Contacts of the strand formed by residues 295 - 301 (chain D) 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 VAL 295 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293D  PRO      3.6     0.2    -      -       -      -
    294D  GLN*     1.3    96.1    -      -       +      +
    296D  TYR*     1.3    73.5    +      -       -      +
    341D  GLY*     3.2     4.3    -      -       -      -
    342D  PHE*     2.8    38.0    +      -       +      +
    344D  GLY*     3.9    18.4    -      -       -      +
    345D  LEU*     5.9     0.2    -      -       -      -
    348D  MET*     4.6    11.0    -      -       -      -
    368D  PRO*     3.7    30.1    -      -       +      -
    369D  THR      3.7     6.5    -      -       -      +
    370D  VAL*     4.3     2.9    -      -       +      -
    451D  VAL*     3.8    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 296 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292D  LYS*     5.9     0.2    -      -       -      +
    293D  PRO*     3.4    30.7    +      -       +      +
    295D  VAL*     1.3    78.2    -      -       -      +
    297D  ALA*     1.3    61.7    -      -       -      +
    325D  PHE*     3.5    19.9    -      +       -      -
    339D  ARG*     3.3    42.6    -      -       +      +
    340D  CYS      3.1    19.7    -      -       -      -
    341D  GLY*     3.7     4.7    -      -       -      -
    342D  PHE*     5.0     0.9    -      -       -      -
    368D  PRO*     3.2     6.1    -      -       -      +
    369D  THR*     2.8    52.4    +      -       +      +
    370D  VAL      5.2     0.2    -      -       -      -
    371D  VAL*     3.6    22.5    -      -       +      +
    385D  ASP*     3.2    36.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 297 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296D  TYR*     1.3    76.5    -      -       -      +
    298D  GLY*     1.3    62.6    +      -       -      +
    299D  LEU*     3.7     4.0    +      -       +      +
    339D  ARG*     4.6     3.6    -      -       -      +
    340D  CYS*     2.8    35.6    +      -       -      +
    342D  PHE*     4.6     6.0    -      -       +      -
    348D  MET*     4.1    24.0    -      -       -      -
    365D  THR*     4.4     9.0    -      -       -      +
    366D  THR*     3.7    20.9    -      -       -      +
    367D  ALA      4.9     0.7    -      -       -      -
    368D  PRO*     4.3     4.0    -      -       +      -
    369D  THR*     5.5     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 298 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297D  ALA*     1.3    69.8    -      -       -      +
    299D  LEU*     1.3    61.9    +      -       -      +
    300D  PHE*     3.6    17.6    -      -       -      -
    329D  GLU*     4.4     4.9    -      -       -      -
    338D  PHE      3.6     6.5    -      -       -      -
    339D  ARG*     4.3     7.5    -      -       -      +
    364D  ILE      3.7     1.2    -      -       -      +
    365D  THR*     3.5     4.9    -      -       -      -
    366D  THR*     2.8    43.8    +      -       -      +
    494D  ALA*     5.2     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 299 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297D  ALA*     4.5     7.6    -      -       +      +
    298D  GLY*     1.3    73.2    -      -       -      +
    300D  PHE*     1.3    61.8    +      -       -      +
    310D  PHE*     3.4    25.4    -      -       +      -
    314D  LEU*     5.2     1.3    -      -       +      -
    337D  GLY*     3.3     1.9    -      -       -      -
    338D  PHE      2.8    41.3    +      -       -      +
    340D  CYS*     4.2    20.2    -      -       +      -
    342D  PHE*     4.7    13.9    -      -       +      -
    348D  MET*     6.2     1.1    -      -       +      -
    351D  ILE*     5.2     0.4    -      -       +      -
    352D  GLN*     4.2    15.7    -      -       +      +
    355D  LEU*     3.8    28.7    -      -       +      -
    363D  LEU*     4.7     9.9    -      -       +      -
    364D  ILE      3.5     2.7    -      -       -      +
    365D  THR*     3.2    33.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 300 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298D  GLY*     3.6    27.1    -      -       -      -
    299D  LEU*     1.3    74.9    -      -       -      +
    301D  PRO*     1.3    68.8    -      -       +      +
    329D  GLU*     3.5    44.2    -      -       +      -
    331D  SER*     4.0     9.9    -      -       -      -
    334D  LEU*     3.7    40.8    -      -       +      +
    335D  GLY      3.6    15.5    -      -       -      -
    336D  PHE      4.0     0.7    -      -       -      -
    337D  GLY*     3.4    23.8    -      -       -      -
    338D  PHE      4.8     0.9    -      -       -      -
    363D  LEU*     3.4     5.4    -      -       -      +
    364D  ILE*     2.7    49.2    +      -       +      +
    366D  THR*     4.1     4.3    -      -       +      -
    494D  ALA*     3.7    14.8    -      -       +      -
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Residues in contact with PRO 301 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300D  PHE*     1.3    88.8    -      -       +      +
    302D  VAL*     1.3    64.4    +      -       -      +
    303D  SER      3.4    23.4    -      -       -      +
    304D  SER*     4.6     5.0    +      -       -      +
    306D  ASP*     4.1    11.7    -      -       +      -
    307D  TYR*     4.2    18.6    -      -       +      -
    310D  PHE*     3.8    25.4    -      -       +      -
    334D  LEU      4.4     8.2    -      -       -      +
    336D  PHE      3.2    25.4    -      -       -      +
    337D  GLY*     4.2     0.2    -      -       -      -
    362D  ASP      3.9     0.4    -      -       -      +
    363D  LEU*     3.6    12.1    -      -       +      -
    364D  ILE*     4.7     0.7    -      -       -      +
    552E  LYS*     4.5     5.4    -      -       -      +
----------------------------------------------------------
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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