Contacts of the strand formed by residues 318 - 324 (chain A) in PDB entry 4MSL


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 318 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283A  SER*     4.7     0.9    -      -       -      -
    292A  ARG*     3.1    23.2    +      -       +      -
    293A  ARG*     3.3    13.7    -      -       -      -
    294A  ILE*     3.4    45.0    +      -       +      -
    309A  LEU*     4.6     4.5    -      -       +      -
    310A  PRO      2.7    29.3    +      -       -      -
    311A  SER*     3.5     1.9    -      -       -      -
    312A  VAL*     3.6    25.8    +      -       +      -
    317A  PHE*     1.3    78.5    -      -       -      +
    319A  SER*     1.3    60.8    +      -       -      +
    330A  MET*     4.2    12.3    -      -       +      -
    331A  HIS      3.4     3.6    -      -       -      +
    332A  VAL*     3.7    27.6    -      -       +      -
    809A  2ET      2.7    62.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  PHE*     3.9     8.3    -      -       -      -
    318A  TYR*     1.3    77.6    -      -       -      +
    320A  ILE*     1.3    69.4    +      -       -      +
    321A  LEU*     3.3     1.8    +      -       -      +
    330A  MET*     3.5     8.1    -      -       -      +
    331A  HIS*     2.8    40.8    +      -       -      +
    362A  TYR*     2.9    42.7    +      -       -      -
    809A  2ET      3.5    15.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  GLY*     5.8     3.8    -      -       -      -
    275A  LEU      5.4     7.6    -      -       -      +
    276A  GLY*     5.2     3.4    -      -       -      +
    281A  PHE*     3.8    26.5    -      -       +      -
    319A  SER*     1.3    76.5    +      -       -      +
    321A  LEU*     1.3    64.0    +      -       -      +
    322A  ALA*     3.8    22.2    -      -       -      +
    323A  ALA*     3.8    18.6    -      -       +      +
    328A  VAL*     4.6     5.8    -      -       +      -
    329A  PHE      3.8     3.8    -      -       -      +
    330A  MET*     3.5    32.3    -      -       +      -
    809A  2ET      4.8    17.4    +      -       +      +
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Residues in contact with LEU 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  SER*     3.3     1.1    +      -       -      +
    320A  ILE*     1.3    77.9    -      -       -      +
    322A  ALA*     1.3    61.6    +      -       -      +
    329A  PHE*     2.7    19.5    +      -       +      +
    331A  HIS*     3.7    24.2    -      -       +      +
    343A  ILE*     3.6    44.2    -      -       +      -
    360A  HIS*     3.9    11.4    -      -       +      -
    362A  TYR*     3.6    32.5    -      -       +      -
    369A  THR*     4.3    10.1    -      -       +      -
    371A  PHE*     3.8    30.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  ILE*     3.4     4.6    -      -       -      +
    321A  LEU*     1.3    82.3    -      -       -      +
    323A  ALA*     1.3    62.6    +      -       -      +
    328A  VAL*     3.2     4.2    -      -       -      +
    329A  PHE*     2.9    39.3    +      -       +      +
    371A  PHE*     4.0    11.7    -      -       +      -
    373A  ASN*     5.1     4.0    -      -       +      +
    381A  TYR*     4.6     4.0    -      -       +      -
      1B  NAG      3.5    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  GLY*     3.5    29.6    -      -       -      -
    277A  GLY*     3.5     6.4    +      -       -      +
    320A  ILE*     3.8     8.7    -      -       +      +
    322A  ALA*     1.3    78.3    -      -       -      +
    324A  ASN*     1.3    61.4    +      -       -      +
    327A  MET      3.3     5.2    -      -       -      -
    328A  VAL*     3.4    22.7    -      -       +      -
      1B  NAG      2.9    12.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277A  GLY*     4.0    13.1    -      -       -      -
    279A  PHE*     4.4     2.9    -      -       -      -
    323A  ALA*     1.3    75.2    -      -       -      +
    325A  ASP*     1.3    57.2    +      -       -      +
    326A  ASP*     2.7    22.1    +      -       -      -
    327A  MET*     2.6    52.7    +      -       -      +
    381A  TYR*     4.7     1.2    +      -       -      -
    400A  GLN*     3.7    19.8    +      -       -      -
      1B  NAG      3.3    47.5    +      -       -      +
      2B  NAG      4.2     8.3    -      -       -      +
----------------------------------------------------------
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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