Contacts of the strand formed by residues 131 - 138 (chain A) in PDB entry 1F4J


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 GLY 131 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  HIS*     3.7    10.8    +      -       -      -
    112A  ARG      3.9     3.4    -      -       -      -
    113A  PHE*     3.0    28.4    -      -       -      +
    114A  SER*     2.7    22.7    +      -       -      -
    130A  ARG*     1.3    74.7    -      -       -      +
    132A  PHE*     1.3    59.0    +      -       -      +
    133A  ALA      3.8     2.2    -      -       -      -
    147A  GLY      3.7     2.5    -      -       -      -
    148A  ASN*     3.8     1.1    -      -       -      -
    600A  HEM      3.4    22.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  VAL*     3.8    18.2    -      -       +      -
    112A  ARG      3.8     2.2    -      -       -      -
    113A  PHE*     3.4    32.1    -      +       +      -
    130A  ARG      3.6     1.1    +      -       -      +
    131A  GLY*     1.3    72.0    -      -       -      +
    133A  ALA*     1.3    57.6    +      -       -      +
    134A  VAL*     4.0     7.9    -      -       +      -
    147A  GLY      2.7    19.6    +      -       -      +
    148A  ASN*     4.0    13.0    -      -       -      -
    149A  ASN      4.6     0.4    -      -       -      +
    212A  MET*     4.4     7.4    -      -       +      -
    213A  ASN      3.9     5.6    -      -       -      -
    214A  GLY*     3.4    22.4    -      -       -      -
    236A  TYR*     3.0    50.4    +      +       +      -
    277A  TRP*     3.3    48.5    -      +       -      -
    316A  LEU*     5.0     2.5    -      -       +      -
    318A  LEU*     5.7     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  VAL*     3.2    10.2    -      -       -      +
    112A  ARG      3.1    32.0    +      -       -      +
    132A  PHE*     1.3    74.8    -      -       -      +
    134A  VAL*     1.3    60.8    +      -       -      +
    145A  LEU      3.7     4.9    -      -       -      -
    146A  VAL*     4.1    10.8    -      -       +      +
    147A  GLY      4.3     0.2    -      -       -      +
    334A  PHE*     3.4    37.8    -      -       +      -
    600A  HEM      4.1    18.4    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
    109A  ILE*     4.2    15.0    -      -       +      -
    110A  ALA      3.5     2.5    -      -       -      +
    111A  VAL*     3.9    19.7    -      -       +      -
    132A  PHE*     4.0    17.9    -      -       +      -
    133A  ALA*     1.3    79.6    -      -       -      +
    135A  LYS*     1.3    62.7    +      -       -      +
    136A  PHE*     3.3    35.6    -      -       +      -
    143A  TRP      3.7     1.0    -      -       -      +
    144A  ASP*     3.6     1.4    -      -       -      -
    145A  LEU*     2.8    41.9    +      -       +      +
    236A  TYR*     4.0    20.4    -      -       +      +
    316A  LEU*     4.3     9.4    -      -       +      -
    334A  PHE*     3.7     3.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  PRO      3.8     0.2    -      -       -      +
    109A  ILE*     3.0     8.8    -      -       -      +
    110A  ALA*     2.8    37.5    +      -       +      +
    134A  VAL*     1.3    73.0    -      -       -      +
    136A  PHE*     1.3    62.4    +      -       -      +
    137A  TYR*     3.4    35.9    +      -       +      +
    142A  ASN*     3.8    23.4    -      -       +      +
    143A  TRP      3.6     0.2    -      -       -      -
    144A  ASP*     3.1    29.9    +      -       -      +
    332A  ILE*     3.9    17.0    -      -       -      -
    333A  ALA      3.0    28.2    +      -       -      -
    334A  PHE*     3.6     8.4    -      -       +      +
    338A  ASN*     4.9     1.4    -      -       -      +
    371A  LEU*     6.1     0.6    -      -       -      +
    375A  VAL      3.5    14.8    -      -       -      +
    376A  ASN*     4.2     6.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  PHE*     3.6    39.5    -      +       +      -
     99A  VAL*     4.3     3.8    -      -       +      -
    107A  THR*     4.1     4.3    -      -       +      -
    108A  PRO      3.8     3.8    -      -       -      -
    109A  ILE*     3.8    12.1    -      -       +      -
    134A  VAL*     3.3    32.1    -      -       +      -
    135A  LYS*     1.3    72.3    -      -       -      +
    137A  TYR*     1.3    62.4    +      -       -      +
    138A  THR*     3.0    15.1    +      -       +      +
    142A  ASN*     3.4     1.9    -      -       -      -
    143A  TRP*     2.8    91.2    +      +       +      +
    145A  LEU*     4.0    14.1    -      -       +      -
    279A  PHE*     4.3    13.0    -      +       -      -
    316A  LEU*     3.9    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  PHE*     4.1     9.4    -      +       -      -
    107A  THR*     3.3     6.9    -      -       -      +
    108A  PRO*     3.0    36.8    +      -       +      +
    109A  ILE      3.8     3.6    -      -       -      -
    110A  ALA*     3.2    38.3    -      -       +      +
    135A  LYS*     3.4    22.4    -      -       +      -
    136A  PHE*     1.3    69.8    -      -       -      +
    138A  THR*     1.3    58.9    +      -       -      +
    142A  ASN*     3.5    20.0    -      -       -      +
    374A  PRO      5.0     0.7    -      -       -      -
    375A  VAL*     2.8    31.2    +      -       -      +
    377A  CYS      3.8    10.1    -      -       -      -
    379A  TYR*     3.4    39.9    -      +       +      -
    380A  ARG*     3.0    34.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  VAL*     4.0    30.5    -      -       +      -
    107A  THR*     4.2     4.3    -      -       +      -
    136A  PHE*     3.0    25.3    +      -       +      +
    137A  TYR*     1.3    75.0    -      -       -      +
    139A  GLU*     1.3    66.5    +      -       -      +
    140A  ASP*     2.8    19.6    +      -       -      +
    141A  GLY*     2.6    39.7    +      -       -      +
    142A  ASN*     5.0     0.7    -      -       -      +
    143A  TRP*     4.1    10.5    -      -       +      -
    340A  PRO*     4.4     4.8    -      -       +      +
    378A  PRO      5.8     0.2    -      -       -      -
    380A  ARG*     3.9     8.1    +      -       -      +
    381A  ALA*     3.7     6.8    -      -       -      +
----------------------------------------------------------
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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