Contacts of the strand formed by residues 244 - 251 (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 THR 244 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  GLY      3.7     2.5    -      -       -      +
    237A  SER*     4.6     2.9    -      -       -      +
    242A  GLY      2.8    16.1    +      -       -      -
    243A  THR*     1.3    74.2    -      -       -      +
    245A  ASN*     1.3    66.4    +      -       -      +
    265A  PHE*     2.8    33.4    +      -       -      +
    274A  ASN*     3.2     8.9    -      -       +      +
    275A  ARG*     2.9    24.6    +      -       -      +
    276A  ASN*     3.3    52.0    -      -       -      +
    279A  LEU*     3.4     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  PHE*     5.2     0.7    -      -       -      +
     67A  ALA      2.8    27.7    +      -       -      -
     68A  MET*     3.1    18.6    +      -       -      +
     69A  CYS*     4.2     0.4    -      -       -      +
     71A  THR*     3.7     7.9    -      -       +      -
    235A  THR*     3.4     5.9    -      -       -      +
    236A  GLY      2.8    33.4    +      -       -      +
    243A  THR*     3.8    10.5    -      -       -      +
    244A  THR*     1.3    84.2    -      -       -      +
    246A  ASP*     1.3    65.2    +      -       -      +
    263A  THR      3.4     4.9    -      -       -      -
    264A  TYR*     3.2    37.8    -      -       +      +
    265A  PHE      3.2     8.3    +      -       -      +
    276A  ASN*     4.8     1.7    -      -       -      +
    279A  LEU*     3.5     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  THR*     4.4     0.4    -      -       -      -
    217A  GLY      4.7     0.3    -      -       -      +
    220A  SER*     3.3    11.3    -      -       -      -
    221A  ILE*     3.0    45.3    +      -       +      +
    222A  ARG      4.6     0.7    +      -       -      -
    233A  ASP*     2.5    34.7    -      -       -      +
    234A  LYS      3.1    17.9    -      -       -      +
    235A  THR*     3.4     3.2    +      -       -      -
    245A  ASN*     1.3    77.6    -      -       -      +
    247A  ILE*     1.3    68.7    +      -       -      +
    263A  THR*     2.9    32.9    +      -       -      +
    279A  LEU*     3.9    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  THR*     4.0    25.4    -      -       +      +
     74A  VAL*     4.1    15.7    -      -       +      -
    186A  MET*     4.0    24.5    -      -       +      -
    190A  LEU*     3.9    26.5    -      -       +      +
    211A  LEU*     5.5     1.0    -      -       +      +
    233A  ASP*     3.1     4.1    -      -       -      +
    234A  LYS*     2.9    45.4    +      -       +      +
    246A  ASP*     1.3    79.4    +      -       -      +
    248A  ALA*     1.3    61.1    +      -       -      +
    261A  LEU      3.5     4.3    -      -       -      -
    262A  VAL*     3.8    18.4    -      -       +      -
    264A  TYR*     3.7    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190A  LEU*     3.6     8.2    -      -       -      +
    221A  ILE*     3.8    32.1    -      -       +      -
    231A  VAL*     4.2     8.3    -      -       +      -
    232A  GLY      3.1    11.2    -      -       -      +
    233A  ASP*     3.9     8.1    -      -       +      -
    247A  ILE*     1.3    75.2    -      -       -      +
    249A  VAL*     1.3    65.1    +      -       -      +
    250A  ILE*     4.3     6.9    -      -       +      +
    259A  LEU      4.1     0.2    -      -       -      +
    260A  VAL*     3.4     3.8    -      -       -      -
    261A  LEU      2.8    35.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190A  LEU*     3.9    13.0    -      -       +      +
    194A  THR*     3.2    34.5    -      -       +      +
    195A  LEU*     3.9    23.1    -      -       +      -
    211A  LEU*     5.0     4.0    -      -       +      -
    231A  VAL*     3.4     4.5    -      -       -      +
    232A  GLY*     2.8    33.6    +      -       -      +
    248A  ALA*     1.3    76.5    -      -       -      +
    250A  ILE*     1.3    64.8    +      -       -      +
    251A  TRP*     3.4    37.6    -      -       +      -
    258A  PRO*     4.6     0.9    -      -       +      -
    259A  LEU      3.6     7.2    -      -       -      +
    260A  VAL*     4.5     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  ILE*     4.3     7.9    -      -       +      -
    225A  LEU*     3.8    30.3    -      -       +      -
    229A  TRP*     3.4    35.4    -      -       +      -
    230A  VAL      3.6     7.9    -      -       -      +
    231A  VAL*     4.4     3.8    -      -       +      +
    248A  ALA*     4.3     9.0    -      -       +      -
    249A  VAL*     1.3    79.5    -      -       -      +
    251A  TRP*     1.3    63.3    +      -       -      +
    252A  PRO*     3.3     6.5    -      -       +      +
    258A  PRO*     3.2     6.9    -      -       -      +
    259A  LEU*     2.8    48.9    +      -       +      +
    261A  LEU*     4.1    30.3    -      -       +      -
    287A  THR*     4.5     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  THR*     5.6     0.4    -      -       +      -
    195A  LEU*     4.1    14.1    -      -       +      +
    204A  ARG*     5.6     1.8    -      -       -      -
    208A  VAL*     3.7    35.4    -      -       +      -
    211A  LEU*     6.4     1.6    -      -       +      -
    212A  LYS*     3.7    19.3    -      -       +      -
    229A  TRP*     4.1     2.7    -      -       -      -
    230A  VAL*     2.8    54.7    +      -       +      +
    232A  GLY*     3.7    12.8    -      -       -      -
    249A  VAL*     3.4    43.3    -      -       +      -
    250A  ILE*     1.3    75.8    -      -       -      +
    252A  PRO*     1.3    70.0    -      -       -      +
    256A  HIS      5.3     0.4    -      -       -      -
    258A  PRO*     3.7    24.2    -      -       +      +
----------------------------------------------------------
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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