Contacts of the strand formed by residues 319 - 329 (chain B) in PDB entry 3L73


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 SER 319 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168B  TYR*     3.2    16.9    +      -       -      -
    172B  LEU*     4.4     2.9    -      -       -      -
    237B  ALA*     4.1    11.0    -      -       -      -
    260B  GLU*     2.8    29.0    +      -       -      -
    261B  GLY      5.3     1.6    -      -       -      -
    262B  ALA      3.7     5.2    -      -       -      -
    263B  ALA*     3.3    10.4    -      -       -      +
    316B  TYR*     2.5    46.9    +      -       -      +
    318B  ASP*     1.3    87.7    +      -       -      +
    320B  GLY*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168B  TYR*     3.5     6.9    +      -       -      -
    260B  GLU*     3.6     5.5    -      -       -      +
    261B  GLY      3.2    20.8    +      -       -      -
    262B  ALA      3.0    19.8    +      -       -      -
    314B  VAL      3.2     7.9    -      -       -      -
    316B  TYR*     4.2     5.4    -      -       -      -
    319B  SER*     1.3    83.0    +      -       -      +
    321B  LEU*     1.3    72.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 321 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  LEU*     4.3    11.2    -      -       +      -
    164B  HIS*     4.3    26.5    -      -       +      +
    167B  ALA*     3.8    22.7    -      -       +      -
    168B  TYR*     3.7    23.6    -      -       +      +
    239B  TYR*     4.5     5.8    -      -       +      -
    258B  VAL*     3.6    25.8    -      -       +      -
    259B  THR      3.6    10.8    -      -       -      +
    261B  GLY*     4.0     2.6    -      -       -      +
    312B  PHE*     4.2     7.6    -      -       +      -
    313B  ASN*     3.4     4.2    -      -       -      +
    314B  VAL*     2.8    47.1    +      -       +      +
    316B  TYR*     5.2     2.5    -      -       +      -
    320B  GLY*     1.3    81.6    -      -       -      +
    322B  PHE*     1.3    60.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 322 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    258B  VAL*     3.0     7.5    -      -       -      +
    259B  THR*     2.7    38.6    +      -       -      +
    261B  GLY*     4.4     7.0    -      -       -      -
    272B  PHE*     3.4    51.1    -      +       +      -
    275B  LEU*     3.5    37.2    -      -       +      -
    276B  GLN*     4.3     9.4    -      -       +      -
    279B  LEU*     4.1    13.7    -      -       +      -
    311B  ALA*     5.1     2.0    -      -       +      -
    312B  PHE      3.4    14.8    -      -       -      -
    313B  ASN*     3.4    23.1    -      -       +      +
    321B  LEU*     1.3    76.8    -      -       -      +
    323B  GLY*     1.3    82.3    +      -       -      +
    344B  LEU*     4.6     7.6    -      -       +      -
    417B  PHE*     3.4    17.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLY 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257B  VAL      3.3    12.6    -      -       -      -
    258B  VAL*     3.9     2.1    -      -       -      +
    279B  LEU*     5.9     1.0    -      -       -      +
    311B  ALA*     3.5     5.4    -      -       -      +
    312B  PHE*     2.5    40.2    +      -       -      +
    322B  PHE*     1.3    87.4    -      -       -      +
    324B  PHE*     1.3    56.2    +      -       -      -
    344B  LEU*     5.2     2.0    -      -       -      -
    417B  PHE*     3.5    13.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255B  ALA*     5.3     2.7    -      -       +      -
    256B  ALA*     3.4     3.1    -      -       -      +
    257B  VAL*     3.2    50.6    +      -       +      +
    258B  VAL*     4.9     0.5    -      -       -      +
    279B  LEU*     6.5     0.2    -      -       +      -
    295B  LEU*     3.7    17.7    -      -       +      -
    310B  SER      3.1    13.9    -      -       -      +
    312B  PHE*     4.0     4.7    -      -       -      +
    323B  GLY*     1.3    74.8    -      -       -      -
    325B  TYR*     1.3    60.9    +      -       -      +
    326B  THR*     3.5    23.6    -      -       +      -
    337B  ILE*     4.0    23.8    -      -       +      -
    340B  ALA*     3.5    26.7    -      -       +      -
    341B  MET*     3.6    34.1    -      -       +      -
    344B  LEU*     3.3    21.1    -      -       +      -
    417B  PHE*     4.1     7.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156B  GLN*     3.5    13.4    -      -       -      -
    159B  VAL*     3.2    34.5    -      -       +      +
    160B  LEU*     4.1     4.9    -      -       +      -
    254B  HIS*     2.4    45.2    +      +       +      -
    255B  ALA      3.2     9.6    -      -       -      -
    256B  ALA*     4.2    11.9    -      -       +      -
    309B  ALA*     3.3     0.7    -      -       -      -
    310B  SER      3.0    30.8    +      -       -      +
    312B  PHE*     4.4     4.9    -      +       +      +
    324B  PHE*     1.3    74.1    -      -       -      +
    326B  THR*     1.3    67.6    +      -       -      +
    327B  ILE*     3.9    11.4    -      -       +      -
     58I  ARG      4.7     0.2    -      -       -      -
     59I  SER*     3.1    18.6    +      -       -      -
     60I  ALA*     3.0    53.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253B  VAL      3.3     4.9    -      -       -      +
    254B  HIS*     3.4     0.5    -      -       -      -
    255B  ALA*     2.7    47.9    +      -       -      +
    308B  ASP      3.3     7.4    -      -       -      -
    309B  ALA*     4.0    14.8    -      -       +      -
    324B  PHE*     3.5    28.7    -      -       +      -
    325B  TYR*     1.3    82.7    -      -       -      +
    327B  ILE*     1.3    63.3    +      -       -      +
    328B  SER*     5.2     2.1    +      -       -      -
    336B  VAL*     4.3    17.4    -      -       +      +
    337B  ILE*     3.7    14.0    -      -       +      +
    340B  ALA*     4.3     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  LEU*     4.3     8.7    -      -       +      -
    253B  VAL      3.4     4.0    -      -       -      +
    254B  HIS*     3.5    36.3    -      -       +      +
    307B  PHE*     3.2     3.3    -      -       -      +
    308B  ASP*     2.8    38.9    +      -       +      +
    325B  TYR*     3.9     5.4    -      -       +      -
    326B  THR*     1.3    74.3    -      -       -      +
    328B  SER*     1.3    67.6    +      -       -      +
    336B  VAL*     5.2     0.3    -      -       -      +
     49I  LEU*     6.3     0.2    -      -       +      -
     55I  MET*     3.2    28.0    -      -       +      +
     58I  ARG*     3.3    50.0    -      -       +      +
     59I  SER*     3.6    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  LEU*     3.6     7.3    -      -       -      -
    253B  VAL*     2.9    30.6    +      -       -      -
    306B  PRO      4.3     2.2    -      -       -      -
    307B  PHE*     4.1    10.5    -      -       -      +
    326B  THR*     5.2     3.0    +      -       -      -
    327B  ILE*     1.3    80.8    -      -       -      +
    329B  GLN*     1.3    68.0    +      -       -      +
    332B  HIS*     4.7     1.3    -      -       -      -
    333B  ALA*     3.2    30.3    -      -       -      +
    336B  VAL*     4.1    27.1    -      -       -      +
     55I  MET*     4.6     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251B  SER      3.8     7.6    -      -       -      +
    252B  LEU*     4.0    11.6    -      -       +      +
    305B  GLN*     3.4    39.6    +      -       +      +
    306B  PRO*     3.9    25.6    +      -       +      +
    328B  SER*     1.3    75.4    -      -       -      +
    330B  ALA*     1.3    67.2    +      -       -      +
    331B  ALA*     3.3     3.7    -      -       +      +
    332B  HIS*     2.8    30.8    +      -       +      +
    333B  ALA      3.2     6.9    +      -       -      -
     50I  LEU      5.0     2.9    -      -       -      +
     55I  MET*     6.5     0.2    -      -       -      -
----------------------------------------------------------
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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