Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 5A91


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 230 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  LYS*     3.7    37.5    -      -       +      +
    228A  SER      3.5     7.2    +      -       -      +
    229A  TRP*     1.3    72.5    -      -       -      +
    231A  VAL*     1.3    66.3    +      -       -      +
    250A  ILE*     4.3     0.3    -      -       -      +
    251A  TRP*     2.8    51.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  LYS*     3.5    17.1    -      -       -      +
    221A  ILE*     5.1     1.3    -      -       +      -
    222A  ARG*     3.0    53.0    +      -       +      +
    225A  LEU*     3.6    29.2    -      -       +      -
    226A  PRO      5.9     0.2    -      -       -      +
    229A  TRP*     3.6    13.2    +      -       +      +
    230A  VAL*     1.3    83.6    -      -       -      +
    232A  GLY*     1.3    74.2    +      -       -      +
    233A  ASP*     4.4     2.0    -      -       +      -
    248A  ALA*     4.2    13.5    -      -       +      -
    249A  VAL      3.4     8.7    -      -       -      +
    250A  ILE*     4.4     7.0    -      -       +      -
    251A  TRP*     4.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211A  LEU*     3.2    30.9    -      -       -      +
    212A  LYS*     3.6     5.4    -      -       -      -
    222A  ARG*     3.9     0.2    -      -       -      -
    231A  VAL*     1.3    73.3    -      -       -      +
    233A  ASP*     1.3    62.0    +      -       -      +
    248A  ALA*     3.1     4.3    -      -       -      +
    249A  VAL*     2.8    36.3    +      -       -      +
    251A  TRP*     3.7     6.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  LEU      4.8     0.7    -      -       -      +
    211A  LEU*     3.1    21.6    +      -       -      +
    214A  ASN*     3.0    43.4    +      -       -      +
    217A  GLY*     3.7     3.9    -      -       -      -
    221A  ILE*     5.7     0.4    -      -       +      -
    222A  ARG*     2.8    34.7    +      -       +      -
    231A  VAL*     4.4     3.6    -      -       +      -
    232A  GLY*     1.3    76.8    -      -       -      +
    234A  LYS*     1.3    62.0    +      -       -      +
    235A  THR*     3.5     7.3    -      -       -      +
    246A  ASP*     2.5    31.9    -      -       -      +
    247A  ILE      3.1    14.4    -      -       -      +
    248A  ALA*     3.9    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  SER*     3.4    21.3    -      -       -      +
     71A  THR*     3.4    10.2    -      -       -      +
     73A  LYS*     3.9     5.6    -      -       -      -
     74A  VAL*     3.5    29.8    -      -       +      -
    126A  ALA      3.5    22.2    -      -       -      -
    127A  LEU*     3.5    31.0    +      -       +      +
    130A  SER*     2.9    27.9    +      -       -      -
    211A  LEU*     4.2     2.6    -      -       +      +
    214A  ASN*     4.4     1.8    -      -       -      +
    216A  THR*     4.6     1.6    +      -       -      -
    233A  ASP*     1.3    74.3    -      -       -      +
    235A  THR*     1.3    90.1    +      -       -      +
    246A  ASP*     3.2     4.3    -      -       -      -
    247A  ILE*     2.9    33.8    +      -       +      +
   1291A  SO4      3.2     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  SER      3.4    10.2    -      -       -      -
     71A  THR*     3.7     3.4    -      -       -      -
    216A  THR*     2.7    40.8    +      -       -      +
    217A  GLY*     3.7     8.1    -      -       -      -
    220A  SER*     4.0    10.8    -      -       -      +
    233A  ASP*     3.5     9.6    +      -       -      +
    234A  LYS*     1.3    97.8    +      -       -      +
    236A  GLY*     1.3    59.3    +      -       -      +
    245A  ASN      3.4     8.7    -      -       -      +
    246A  ASP*     3.5    17.3    -      -       -      +
    276A  ASN*     5.1     2.0    -      -       -      +
   1291A  SO4      2.5    23.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  CYS*     3.8     6.5    -      -       -      -
     70A  SER*     3.6    19.3    -      -       -      -
     71A  THR*     3.7     7.0    -      -       -      +
    235A  THR*     1.3    77.0    -      -       -      +
    237A  SER*     1.3    61.6    +      -       -      -
    244A  THR*     3.7     0.7    -      -       -      +
    245A  ASN*     2.8    38.8    +      -       -      +
   1291A  SO4      3.6     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  CYS*     3.7     6.0    -      -       -      +
    170A  ASN*     3.4    21.0    +      -       -      +
    236A  GLY*     1.3    75.8    -      -       -      -
    238A  GLY*     1.3    59.0    +      -       -      +
    243A  THR      3.1    11.9    -      -       -      -
    244A  THR*     4.7     4.9    -      -       -      -
    274A  ASN*     3.7    20.0    +      -       -      -
    276A  ASN*     5.8     2.0    -      -       -      -
   1291A  SO4      2.8    26.4    +      -       -      -
----------------------------------------------------------
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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