Contacts of the strand formed by residues 5 - 12 (chain E) in PDB entry 1ZMD


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 ILE 5 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3E  GLN      4.1     5.8    -      -       -      +
      4E  PRO*     1.3    79.1    -      -       -      +
      6E  ASP*     1.3    72.9    +      -       -      +
     31E  LYS*     6.0     0.7    -      -       -      -
     33E  VAL*     4.0    16.4    -      -       +      -
    113E  VAL*     5.3    10.8    -      -       +      -
    115E  VAL*     5.4     5.6    -      -       +      -
    137E  GLN*     3.3    27.6    -      -       +      +
    138E  VAL      2.7    11.8    +      -       -      +
    139E  ILE*     3.8    20.9    -      -       +      -
    140E  ASP*     2.9    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 6 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  PRO      4.3     0.6    +      -       -      +
      5E  ILE*     1.3    81.2    -      -       -      +
      7E  ALA*     1.3    68.7    +      -       -      +
     31E  LYS*     3.2    31.3    -      -       -      +
     33E  VAL*     5.1     0.3    -      -       -      +
    140E  ASP*     3.5    12.8    -      -       -      +
    142E  LYS*     5.5     6.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 7 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  ASP*     1.3    81.8    +      -       -      +
      8E  ASP*     1.3    62.8    +      -       -      +
      9E  VAL      4.1     2.5    -      -       -      +
     10E  THR*     3.6    22.7    -      -       -      +
     31E  LYS*     3.7    15.7    -      -       +      +
     33E  VAL*     3.7    23.1    -      -       +      -
    139E  ILE*     3.9     4.5    -      -       +      -
    140E  ASP      3.0     7.9    +      -       -      +
    141E  THR*     2.9    25.1    -      -       -      -
    142E  LYS*     3.2     6.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 8 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  ALA*     1.3    73.2    -      -       -      +
      9E  VAL*     1.3    60.4    -      -       -      +
     29E  GLY      4.7     1.4    -      -       -      +
     30E  PHE*     3.8    24.5    -      -       +      -
     31E  LYS*     2.9    39.1    +      -       -      +
    141E  THR*     3.4     1.1    -      -       -      -
    142E  LYS*     2.8    41.0    +      -       +      +
    143E  ASN*     3.0    37.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 9 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  ALA*     4.1     0.7    -      -       -      +
      8E  ASP*     1.3    83.5    -      -       -      +
     10E  THR*     1.3    65.3    +      -       -      +
     11E  VAL*     3.9    21.8    -      -       +      -
     25E  ALA*     4.2    10.8    -      -       +      -
     30E  PHE*     3.6    28.0    -      -       +      -
     31E  LYS      3.1     2.9    +      -       -      +
     32E  THR*     3.4    13.9    -      -       +      +
     33E  VAL      2.9    25.3    +      -       -      +
    143E  ASN*     3.7     5.6    -      -       -      +
    145E  LEU*     5.0     5.4    -      -       +      -
    339E  VAL*     4.7     1.1    -      -       +      -
    342E  MET*     3.3    42.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 10 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  ALA*     3.6     4.7    -      -       -      +
      9E  VAL*     1.3    74.8    -      -       -      +
     11E  VAL*     1.3    64.2    +      -       -      +
     12E  ILE*     3.8     1.9    +      -       +      +
     33E  VAL*     3.3    14.2    -      -       +      +
     35E  ILE*     4.1    23.1    -      -       +      -
    127E  VAL*     4.2    23.3    -      -       +      -
    139E  ILE*     3.5    16.2    -      -       +      +
    141E  THR*     3.2    31.8    +      -       -      +
    143E  ASN      3.0     9.5    +      -       -      -
    144E  ILE*     3.7     4.9    -      -       -      +
    145E  LEU      3.0    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 11 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  VAL*     3.9    21.3    -      -       +      -
     10E  THR*     1.3    73.6    -      -       -      +
     12E  ILE*     1.3    56.8    +      -       -      +
     13E  GLY      3.5     8.6    +      -       -      +
     18E  GLY*     3.5    36.8    -      -       -      +
     21E  ALA*     4.6     0.9    -      -       +      -
     22E  ALA*     4.2    22.0    -      -       -      +
     32E  THR*     4.6     1.1    -      -       +      -
     33E  VAL      2.6    15.2    +      -       -      +
     34E  CYS*     3.1     8.2    -      -       +      -
     35E  ILE*     2.7    33.8    +      -       -      +
    145E  LEU*     3.4    26.2    -      -       +      +
    147E  ALA*     4.4     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 12 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  THR*     4.3     6.5    -      -       +      +
     11E  VAL*     1.3    73.4    -      -       -      +
     13E  GLY*     1.3    59.1    +      -       -      +
     35E  ILE*     3.9     8.5    -      -       +      -
    119E  GLY*     4.6     7.2    -      -       -      -
    121E  ILE*     3.9    20.4    -      -       +      +
    127E  VAL*     3.9    23.3    -      -       +      -
    144E  ILE*     3.8    24.2    -      -       +      -
    145E  LEU      2.9    12.3    +      -       -      +
    146E  ILE*     4.6     5.8    -      -       +      -
    147E  ALA      3.0    28.8    +      -       -      -
    148E  THR*     3.4    12.4    +      -       +      +
    287E  LEU*     4.0    13.5    -      -       +      -
    480E  FAD      3.7    34.3    -      -       +      +
----------------------------------------------------------
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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