Contacts of the strand formed by residues 270 - 275 (chain I) in PDB entry 1SXG


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 GLU 270 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172I  LEU*     4.4     9.8    -      -       +      +
    175I  SER*     4.1     8.2    +      -       -      -
    177I  HIS*     2.8    37.0    +      -       +      +
    241I  THR      2.9     7.1    +      -       -      -
    242I  ALA*     2.9    10.8    -      -       +      +
    243I  ILE      2.8    24.3    +      -       -      +
    266I  PRO*     3.1    25.7    -      -       +      +
    269I  LEU*     1.3    73.5    -      -       -      +
    271I  ILE*     1.3    61.6    +      -       -      +
    330I  SER      3.7     6.7    -      -       -      +
    331I  THR*     3.3    10.2    +      -       -      +
    332I  LYS*     2.9    49.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 271 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243I  ILE*     3.2    18.2    -      -       +      +
    245I  VAL*     4.4    10.1    -      -       +      -
    251I  ALA*     4.5     2.2    -      -       +      +
    254I  VAL*     3.4    30.5    -      -       +      +
    255I  ILE*     4.0    16.6    -      -       +      -
    265I  VAL*     4.2    16.6    -      -       +      -
    269I  LEU*     3.2    34.5    +      -       +      -
    270I  GLU*     1.3    72.7    -      -       -      +
    272I  ILE*     1.3    71.6    +      -       -      +
    287I  LEU*     3.5    25.6    -      -       +      -
    288I  THR*     4.3     0.3    -      -       -      -
    330I  SER*     2.5    38.3    +      -       -      +
    331I  THR*     4.5     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 272 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168I  ALA*     3.5    42.0    -      -       +      +
    171I  SER*     3.7    17.5    -      -       -      +
    172I  LEU*     3.8    21.8    -      -       +      -
    243I  ILE      3.0     9.3    +      -       -      +
    244I  PHE*     3.6     9.8    -      -       +      -
    245I  VAL*     2.9    26.0    +      -       -      +
    271I  ILE*     1.3    81.9    -      -       -      +
    273I  GLY*     1.3    71.9    +      -       -      +
    288I  THR*     3.2    30.7    -      -       +      +
    289I  SER*     4.5     0.7    -      -       -      -
    290I  VAL*     4.4     5.6    -      -       +      -
    325I  ILE*     5.1     2.2    -      -       +      -
    327I  PHE*     4.9     1.6    -      -       +      -
    331I  THR*     4.5     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 273 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244I  PHE*     4.2     1.6    -      -       -      -
    245I  VAL      3.5     9.5    -      -       -      +
    251I  ALA*     4.0     9.2    -      -       -      -
    272I  ILE*     1.3    81.4    -      -       -      +
    274I  PHE*     1.3    63.5    +      -       -      +
    287I  LEU*     3.7    21.7    -      -       -      +
    288I  THR      2.6    15.3    +      -       -      -
    289I  SER*     3.4     6.5    -      -       -      -
    290I  VAL*     3.1    17.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 274 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159I  ILE*     4.0     4.7    -      -       +      -
    161I  TYR*     3.7    31.6    -      +       -      -
    164I  ALA*     3.7    29.4    -      -       +      -
    165I  ALA*     4.2     8.3    -      -       -      -
    196I  LYS*     4.1    21.5    -      -       +      -
    244I  PHE*     3.9    16.6    -      +       -      -
    245I  VAL      3.7     3.6    +      -       -      +
    246I  GLY*     3.4    21.8    -      -       -      +
    247I  THR*     3.7     0.5    -      -       -      -
    248I  ASP*     2.9    22.2    +      -       -      +
    273I  GLY*     1.3    72.2    -      -       -      -
    275I  ASP*     1.3    97.7    +      -       -      +
    289I  SER*     3.1     9.8    +      -       -      -
    290I  VAL*     3.6    24.5    -      -       +      +
    292I  GLN*     3.6    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 275 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74I  PHE*     3.3    35.1    -      -       +      +
    196I  LYS*     5.2     1.7    +      -       -      -
    246I  GLY      5.0     0.8    -      -       -      +
    247I  THR*     4.1    13.7    +      -       -      +
    248I  ASP      4.6     1.9    +      -       -      -
    274I  PHE*     1.3    90.9    -      -       -      +
    276I  ASN*     1.3    69.4    +      -       -      +
    277I  THR*     3.4    20.7    -      -       +      +
    290I  VAL      2.7    13.4    +      -       -      -
    292I  GLN*     2.7    54.5    +      -       -      +
    294I  MET*     3.8     4.7    -      -       -      +
----------------------------------------------------------
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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