Contacts of the strand formed by residues 389 - 397 (chain A) in PDB entry 2PME


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 ASP 389 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  ASN*     3.6    28.6    +      -       +      +
    352A  LEU*     3.6    18.1    -      -       -      +
    377A  GLN*     3.1    28.6    +      -       -      +
    388A  CYS*     1.3    69.6    -      -       -      +
    390A  CYS*     1.3    61.7    +      -       -      +
    391A  TRP*     3.7     7.9    +      -       -      -
    409A  ASP*     2.8    43.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 390 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    377A  GLN*     3.4    29.5    -      -       -      +
    378A  HIS*     3.2    38.1    +      -       +      +
    388A  CYS*     3.2    38.3    +      -       -      -
    389A  ASP*     1.3    76.0    +      -       -      +
    391A  TRP*     1.3    62.8    +      -       -      +
    392A  ASP*     4.2     1.1    -      -       -      +
    407A  CYS      3.5     9.0    -      -       -      +
    408A  ALA*     3.6    20.9    -      -       +      +
    410A  ARG*     5.4     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 391 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321A  LEU*     3.7    24.0    -      -       +      -
    322A  TYR      4.1     3.1    -      -       -      -
    323A  SER*     4.1    13.0    -      -       -      -
    346A  VAL*     3.1    34.6    +      -       +      -
    347A  ILE*     4.1    11.7    -      -       +      +
    352A  LEU*     3.9    28.1    -      -       +      +
    356A  ILE*     4.0    22.7    -      -       +      -
    375A  PHE*     3.2    44.0    -      -       +      -
    376A  ARG      3.5     3.4    -      -       -      -
    377A  GLN*     3.6    37.0    -      -       +      +
    389A  ASP*     3.7    18.0    +      -       -      -
    390A  CYS*     1.3    76.2    -      -       -      +
    392A  ASP*     1.3    63.9    +      -       -      +
    393A  ALA      3.9     0.9    +      -       -      -
    407A  CYS*     2.7    38.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 392 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A  PHE*     3.5     2.4    -      -       -      -
    376A  ARG*     2.6    51.4    +      -       -      +
    378A  HIS*     2.7    39.2    +      -       +      -
    390A  CYS*     4.4     0.5    -      -       -      +
    391A  TRP*     1.3    76.5    -      -       -      +
    393A  ALA*     1.3    62.8    +      -       -      +
    394A  GLU*     3.4    10.4    +      -       +      +
    403A  GLU*     3.5    39.0    -      -       +      +
    405A  VAL      3.6     2.7    -      -       -      -
    406A  GLY*     3.5    11.4    -      -       -      -
    407A  CYS      3.9     3.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 393 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359A  ILE*     4.3     1.8    -      -       +      -
    363A  LEU*     4.0    17.5    -      -       +      -
    373A  LEU*     4.9     1.8    -      -       +      -
    374A  ARG      3.6     5.2    -      -       -      +
    375A  PHE*     3.6    27.7    -      -       +      -
    391A  TRP      3.9     1.6    +      -       -      -
    392A  ASP*     1.3    71.1    -      -       -      +
    394A  GLU*     1.3    59.6    +      -       -      +
    403A  GLU*     3.7     2.8    -      -       -      -
    404A  ILE*     3.0    28.0    +      -       +      +
    405A  VAL*     2.6    34.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 394 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373A  LEU*     3.5     5.5    -      -       -      +
    374A  ARG*     2.7    79.7    +      -       +      +
    376A  ARG*     3.2    37.6    +      -       +      -
    392A  ASP*     3.8    11.5    -      -       +      +
    393A  ALA*     1.3    77.9    -      -       -      +
    395A  SER*     1.3    61.5    +      -       -      +
    401A  TRP*     3.7    14.4    -      -       +      +
    402A  ILE      3.1    19.3    -      -       -      +
    403A  GLU*     4.1    11.0    +      -       -      +
    404A  ILE*     4.7     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 395 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368A  ILE*     4.5     4.0    -      -       -      -
    372A  LYS      3.2     9.4    -      -       -      -
    373A  LEU*     5.1     0.7    -      -       -      -
    394A  GLU*     1.3    74.7    -      -       -      +
    396A  LYS*     1.3    62.1    +      -       -      +
    397A  THR*     3.5     1.2    +      -       -      +
    400A  GLY      3.2     3.6    -      -       -      +
    401A  TRP*     3.4     5.2    -      -       -      -
    402A  ILE*     3.1    32.1    +      -       -      +
    404A  ILE*     3.5    21.6    -      -       -      +
    533A  THR*     3.2    41.3    +      -       -      +
    537A  HIS*     4.3     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 396 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ILE*     5.5    12.5    -      -       +      +
    371A  ASP      6.0     0.4    -      -       -      +
    372A  LYS*     3.0    30.0    +      -       +      +
    395A  SER*     1.3    69.8    -      -       -      +
    397A  THR*     1.3    68.3    +      -       -      +
    400A  GLY*     3.7     7.2    -      -       -      -
    401A  TRP*     3.4    47.0    -      -       +      +
    537A  HIS*     3.0    23.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 397 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ILE*     4.4    10.2    -      -       -      +
    395A  SER*     3.9    16.2    -      -       -      +
    396A  LYS*     1.3    84.7    -      -       -      +
    398A  SER*     1.3    58.3    +      -       -      +
    399A  TYR*     2.9    21.7    +      -       -      +
    400A  GLY*     2.8    36.1    +      -       -      -
    402A  ILE*     3.9    23.2    -      -       +      +
    532A  TYR*     4.9     4.5    -      -       +      -
    533A  THR*     4.5    15.9    -      -       +      +
    536A  GLU*     3.3    22.2    -      -       -      +
    537A  HIS*     4.8     0.9    -      -       -      +
----------------------------------------------------------
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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