Contacts of the strand formed by residues 535 - 542 (chain A) in PDB entry 3CB4


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 HIS 535 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    531A  ALA*     4.0     0.9    -      -       -      -
    532A  ILE*     2.8    37.3    +      -       +      +
    534A  THR*     1.3    88.7    +      -       +      +
    536A  ILE*     1.3    63.1    +      -       -      +
    537A  ILE*     3.6     4.5    +      -       +      +
    166C  GLY      5.1     2.7    -      -       -      +
    167C  VAL*     4.0    28.4    -      -       +      +
    168C  GLY*     3.8    25.9    +      -       -      -
    170C  GLN*     4.0    12.1    -      -       +      -
    171C  ASP*     4.3    21.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 536 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    529A  GLN*     3.2    30.1    -      -       -      +
    530A  ALA      3.7    10.5    -      -       -      +
    531A  ALA*     3.9     5.2    -      -       +      -
    534A  THR      4.1     9.0    -      -       -      +
    535A  HIS*     1.3    71.6    -      -       -      +
    537A  ILE*     1.3    62.5    +      -       -      +
    538A  ALA      3.9    18.2    -      -       -      +
    539A  ARG*     3.3    38.1    -      -       +      +
     27C  ILE*     3.4    29.4    -      -       +      +
    166C  GLY      4.8     8.3    -      -       -      +
    170C  GLN*     3.3    31.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 537 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    483A  VAL*     4.0    22.7    -      -       +      -
    504A  SER      3.5    23.1    -      -       -      +
    505A  GLN*     3.0    36.8    -      -       -      +
    508A  GLY*     3.9    16.8    -      -       -      -
    530A  ALA*     3.0    19.5    +      -       +      +
    531A  ALA*     3.9     4.0    -      -       -      -
    532A  ILE*     4.2    20.4    -      -       +      -
    535A  HIS*     4.5     5.6    -      -       +      +
    536A  ILE*     1.3    76.2    -      -       -      +
    538A  ALA*     1.3    62.0    +      -       +      +
     26C  GLN*     3.9     7.4    -      -       -      +
     27C  ILE*     3.5    15.6    -      -       -      +
    165C  THR*     3.6    17.9    -      -       -      +
    166C  GLY*     5.3     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 538 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    508A  GLY      4.2     2.9    -      -       -      +
    509A  ARG*     4.0    29.6    -      -       +      +
    512A  VAL*     3.8    22.2    -      -       +      -
    529A  GLN*     3.2     3.8    -      -       -      +
    530A  ALA*     2.8    30.9    +      -       +      +
    536A  ILE*     3.8     2.8    -      -       -      +
    537A  ILE*     1.3    81.8    -      -       -      +
    539A  ARG*     1.3    61.8    +      -       -      +
     26C  GLN      3.3    11.4    -      -       -      +
     27C  ILE*     4.2     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 539 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    512A  VAL*     4.7     1.1    -      -       -      +
    527A  ALA*     5.8     6.7    -      -       +      -
    528A  ILE      3.4    12.3    -      -       -      +
    529A  GLN*     3.1    32.2    -      -       +      +
    536A  ILE*     3.3    33.1    -      -       +      +
    538A  ALA*     1.3    76.4    -      -       -      +
    540A  SER*     1.3    62.4    +      -       -      +
    541A  THR*     6.4     2.5    -      -       -      -
     26C  GLN      3.5     6.7    +      -       -      -
     27C  ILE      3.3    19.3    +      -       -      +
     28C  CYS*     2.6    32.6    -      -       -      +
     29C  GLY      3.3     1.4    +      -       -      +
     30C  GLY*     5.8     0.4    -      -       -      -
     62C  ASP      6.0     1.8    -      -       -      -
     63C  TYR*     4.5     8.4    -      -       -      +
     64C  LYS*     3.8    47.6    +      -       -      +
    170C  GLN*     4.2     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 540 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    512A  VAL*     3.5    23.1    -      -       -      +
    513A  GLU*     5.2     1.8    -      -       -      -
    516A  LYS*     3.1    31.7    -      -       -      +
    527A  ALA*     4.8     0.2    -      -       -      -
    528A  ILE*     2.8    41.5    +      -       -      +
    539A  ARG*     1.3    77.0    -      -       -      +
    541A  THR*     1.3    65.5    +      -       -      +
     29C  GLY*     3.5    18.1    +      -       -      -
     30C  GLY*     5.4     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 541 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516A  LYS*     4.9     2.9    -      -       -      +
    525A  ASP*     4.5     9.7    -      -       -      +
    526A  ILE      3.4    12.3    +      -       -      -
    527A  ALA*     4.4    11.7    +      -       -      +
    539A  ARG*     6.4     2.7    -      -       -      -
    540A  SER*     1.3    80.8    +      -       -      +
    542A  VAL*     1.3    67.9    +      -       -      +
    543A  LYS*     3.4    36.9    +      -       -      +
     29C  GLY*     5.0     2.7    +      -       -      -
     62C  ASP*     6.3     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 542 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516A  LYS*     4.0    22.0    -      -       +      +
    519A  ILE*     3.8    22.2    -      -       +      +
    520A  PRO      3.6    24.7    -      -       -      +
    521A  ARG*     3.8    18.4    -      -       +      +
    522A  GLN      4.9     0.4    -      -       -      +
    524A  PHE      4.1     2.5    -      -       -      +
    525A  ASP*     3.7     1.9    -      -       -      -
    526A  ILE*     2.8    39.7    +      -       +      +
    528A  ILE*     3.6    28.3    -      -       +      -
    541A  THR*     1.3    70.4    +      -       -      +
    543A  LYS*     1.3    64.2    +      -       -      +
    544A  GLN      3.5     1.2    +      -       -      -
----------------------------------------------------------
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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