Contacts of the strand formed by residues 148 - 157 (chain D) in PDB entry 3F12


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 ALA 148 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117C  PHE*     4.3     4.0    -      -       -      -
    147D  THR*     1.3    79.0    +      -       -      +
    149D  ALA*     1.3    59.8    +      -       -      +
    150D  LEU*     5.8     1.3    -      -       +      -
    195D  THR*     3.1     6.2    -      -       -      -
    196D  VAL*     2.6    51.9    +      -       +      +
    198D  SER*     4.3    10.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 149 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117C  PHE*     3.7    39.6    -      -       +      -
    119C  PHE*     3.6    19.9    -      -       +      -
    136C  LEU*     4.2     9.4    -      -       +      -
    137D  ALA      3.5    19.6    -      -       -      +
    148D  ALA*     1.3    76.6    -      -       -      +
    150D  LEU*     1.3    63.4    +      -       -      +
    194D  VAL      3.1    10.3    -      -       -      +
    195D  THR*     4.6     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119C  PHE*     4.4     3.3    -      -       -      -
    136D  LEU*     4.3     8.3    -      -       -      +
    137D  ALA      4.5    16.2    -      -       -      +
    148D  ALA*     5.8     1.1    -      -       +      -
    149D  ALA*     1.3    78.4    -      -       -      +
    151D  GLY*     1.3    60.8    +      -       -      +
    166D  TRP*     4.5     6.7    -      -       +      -
    193D  VAL*     3.3    22.3    -      -       -      +
    194D  VAL*     2.8    24.2    +      -       +      -
    196D  VAL*     3.2    49.1    -      -       +      -
    206D  TYR*     3.3    27.1    -      -       +      -
    223D  VAL*     3.9    24.7    -      -       +      +
    224D  GLU*     4.9     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 151 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135D  PRO*     3.7     2.9    -      -       -      +
    136D  LEU*     2.9    35.2    +      -       -      +
    137D  ALA      4.9     0.2    -      -       -      +
    150D  LEU*     1.3    82.6    -      -       -      +
    152D  CYS*     1.3    62.4    +      -       -      +
    166D  TRP*     3.3    17.9    -      -       -      -
    192D  SER      3.1    13.9    -      -       -      -
    193D  VAL*     3.7     0.7    -      -       -      -
    223D  VAL*     4.0     6.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 152 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133D  VAL*     3.5    24.9    -      -       +      -
    134D  PHE      3.1     9.0    -      -       -      +
    135D  PRO*     4.5     0.2    -      -       -      -
    136D  LEU*     4.1     4.6    -      -       -      +
    151D  GLY*     1.3    75.9    -      -       -      -
    153D  LEU*     1.3    59.9    +      -       -      +
    154D  VAL*     3.7     8.1    +      -       +      +
    164D  VAL*     5.7     0.4    -      -       +      -
    166D  TRP*     3.8     2.8    -      -       +      -
    191D  SER*     3.4     5.4    -      -       -      -
    192D  SER*     2.9    31.2    +      -       -      +
    208D  CYS*     2.0    50.7    -      -       +      -
    221D  LYS*     4.1    10.1    -      -       -      -
    223D  VAL*     4.2     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 153 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125C  GLN*     5.3     0.2    -      -       -      +
    132C  SER*     3.6    28.3    -      -       -      +
    134C  VAL*     3.2    33.7    -      -       +      -
    179C  THR*     4.2    15.7    -      -       +      +
    132D  SER      3.3     2.6    -      -       -      +
    133D  VAL*     4.6     0.7    -      -       -      -
    134D  PHE*     2.9    43.4    +      -       +      +
    136D  LEU*     4.8    10.4    -      -       +      +
    152D  CYS*     1.3    70.6    -      -       -      +
    154D  VAL*     1.3    61.9    +      -       -      +
    155D  LYS*     3.2    38.2    +      -       +      -
    189D  SER*     4.7     6.1    -      -       -      +
    190D  LEU      3.6     8.3    -      -       -      +
    191D  SER*     4.1    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 154 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131D  PRO*     3.4    24.0    -      -       +      -
    132D  SER      4.0     2.5    -      -       -      -
    133D  VAL*     4.4     6.1    -      -       +      +
    152D  CYS*     3.7     8.5    -      -       +      +
    153D  LEU*     1.3    70.1    -      -       -      +
    155D  LYS*     1.3    56.4    +      -       -      +
    157D  TYR*     4.0     4.7    -      -       +      -
    162D  VAL*     4.3    11.4    -      -       +      -
    164D  VAL*     4.1     7.4    -      -       +      -
    189D  SER*     3.2     3.1    -      -       -      -
    190D  LEU*     2.7    63.6    +      -       +      +
    192D  SER      5.4     0.2    -      -       -      +
    210D  VAL*     3.4    47.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 155 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125C  GLN*     4.0    10.1    -      -       -      +
    130C  THR*     5.3     7.5    -      -       -      +
    132C  SER*     3.5    25.4    -      -       -      +
    179C  THR*     5.7     2.5    -      -       -      -
    181C  THR*     4.3    14.6    -      -       -      +
    131D  PRO*     3.4     3.0    -      -       -      +
    132D  SER*     2.9    43.5    +      -       -      +
    134D  PHE*     4.5    11.9    -      -       +      -
    153D  LEU*     3.2    18.8    +      -       +      +
    154D  VAL*     1.3    74.9    -      -       -      +
    156D  ASP*     1.3   102.7    +      -       -      +
    157D  TYR*     3.9     0.7    -      -       -      -
    183D  GLN*     3.4    21.8    +      -       -      +
    188D  TYR      4.0     0.2    -      -       -      -
    189D  SER*     3.9    12.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 156 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129D  LYS*     3.0    29.8    +      -       -      +
    130D  GLY      3.2    10.6    -      -       -      +
    132D  SER*     4.4     5.1    +      -       -      +
    155D  LYS*     1.3   110.3    +      -       -      +
    157D  TYR*     1.3    56.9    +      -       -      +
    183D  GLN*     3.1    13.3    +      -       -      -
    185D  SER*     5.9     0.7    -      -       -      -
    187D  LEU*     3.9    16.8    -      -       +      +
    188D  TYR      3.0    15.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 157 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129D  LYS      3.1    14.1    -      -       -      +
    131D  PRO*     3.6    31.0    -      -       +      -
    154D  VAL*     4.0    13.5    -      -       +      -
    156D  ASP*     1.3    75.4    -      -       -      +
    158D  PHE*     1.3    64.5    +      -       -      +
    159D  PRO      3.2    24.9    -      -       -      -
    160D  GLU*     2.9    28.6    +      -       -      -
    162D  VAL*     3.7    30.7    -      -       +      +
    180D  ALA*     3.1    19.1    -      -       -      +
    187D  LEU*     3.6     6.1    -      -       -      +
    188D  TYR*     2.9    43.3    +      -       +      -
    189D  SER*     3.6    22.0    -      -       -      -
    190D  LEU*     3.9     3.3    -      -       -      +
    212D  HIS*     3.6     9.6    -      +       +      -
----------------------------------------------------------
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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