Contacts of the strand formed by residues 141 - 148 (chain A) in PDB entry 5F4T


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 141 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  ASN*     4.0     0.4    -      -       -      -
    139A  CYS      4.0     0.2    +      -       -      -
    140A  GLY*     1.3    79.5    -      -       -      +
    142A  MET*     1.3    61.9    +      -       -      +
    143A  LEU*     4.0    23.5    +      -       +      +
    158A  ALA*     4.6     6.3    -      -       +      -
    159A  CYS      3.2     7.9    -      -       -      +
    160A  ARG*     4.3    24.7    -      -       +      +
    161A  LYS      5.7     0.9    -      -       -      +
    186A  TRP*     3.7     5.2    -      -       -      -
    190A  SER*     4.2     1.6    +      -       -      -
    241A  SER*     4.8    10.1    -      -       -      +
    242A  PRO      4.4    10.8    -      -       -      +
    243A  ALA*     3.0    37.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  PRO*     3.6    27.6    -      -       +      -
    137A  ASN*     3.2    19.0    -      -       -      +
    141A  VAL*     1.3    73.1    -      -       -      +
    143A  LEU*     1.3    66.2    +      -       -      +
    144A  GLN*     3.3    42.8    +      -       +      +
    157A  HIS      3.1     4.2    -      -       -      +
    159A  CYS*     2.9    39.7    +      -       +      +
    186A  TRP*     3.5    34.5    -      -       +      +
    189A  ALA*     4.0    29.8    -      -       +      +
    190A  SER*     3.8     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  VAL*     4.0    15.9    +      -       +      +
    142A  MET*     1.3    72.9    -      -       -      +
    144A  GLN*     1.3    59.5    +      -       -      +
    156A  VAL*     3.7    22.0    -      -       +      -
    157A  HIS      3.6     3.4    -      -       -      +
    158A  ALA*     4.1    23.8    -      -       +      +
    190A  SER*     3.3    12.7    +      -       -      +
    191A  GLU*     3.2    56.1    +      -       +      +
    192A  GLY*     4.5     4.7    -      -       -      -
    237A  SER*     4.3    15.7    -      -       -      +
    238A  VAL      5.8     1.8    -      -       -      +
    240A  SER*     6.1     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  ASP*     4.6     8.2    +      -       +      +
    129A  PHE*     4.4     6.1    -      -       -      -
    133A  ALA*     2.6    27.3    +      -       -      +
    134A  TYR*     3.9     4.1    -      -       -      -
    135A  CYS*     3.0    24.5    +      -       -      -
    136A  PRO*     4.8     0.2    -      -       -      +
    142A  MET*     3.3    31.6    +      -       +      +
    143A  LEU*     1.3    72.1    -      -       -      +
    145A  THR*     1.3    69.0    +      -       -      +
    146A  LEU*     3.2    24.6    +      -       +      +
    156A  VAL*     4.4     1.3    -      -       -      -
    157A  HIS*     2.9    42.3    +      -       +      +
    159A  CYS*     3.8    10.4    -      -       -      -
    189A  ALA      4.9     2.7    -      -       -      +
    191A  GLU*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  ASP*     4.0    16.6    -      -       -      +
     80A  GLU*     4.8     5.0    +      -       +      +
    144A  GLN*     1.3    72.0    -      -       -      +
    146A  LEU*     1.3    71.1    +      -       -      +
    147A  ILE*     5.2     3.1    -      -       +      +
    154A  LYS*     4.1    31.2    -      -       +      +
    155A  GLU      3.7     8.1    -      -       -      +
    156A  VAL*     4.2     9.1    -      -       +      +
    191A  GLU*     2.4    43.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  VAL*     3.5    22.4    -      -       +      -
     78A  VAL      3.3    13.5    -      -       -      +
     79A  ASP*     4.5     1.1    -      -       +      -
    129A  PHE*     3.5    24.9    -      -       +      -
    134A  TYR*     3.7    26.7    -      -       +      -
    144A  GLN*     3.2    24.2    +      -       +      +
    145A  THR*     1.3    80.6    -      -       -      +
    147A  ILE*     1.3    63.1    +      -       -      +
    148A  TRP      4.1     0.6    +      -       -      -
    153A  LYS      3.9     0.3    -      -       -      +
    154A  LYS*     3.4     5.2    -      -       -      +
    155A  GLU*     2.9    44.3    +      -       +      +
    157A  HIS*     3.7    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  CYS*     5.6     0.9    -      -       +      -
     25A  CYS*     4.3    13.2    -      -       +      +
     77A  VAL*     3.4     6.7    -      -       -      -
     78A  VAL*     2.8    44.3    +      -       +      +
     79A  ASP      4.5     1.8    -      -       -      -
     80A  GLU*     3.9    37.0    -      -       +      +
     83A  LEU*     4.0    22.2    -      -       +      -
    145A  THR*     5.2     3.1    -      -       +      -
    146A  LEU*     1.3    77.3    -      -       -      +
    148A  TRP*     1.3    73.6    +      -       -      +
    149A  CYS*     3.4     4.4    +      -       -      -
    152A  CYS*     4.1    15.7    -      -       -      +
    153A  LYS      3.5     8.7    -      -       -      +
    154A  LYS*     4.3    21.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  MET      4.0    18.8    -      -       -      -
     76A  GLY*     3.6    17.0    -      -       -      -
     77A  VAL*     4.5    11.9    -      -       +      +
    147A  ILE*     1.3    70.6    -      -       -      +
    149A  CYS*     1.3    56.6    +      -       -      +
    150A  LYS*     3.4     4.9    -      -       +      +
    151A  ASN*     3.2    26.9    -      -       -      +
    152A  CYS*     2.8    32.3    +      -       -      -
    153A  LYS*     2.8    22.5    +      -       +      +
    154A  LYS      5.1     0.2    -      -       -      -
    155A  GLU*     2.3    51.2    +      -       +      -
----------------------------------------------------------
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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