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65D  ASP      5.1     0.7    -      -       -      +
     66D  LYS*     1.3    76.3    -      -       -      +
     68D  THR*     1.3    60.3    +      -       -      +
     69D  VAL*     3.8     6.4    +      -       +      +
     82D  LYS*     3.3     4.0    -      -       -      -
     83D  GLY      2.7    45.8    +      -       -      +
     85D  VAL*     4.0    22.8    -      -       +      +
    156D  LEU*     3.9    30.5    -      -       +      -
    157D  THR      3.8    11.9    -      -       -      +
    158D  LYS*     4.4    15.9    -      -       +      +
    160D  MET*     3.8    15.7    -      -       +      +
    161D  ASP*     3.2    40.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 68 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66D  LYS      5.3     0.7    +      -       -      -
     67D  ILE*     1.3    74.1    -      -       -      +
     69D  VAL*     1.3    65.4    +      -       -      +
     70D  HIS*     3.9     7.9    -      -       +      +
     80D  THR*     3.7    24.7    -      -       +      -
     81D  THR      3.4    12.8    -      -       -      +
     82D  LYS*     4.0    14.9    -      -       +      +
    160D  MET      3.8     1.2    -      -       -      +
    161D  ASP*     2.7    18.9    +      -       -      -
    162D  ASN*     2.6    50.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 69 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67D  ILE*     3.8    10.7    +      -       +      +
     68D  THR*     1.3    79.7    -      -       -      +
     70D  HIS*     1.3    72.6    +      -       -      +
     71D  PHE*     3.6    25.4    +      -       +      -
     79D  LEU      3.8     1.2    -      -       -      +
     80D  THR*     3.8     0.3    -      -       -      -
     81D  THR*     3.0    38.6    +      -       +      +
     83D  GLY      5.4     1.6    -      -       -      +
     89D  LEU*     4.1     7.6    -      -       +      -
     92D  VAL*     5.4     2.7    -      -       +      -
    156D  LEU*     3.8    34.3    -      -       +      -
    163D  MET*     3.8    28.0    -      -       +      +
    165D  VAL*     4.4     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 70 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68D  THR*     3.9     7.8    -      -       +      +
     69D  VAL*     1.3    74.7    -      -       -      +
     71D  PHE*     1.3    62.5    +      -       -      +
     78D  THR*     4.3    13.4    -      -       +      +
     79D  LEU      3.5     3.1    -      -       -      -
     80D  THR*     2.8    41.7    +      -       +      +
    162D  ASN*     3.3    44.2    +      -       -      +
    163D  MET      2.9     8.9    +      -       -      +
    164D  THR*     3.2    19.7    -      -       +      +
    165D  VAL*     2.9    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 71 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  VAL*     3.6    20.4    -      -       +      -
     70D  HIS*     1.3    77.7    -      -       -      +
     72D  ILE*     1.3    64.9    +      -       -      +
     73D  ASN*     3.8     0.6    +      -       -      +
     77D  GLU      3.5     1.4    -      -       -      +
     78D  THR*     3.2     4.8    -      -       -      -
     79D  LEU*     2.7    57.0    +      -       +      +
     81D  THR*     3.9    14.1    -      -       +      -
     89D  LEU*     4.0    22.9    -      -       +      -
     92D  VAL*     4.0     8.3    -      -       +      -
     93D  VAL*     3.7    29.2    -      -       +      -
     98D  LEU*     3.9    20.4    -      -       +      -
    100D  ILE*     4.3    13.5    -      -       +      -
    117D  LEU*     4.6     9.6    -      -       +      -
    165D  VAL*     3.4    23.1    -      -       +      -
    167D  VAL*     4.5    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 72 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71D  PHE*     1.3    72.2    -      -       -      +
     73D  ASN*     1.3    71.7    +      -       -      +
     76D  GLY*     4.3    17.9    -      -       -      +
     77D  GLU      3.6     2.7    -      -       -      +
     78D  THR*     4.3    15.3    -      -       +      +
    164D  THR*     3.8    26.9    -      -       +      -
    165D  VAL      2.9    11.4    +      -       -      +
    166D  ARG*     3.7    20.0    -      -       +      +
    167D  VAL*     2.8    32.4    +      -       -      +
    183E  THR*     3.6    24.2    -      -       -      +
    184E  SER*     4.8     8.7    -      -       -      -
----------------------------------------------------------
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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