Contacts of the strand formed by residues 327 - 333 (chain D) in PDB entry 1SAE


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 TYR 327 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331B  GLN*     3.4    37.0    -      -       -      +
    332B  ILE      4.1     3.4    -      -       -      -
    333B  ARG*     4.0    41.5    +      -       +      +
    322D  PRO*     2.4    48.6    +      -       +      +
    323D  LEU*     4.9     3.1    -      -       +      -
    324D  ASP      4.4     1.1    +      -       -      -
    325D  GLY      3.2    16.4    -      -       -      -
    326D  GLU*     1.3    73.3    -      -       -      +
    328D  PHE*     1.3    76.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 328 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331B  GLN*     3.1    20.6    -      -       -      +
    332B  ILE      3.2    15.5    +      -       -      +
    334B  GLY      3.4    14.6    -      -       -      -
    335B  ARG*     3.3    44.9    -      -       +      -
    338B  PHE*     3.5    33.7    -      +       +      -
    326D  GLU*     3.1    44.4    -      -       +      -
    327D  TYR*     1.3    80.3    -      -       -      +
    329D  THR*     1.3    75.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 329 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329B  THR*     5.7     5.8    -      -       -      -
    330B  LEU      3.3    10.5    -      -       -      -
    331B  GLN*     4.5    14.1    -      -       +      +
    332B  ILE*     4.7     0.4    -      -       -      +
    338B  PHE*     3.3    16.9    -      -       -      -
    328D  PHE*     1.3    88.4    -      -       -      +
    330D  LEU*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 330 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329B  THR*     3.3     4.6    -      -       -      -
    330B  LEU*     3.0    31.4    +      -       +      +
    332B  ILE*     3.9    26.7    -      -       +      -
    338B  PHE*     4.1    11.4    -      -       +      -
    341B  PHE*     4.3     4.3    -      -       +      +
    342B  ARG*     4.1    42.4    -      -       +      +
    345B  ASN*     4.2    20.2    -      -       +      +
    329D  THR*     1.3    76.4    -      -       -      +
    331D  GLN*     1.3    78.5    +      -       -      +
    332D  ILE*     3.6    15.7    +      -       +      +
    341D  PHE*     5.1     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 331 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327B  TYR*     3.5    40.8    -      -       +      +
    328B  PHE      3.1    19.5    -      -       -      +
    329B  THR*     4.3     8.6    -      -       +      +
    345B  ASN*     2.9    22.0    +      -       -      -
    330D  LEU*     1.3    79.1    -      -       -      +
    332D  ILE*     1.3    61.1    +      -       -      +
    333D  ARG      4.1     0.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 332 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328B  PHE*     3.2    34.7    +      -       -      -
    330B  LEU*     3.9    27.4    -      -       +      +
    345B  ASN*     4.3     9.0    -      -       -      +
    330D  LEU*     3.8    18.8    -      -       +      +
    331D  GLN*     1.3    78.6    -      -       -      +
    333D  ARG*     1.3    72.0    +      -       -      +
    334D  GLY      3.8     0.2    -      -       -      +
    337D  ARG*     4.3    17.0    -      -       +      +
    338D  PHE*     4.1    34.8    -      -       +      +
    341D  PHE*     3.6    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 333 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322B  PRO*     5.7     1.2    -      -       -      +
    324B  ASP*     2.8    42.7    +      -       -      +
    325B  GLY*     3.9    17.6    -      -       -      +
    326B  GLU      4.2     3.8    -      -       -      -
    327B  TYR*     4.0    39.8    +      -       +      -
    345B  ASN*     4.9     5.0    +      -       -      +
    349B  GLU*     6.0     5.8    -      -       +      -
    331D  GLN*     4.1     2.0    +      -       -      +
    332D  ILE*     1.3    75.1    -      -       -      +
    334D  GLY*     1.3    69.1    +      -       -      +
    337D  ARG*     3.6    34.8    +      -       -      +
----------------------------------------------------------
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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