Contacts of the strand formed by residues 70 - 76 (chain A) in PDB entry 4FPR


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 MET 70 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  THR*     3.9    19.7    -      -       +      +
     55A  LEU*     3.7    40.2    -      -       -      +
     56A  ILE*     3.8    20.1    -      -       +      +
     59A  SER*     4.0     0.4    -      -       -      -
     66A  TRP*     3.4    30.5    -      -       +      +
     67A  GLY      3.3    24.0    -      -       -      +
     68A  ILE      3.6     3.6    +      -       -      -
     69A  ASP*     1.3    82.8    +      -       -      +
     71A  THR*     1.3    69.8    +      -       -      +
     94A  ILE*     4.0    19.3    -      -       +      -
     95A  THR      3.3     5.4    -      -       -      +
     96A  ALA*     4.1    11.2    -      -       +      -
    131A  TRP*     4.3     4.5    -      -       +      -
     42B  THR*     3.4    10.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ASN*     5.5     0.4    -      -       -      -
     52A  THR*     4.8     2.5    -      -       -      -
     70A  MET*     1.3    82.0    -      -       -      +
     72A  ALA*     1.3    62.1    +      -       -      +
     73A  LYS*     5.6     1.4    -      -       -      +
     93A  LYS      3.8     0.9    -      -       -      +
     94A  ILE*     3.5     3.6    -      -       -      -
     95A  THR*     2.9    33.6    +      -       -      -
     97A  HIS*     2.7    31.1    +      -       -      +
     41B  LYS*     4.0    29.4    -      -       +      +
     42B  THR*     4.2     5.4    -      -       +      +
     45B  LEU*     4.2    21.1    -      -       +      -
     74B  VAL*     6.0     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  LEU*     3.8    12.3    -      -       +      +
     48A  CYS*     3.8    21.3    -      -       -      -
     49A  ASN*     3.3    31.9    +      -       -      +
     52A  THR*     3.4    14.1    -      -       -      +
     71A  THR*     1.3    74.9    -      -       -      +
     73A  LYS*     1.3    67.9    +      -       -      +
     93A  LYS      3.6     4.9    -      -       -      +
     94A  ILE*     4.4     2.7    -      -       +      +
     45B  LEU*     4.8    11.9    -      -       -      +
     73B  LYS*     5.7     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  LEU*     4.3     5.2    -      -       -      -
     48A  CYS*     3.8     3.8    -      -       -      -
     71A  THR      5.6     1.6    -      -       -      +
     72A  ALA*     1.3    78.8    -      -       -      +
     74A  VAL*     1.3    64.0    +      -       -      +
     93A  LYS*     3.1    44.2    +      -       +      +
     95A  THR*     6.0     2.5    -      -       -      +
     73B  LYS*     4.1    42.0    -      -       +      +
     74B  VAL      5.9     2.5    -      -       -      -
     75B  GLN*     5.4     7.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  LYS*     4.7     4.7    -      -       +      +
     44A  ALA*     4.2     9.6    -      -       +      +
     45A  LEU*     3.5    40.8    -      -       +      +
     48A  CYS*     4.4    10.1    -      -       +      -
     73A  LYS*     1.3    78.0    -      -       -      +
     75A  GLN*     1.3    78.3    +      -       -      +
     76A  CYS*     4.3     4.9    -      -       -      -
     90A  CYS*     3.9    18.2    -      -       +      -
     91A  THR      3.2    16.8    -      -       -      +
     92A  CYS*     4.4     3.8    -      -       +      -
     71B  THR*     6.1     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  VAL*     1.3    77.8    -      -       -      +
     76A  CYS*     1.3    62.3    +      -       -      +
     90A  CYS*     3.3     2.8    -      -       -      +
     91A  THR*     2.8    38.1    +      -       -      +
    134D  ASN*     4.9     6.7    +      -       -      +
    136D  LYS*     3.5    37.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  PRO*     5.5     2.0    -      -       +      -
     41A  LYS*     4.0    29.0    +      -       +      +
     44A  ALA*     3.7    19.1    -      -       -      -
     74A  VAL*     4.3     3.8    -      -       -      -
     75A  GLN*     1.3    75.1    -      -       -      +
     77A  ALA*     1.3    71.5    +      -       -      +
     78A  PRO*     3.9     1.4    -      -       -      +
     88A  VAL*     4.6     4.0    -      -       +      -
     89A  LEU      3.6     4.0    -      -       -      -
     90A  CYS*     2.0    46.7    -      -       -      -
    136D  LYS*     3.8    14.3    -      -       -      +
----------------------------------------------------------
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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