Contacts of the strand formed by residues 71 - 81 (chain A) in PDB entry 3A46


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 ASP 71 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  ASP*     2.7    33.2    +      -       +      +
     70A  ASN*     1.3    73.8    -      -       +      +
     72A  LYS*     1.3    56.4    +      -       -      +
     73A  SER*     2.8    28.6    +      -       -      -
     74A  ASN*     2.9    35.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  PHE*     4.1    23.8    -      -       +      +
     68A  ASP      3.8     3.4    -      -       -      -
     69A  PRO      3.8    17.3    -      -       -      +
     70A  ASN      3.9     2.8    +      -       -      -
     71A  ASP*     1.3    71.3    -      -       -      +
     73A  SER*     1.3    60.3    +      -       -      +
     74A  ASN      3.4     2.0    -      -       -      -
     75A  LYS*     3.6    25.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ASP*     2.8    13.0    +      -       -      -
     72A  LYS*     1.3    77.2    -      -       -      +
     74A  ASN*     1.3    61.1    +      -       -      +
     75A  LYS*     3.0    15.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  ASN*     3.7    15.5    +      -       -      +
     50A  LEU*     4.7     2.0    -      -       -      +
     67A  PHE*     3.2    24.0    -      -       -      +
     68A  ASP*     3.4    17.6    +      -       +      +
     71A  ASP*     2.9    29.9    +      -       +      +
     73A  SER*     1.3    74.4    -      -       -      +
     75A  LYS*     1.3    61.0    +      -       -      +
     76A  TRP*     2.7    37.2    +      -       -      +
    123A  ASN*     4.7     7.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  GLU*     4.1    19.5    +      -       +      +
     66A  LEU      3.3     9.0    -      -       -      +
     67A  PHE*     4.3     9.4    -      -       +      -
     72A  LYS      3.6    18.6    -      -       -      +
     73A  SER*     3.0    13.8    +      -       -      +
     74A  ASN*     1.3    76.7    -      -       -      +
     76A  TRP*     1.3    63.5    +      -       -      +
     77A  TYR*     4.0    26.9    -      -       +      +
    123A  ASN*     3.3    27.9    -      -       -      +
    125A  GLU*     5.9     2.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLY*     4.5     3.6    -      -       -      -
     43A  ASP*     3.6    27.6    -      -       +      -
     44A  PHE*     3.5    39.0    -      +       +      -
     47A  ASN*     3.1    30.3    -      -       +      -
     50A  LEU*     3.7    31.2    -      -       +      -
     64A  PHE      3.7     0.2    -      -       -      +
     65A  GLU*     3.5     4.3    -      -       -      +
     66A  LEU*     2.7    41.6    +      -       +      +
     74A  ASN*     2.7    40.8    +      -       -      +
     75A  LYS*     1.3    72.8    -      -       -      +
     77A  TYR*     1.3    65.4    +      -       -      +
    121A  PHE      4.8     0.4    -      -       -      -
    122A  SER*     3.5    28.0    -      -       -      -
    123A  ASN*     3.4    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  PHE*     4.9     1.2    -      -       -      -
     63A  TRP*     4.1     5.8    -      +       +      -
     64A  PHE      3.1     9.2    -      -       -      +
     65A  GLU*     3.4    37.8    -      -       +      -
     66A  LEU*     4.7     0.2    -      -       -      -
     75A  LYS*     4.0    32.3    -      -       +      +
     76A  TRP*     1.3    79.4    -      -       -      +
     78A  ILE*     1.3    65.8    +      -       -      +
     79A  TRP*     3.9    19.7    -      -       +      +
    121A  PHE*     3.4     6.4    -      -       -      +
    122A  SER*     2.6    45.7    +      -       -      +
    123A  ASN      4.6     0.2    -      -       -      -
    124A  SER      4.2     9.0    -      -       -      -
    125A  GLU*     3.4    47.2    +      -       +      +
    128A  LEU*     3.3    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     4.3    12.3    -      -       +      -
     26A  ILE*     5.1     2.5    -      -       +      -
     44A  PHE*     3.8    20.9    -      -       +      -
     63A  TRP*     3.1     7.7    -      -       -      -
     64A  PHE*     2.9    53.8    +      -       +      -
     66A  LEU*     3.8    20.4    -      -       +      -
     77A  TYR*     1.3    76.6    -      -       -      +
     79A  TRP*     1.3    64.2    +      -       -      +
     80A  ASN*     3.8     1.5    +      -       +      -
     88A  TRP*     6.2     0.2    -      -       +      -
    100A  LEU*     4.9    10.1    -      -       +      -
    119A  PHE*     4.1    24.5    -      -       +      -
    120A  LYS      3.4     3.4    -      -       -      +
    121A  PHE*     3.7    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  PHE*     3.7    20.4    -      +       +      -
     62A  LEU      3.9     4.0    -      -       -      -
     63A  TRP*     4.4     1.3    -      -       +      -
     77A  TYR*     3.9    24.8    -      -       +      +
     78A  ILE*     1.3    77.0    -      -       -      +
     80A  ASN*     1.3    61.6    +      -       -      +
    118A  THR*     4.4     0.9    -      -       -      -
    119A  PHE*     3.2     9.7    -      -       -      -
    120A  LYS*     2.6    82.8    +      -       +      +
    122A  SER*     4.0    10.9    -      -       -      -
    127A  GLU*     3.7    19.7    -      -       +      -
    128A  LEU*     3.6    35.5    -      -       +      +
    131A  LYS*     3.6    41.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  LYS      4.4     0.3    -      -       -      +
     61A  PHE*     3.7     9.2    -      -       -      -
     62A  LEU*     2.8    53.6    +      -       +      +
     64A  PHE*     5.4     0.4    -      -       +      -
     78A  ILE*     3.8     4.2    +      -       +      +
     79A  TRP*     1.3    76.8    -      -       -      +
     81A  THR*     1.3    71.2    +      -       -      +
     82A  PHE*     3.1    18.9    +      -       -      -
     88A  TRP*     3.0    29.1    +      -       +      -
    110A  PHE*     3.9     5.7    -      -       -      -
    118A  THR*     3.0    21.6    +      -       -      -
    119A  PHE*     3.5    32.2    -      -       +      -
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Residues in contact with THR 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  LYS      4.6     8.8    +      -       -      -
     61A  PHE*     4.8     8.6    -      -       -      +
     80A  ASN*     1.3    83.4    +      -       -      +
     82A  PHE*     1.3    62.8    +      -       -      +
     83A  GLY*     3.8     8.1    -      -       -      +
    110A  PHE*     4.1     1.0    -      -       -      -
    116A  PHE      4.0     3.4    -      -       -      +
    117A  GLY*     3.0    11.2    -      -       -      -
    118A  THR*     2.9    60.9    +      -       +      +
     22D    T      5.5    11.8    +      -       -      -
----------------------------------------------------------
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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