Contacts of the strand formed by residues 130 - 140 (chain A) 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 THR 130 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  GLN*     3.4    43.9    +      -       -      +
    126A  LEU*     3.8     4.5    +      -       -      -
    128A  SER*     3.8     9.1    +      -       -      -
    129A  GLY*     1.3    80.4    +      -       -      +
    131A  ALA*     1.3    69.1    +      -       -      +
    181A  THR*     4.2     9.7    -      -       +      +
    182A  LEU      3.5    14.1    +      -       -      +
    183A  SER*     4.6     2.3    -      -       -      -
    184A  LYS*     3.9     4.2    -      -       -      +
    155B  LYS*     4.1    20.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  PRO*     4.0    11.9    -      -       +      -
    125A  GLN*     3.7     5.2    -      -       -      +
    126A  LEU*     4.3     4.0    -      -       +      -
    130A  THR*     1.3    79.1    -      -       -      +
    132A  SER*     1.3    60.7    +      -       -      +
    133A  VAL*     4.0     2.0    +      -       +      +
    180A  LEU      4.0     0.3    -      -       -      +
    181A  THR*     3.7     1.4    -      -       -      -
    182A  LEU*     2.8    37.3    +      -       +      +
    183A  SER      3.8    10.5    -      -       -      +
    184A  LYS*     4.3     3.1    -      -       -      -
    187A  TYR*     3.7    36.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  PHE      4.3     1.0    -      -       -      +
    120A  PRO      4.8     0.2    -      -       -      -
    121A  PRO*     3.9    16.4    -      -       -      +
    125A  GLN*     3.1    23.8    +      -       -      +
    131A  ALA*     1.3    72.7    -      -       -      +
    133A  VAL*     1.3    62.5    +      -       -      +
    134A  VAL*     3.8     7.8    -      -       -      +
    179A  THR*     3.4    12.5    -      -       -      +
    180A  LEU      3.4     2.7    -      -       -      -
    181A  THR*     3.0    22.7    +      -       -      +
    136B  LEU*     5.4     0.7    -      -       -      +
    153B  LEU*     3.8    23.8    -      -       -      +
    155B  LYS*     3.9    14.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ILE*     4.5     1.1    -      -       +      -
    119A  PHE      3.7     7.9    -      -       -      +
    121A  PRO*     4.3    13.2    -      -       +      -
    131A  ALA      4.9     2.9    -      -       -      +
    132A  SER*     1.3    75.2    -      -       -      +
    134A  VAL*     1.3    61.3    +      -       -      +
    149A  TRP*     3.8    22.8    -      -       +      -
    179A  THR*     3.4     3.6    -      -       -      +
    180A  LEU*     2.8    55.1    +      -       +      +
    182A  LEU*     4.9     2.9    -      -       +      -
    187A  TYR*     4.5    10.1    -      -       +      -
    193A  TYR*     4.5    13.9    -      -       +      -
    210A  PHE*     3.5    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ILE*     3.5     4.0    -      -       -      +
    119A  PHE*     2.8    47.2    +      -       +      -
    132A  SER      3.8     9.9    -      -       -      +
    133A  VAL*     1.3    80.3    -      -       -      +
    135A  CYS*     1.3    67.7    +      -       -      +
    136A  LEU*     5.8     1.1    -      -       +      -
    149A  TRP*     3.5     5.2    -      -       -      -
    177A  SER*     3.9    21.8    -      -       -      +
    178A  SER      3.6     1.8    -      -       -      +
    179A  THR*     3.9    14.8    -      -       +      +
    136B  LEU*     3.5    31.2    -      -       +      -
    153B  LEU*     3.8    15.3    -      -       +      -
    191B  SER*     4.2    10.3    -      -       -      +
    193B  VAL*     6.2     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  VAL*     4.0    12.3    -      -       -      -
    117A  PHE      3.4    15.5    -      -       -      -
    118A  ILE*     5.0     1.1    -      -       -      -
    134A  VAL*     1.3    78.1    -      -       -      +
    136A  LEU*     1.3    61.1    +      -       -      +
    137A  LEU*     4.2     7.4    -      -       +      +
    147A  VAL*     4.8     0.2    -      -       +      -
    149A  TRP*     3.3    18.1    -      -       +      -
    176A  LEU      3.5     3.1    -      -       -      +
    177A  SER*     3.6     3.5    -      -       -      -
    178A  SER*     2.7    41.0    +      -       -      +
    195A  CYS*     2.0    49.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  SER      3.3     7.3    -      -       -      +
    116A  VAL*     3.3     2.6    -      -       -      +
    117A  PHE*     3.0    56.0    +      -       +      +
    119A  PHE*     3.9    25.4    -      -       +      -
    134A  VAL*     4.3     1.1    +      -       +      -
    135A  CYS*     1.3    75.1    -      -       -      +
    137A  LEU*     1.3    71.1    +      -       -      +
    138A  ASN*     4.5    15.5    -      -       +      +
    176A  LEU      3.5     1.6    -      -       -      +
    177A  SER*     5.4     0.7    -      -       -      -
    149B  ALA*     4.4     7.0    -      -       +      -
    178B  PHE*     3.6    33.7    -      -       +      -
    193B  VAL*     3.6    36.8    -      -       +      -
    194B  VAL      5.8     0.4    -      -       -      +
    195B  THR*     6.1     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  PRO*     4.1    11.4    -      -       +      -
    115A  SER      3.8     3.6    -      -       -      -
    116A  VAL*     4.4     1.6    -      -       +      -
    135A  CYS*     4.2    11.4    -      -       -      -
    136A  LEU*     1.3    78.5    -      -       -      +
    138A  ASN*     1.3    59.4    +      -       -      +
    140A  PHE*     3.2    24.7    -      -       +      -
    145A  ALA*     5.0    10.1    -      -       +      -
    146A  LYS      5.1     2.5    -      -       -      +
    147A  VAL*     3.6    25.8    -      -       +      -
    175A  SER*     3.3     2.4    -      -       -      -
    176A  LEU*     3.0    52.9    +      -       +      -
    197A  VAL*     3.2    48.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  PRO*     3.6     1.7    -      -       -      +
    115A  SER*     2.9    47.5    +      -       -      +
    117A  PHE*     4.1    11.1    -      -       +      -
    136A  LEU*     3.7    11.5    -      -       +      +
    137A  LEU*     1.3    72.2    -      -       -      +
    139A  ASN*     1.3   100.7    +      -       -      +
    140A  PHE*     3.8     0.9    -      -       -      -
    175A  SER*     3.3     2.4    +      -       -      -
    176B  HIS*     3.1    26.7    +      -       -      -
    193B  VAL*     5.6     0.6    -      -       -      +
    195B  THR*     3.5    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  ALA*     4.5     4.7    -      -       -      +
    113A  ALA      3.9     8.7    -      -       -      +
    115A  SER*     4.6     2.7    +      -       -      +
    138A  ASN*     1.3   110.6    +      -       -      +
    140A  PHE*     1.3    59.6    +      -       -      +
    168A  ASP*     5.1     0.9    -      -       -      +
    171A  ASP*     3.3    20.7    -      -       -      +
    173A  THR*     3.7    20.8    +      -       +      +
    174A  TYR      3.1     9.5    +      -       -      -
    175A  SER*     3.3     6.8    +      -       -      -
    176B  HIS*     3.2    23.7    +      -       -      -
    195B  THR*     5.2     2.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  ALA      3.1    18.4    -      -       -      +
    114A  PRO*     3.5    28.0    -      -       +      -
    137A  LEU*     3.2    36.6    -      -       +      -
    138A  ASN      4.0     0.2    -      -       -      -
    139A  ASN*     1.3    73.6    -      -       -      +
    141A  TYR*     1.3    59.6    +      -       -      +
    142A  PRO      3.4    12.0    -      -       -      +
    143A  ARG*     3.3    25.1    -      -       -      -
    145A  ALA*     4.0     8.3    -      -       +      -
    164A  VAL*     5.2     2.5    -      -       +      -
    173A  THR*     3.6     8.4    -      -       -      -
    174A  TYR*     3.0    45.3    +      -       +      +
    175A  SER*     3.6     5.2    -      -       -      -
    176A  LEU*     4.1    23.6    -      -       +      -
    199A  HIS*     3.4    13.0    -      +       -      +
----------------------------------------------------------
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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