Contacts of the strand formed by residues 71 - 81 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  ASP*     2.6    28.7    +      -       +      +
     70B  ASN*     1.3    74.9    -      -       +      +
     72B  LYS*     1.3    51.7    +      -       -      +
     73B  SER*     3.0     8.0    +      -       -      -
     74B  ASN*     2.6    63.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 72 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  PHE*     3.6    36.4    -      -       +      +
     68B  ASP      2.8    14.1    +      -       -      +
     69B  PRO      4.1     6.7    +      -       -      +
     70B  ASN      3.7     2.0    -      -       -      -
     71B  ASP*     1.3    69.7    -      -       -      +
     73B  SER*     1.3    78.1    +      -       -      +
     74B  ASN      3.4     0.9    +      -       -      -
     75B  LYS*     4.2     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 73 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  ASP*     2.8    10.3    +      -       -      -
     72B  LYS*     1.3    91.3    +      -       -      +
     74B  ASN*     1.3    57.1    +      -       -      -
     75B  LYS*     3.1    22.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 74 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  ASN*     4.5     7.4    -      -       -      +
     50B  LEU*     5.4     1.0    -      -       -      +
     67B  PHE*     3.7    17.7    -      -       -      -
     68B  ASP*     4.0     7.2    +      -       +      +
     71B  ASP*     2.6    42.8    +      -       +      +
     72B  LYS      4.4     1.3    -      -       -      -
     73B  SER*     1.3    67.0    -      -       -      +
     75B  LYS*     1.3    65.5    +      -       -      +
     76B  TRP*     3.5    28.9    +      -       -      +
    123B  ASN*     4.2    15.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 75 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  GLU*     3.3    26.1    +      -       +      +
     66B  LEU      3.3     7.4    -      -       -      +
     67B  PHE*     4.7     3.8    -      -       +      -
     72B  LYS      4.2    11.4    -      -       -      +
     73B  SER*     3.1    17.1    +      -       -      +
     74B  ASN*     1.3    74.9    +      -       -      +
     76B  TRP*     1.3    62.4    +      -       -      +
     77B  TYR*     3.2    23.9    +      -       +      +
    123B  ASN*     3.4    28.9    -      -       -      +
    125B  GLU*     2.7    37.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 76 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  GLY      4.7     2.0    -      -       -      -
     43B  ASP*     3.6    33.2    -      -       +      -
     44B  PHE*     3.7    37.0    -      +       +      -
     47B  ASN*     3.2    33.2    -      -       +      +
     50B  LEU*     3.8    35.2    -      -       +      +
     65B  GLU*     3.5     1.0    -      -       -      +
     66B  LEU*     2.7    39.7    +      -       +      +
     74B  ASN*     3.5    31.2    +      -       -      +
     75B  LYS*     1.3    76.6    -      -       -      +
     77B  TYR*     1.3    67.5    +      -       -      +
    121B  PHE      4.9     0.4    -      -       -      -
    122B  SER*     3.4    17.7    -      -       -      -
    123B  ASN*     3.3    42.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 77 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  PHE*     5.0     1.7    -      -       -      -
     63B  TRP*     4.1     7.9    -      +       +      -
     64B  PHE      3.2    12.8    -      -       -      +
     65B  GLU*     3.5    26.4    +      -       +      -
     66B  LEU*     4.7     0.4    -      -       -      -
     75B  LYS*     3.2    51.8    +      -       +      +
     76B  TRP*     1.3    78.4    -      -       -      +
     78B  ILE*     1.3    65.1    +      -       -      +
     79B  TRP*     4.0    18.6    -      -       +      +
    120B  LYS      3.7     0.5    -      -       -      +
    121B  PHE*     3.3     6.1    -      -       -      +
    122B  SER*     2.6    44.3    +      -       -      +
    124B  SER      4.1    10.3    -      -       -      -
    125B  GLU*     3.4    37.4    +      -       +      +
    128B  LEU*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  LEU*     4.2    12.3    -      -       +      -
     26B  ILE*     5.4     2.2    -      -       +      -
     44B  PHE*     3.8    26.2    -      -       +      -
     63B  TRP*     3.1     7.8    -      -       -      +
     64B  PHE*     3.0    51.8    +      -       +      -
     66B  LEU*     4.1    14.8    -      -       +      -
     77B  TYR*     1.3    75.4    -      -       -      +
     79B  TRP*     1.3    63.4    +      -       -      +
     80B  ASN*     5.1     0.4    -      -       +      -
    100B  LEU*     4.9    11.2    -      -       +      -
    119B  PHE*     4.0    25.1    -      -       +      -
    120B  LYS      3.5     3.8    -      -       -      +
    121B  PHE*     3.7    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  PHE*     3.7    27.1    -      +       +      -
     62B  LEU      3.9     3.6    -      -       -      -
     63B  TRP*     4.4     0.9    -      -       +      -
     77B  TYR*     4.0    18.3    -      -       +      +
     78B  ILE*     1.3    78.2    -      -       -      +
     80B  ASN*     1.3    60.8    +      -       -      +
    118B  THR*     4.3     0.4    -      -       -      -
    119B  PHE*     3.2     9.8    -      -       -      -
    120B  LYS*     2.7    79.4    +      -       +      +
    122B  SER*     4.0    16.7    -      -       -      -
    127B  GLU*     3.6    30.1    -      -       +      -
    128B  LEU*     3.7    40.2    -      -       +      +
    131B  LYS*     3.6    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  PHE*     3.7     2.3    -      -       -      -
     62B  LEU*     2.8    53.7    +      -       +      +
     64B  PHE*     5.3     0.4    -      -       +      -
     78B  ILE*     4.8     3.6    -      -       +      +
     79B  TRP*     1.3    77.3    -      -       -      +
     81B  THR*     1.3    76.0    +      -       -      +
     82B  PHE*     3.3    16.1    -      -       -      -
     88B  TRP*     3.0    30.7    +      -       +      -
    110B  PHE*     4.1     4.9    -      -       -      -
    118B  THR*     2.9    23.7    +      -       -      -
    119B  PHE*     3.4    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LYS*     4.3     6.5    -      -       -      +
     61B  PHE*     3.9    24.9    -      -       +      -
     80B  ASN*     1.3    86.3    +      -       -      +
     82B  PHE*     1.3    65.6    +      -       -      +
     83B  GLY*     4.6     4.0    +      -       -      -
    110B  PHE*     4.2     0.5    -      -       -      -
    116B  PHE      4.6     1.2    +      -       -      -
    117B  GLY*     3.1     4.9    -      -       -      -
    118B  THR*     2.3    62.9    +      -       -      +
    131B  LYS*     5.5     5.6    -      -       -      +
     22F    T      6.1     6.7    -      -       -      +
----------------------------------------------------------
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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