Contacts of the strand formed by residues 349 - 359 (chain A) in PDB entry 5X61


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 GLY 349 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  ASN*     3.7     1.2    +      -       -      -
    270A  ALA      3.5    11.0    -      -       -      -
    272A  VAL*     3.7    15.3    -      -       -      -
    303A  ILE*     3.9     6.7    -      -       -      +
    344A  ILE*     2.8    16.4    +      -       -      -
    345A  HIS*     3.2    29.8    +      -       -      +
    347A  PHE      3.6     1.0    -      -       -      -
    348A  GLY*     1.3    79.3    -      -       -      +
    350A  ASP*     1.3    60.0    +      -       -      -
    351A  PRO*     3.5     1.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  ASN*     3.0    31.4    +      -       -      +
    270A  ALA      2.8    17.1    +      -       -      +
    272A  VAL*     3.8     3.9    -      -       -      +
    344A  ILE*     4.1     2.0    -      -       -      -
    349A  GLY*     1.3    72.5    -      -       -      -
    351A  PRO*     1.3    62.2    -      -       -      +
    352A  SER*     2.9    27.2    +      -       -      -
    353A  ARG*     2.8    59.0    +      -       +      -
    354A  VAL*     3.8     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 351 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  ASN*     4.7     1.1    -      -       -      +
    341A  ARG*     3.5    59.8    +      -       -      +
    344A  ILE*     3.8    17.5    -      -       +      -
    345A  HIS*     4.1    21.3    -      -       +      +
    349A  GLY      3.5     9.4    -      -       -      +
    350A  ASP*     1.3    87.9    -      -       -      +
    352A  SER*     1.3    55.9    +      -       -      +
    353A  ARG      3.5     0.4    -      -       -      -
    354A  VAL*     4.0    13.0    +      -       +      +
    378A  LEU      4.7     3.5    -      -       -      +
    379A  PHE*     5.7     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  ARG*     5.1     5.8    -      -       -      +
    350A  ASP*     2.8    23.7    +      -       -      -
    351A  PRO*     1.3    78.2    -      -       -      +
    353A  ARG*     1.3    63.3    +      -       -      +
    354A  VAL      3.5     2.7    -      -       -      -
    379A  PHE      5.2     0.6    -      -       -      -
    380A  GLN*     3.3    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  ASN*     4.6     4.8    +      -       -      -
    270A  ALA*     4.0     6.7    -      -       -      +
    271A  ALA*     3.8    25.9    -      -       +      +
    272A  VAL      3.2    20.0    +      -       -      +
    350A  ASP*     2.8    39.4    +      -       +      +
    352A  SER*     1.3    85.1    -      -       -      +
    354A  VAL*     1.3    60.2    +      -       -      +
    355A  THR*     3.6     5.5    +      -       -      -
    380A  GLN*     3.4    23.7    +      -       -      +
    381A  ARG*     5.7     0.4    -      -       -      +
    637A  ALA      4.5     3.0    +      -       -      +
    638A  LYS*     3.0    38.8    +      -       -      +
    802A  SO4      2.9    42.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  VAL*     3.5    16.6    -      -       +      +
    274A  LEU*     4.2    19.7    -      -       +      -
    337A  LEU*     5.4     0.9    -      -       +      -
    340A  VAL*     4.0    21.5    -      -       +      -
    341A  ARG*     5.7     1.1    -      -       -      +
    350A  ASP      3.9    13.7    -      -       -      +
    351A  PRO*     4.0    15.9    -      -       +      +
    352A  SER      3.5     3.2    +      -       -      -
    353A  ARG*     1.3    74.4    -      -       -      +
    355A  THR*     1.3    60.9    +      -       -      +
    356A  LEU*     4.0    22.7    -      -       +      -
    378A  LEU      4.6     6.7    -      -       -      +
    379A  PHE*     3.5    17.6    -      -       +      +
    380A  GLN*     2.7    28.2    +      -       -      +
    381A  ARG      3.3     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  VAL      2.7    12.3    +      -       -      -
    273A  MET*     3.5     5.1    -      -       +      -
    274A  LEU      2.9    26.7    +      -       -      -
    353A  ARG      3.6     2.6    +      -       -      -
    354A  VAL*     1.3    71.6    -      -       -      +
    356A  LEU*     1.3    71.6    +      -       -      +
    357A  PHE*     3.6     2.1    +      -       +      -
    380A  GLN*     5.1     0.2    +      -       -      -
    381A  ARG*     3.4    31.2    +      -       +      +
    383A  ILE*     4.1    22.0    -      -       +      -
    636A  PHE*     4.6     0.9    -      -       +      -
    637A  ALA*     3.3    45.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  LEU*     3.6    22.2    -      -       +      +
    276A  ILE*     4.5     4.9    -      -       +      -
    337A  LEU*     3.6    28.5    -      -       +      -
    354A  VAL*     4.0    11.9    -      -       +      -
    355A  THR*     1.3    72.9    -      -       -      +
    357A  PHE*     1.3    53.4    +      -       -      +
    366A  VAL*     3.7    20.7    -      -       +      +
    369A  HIS*     3.8    33.7    -      -       +      -
    379A  PHE*     3.7    37.5    -      -       +      -
    381A  ARG      3.0     9.8    +      -       -      +
    382A  ALA*     3.2     2.4    -      -       -      -
    383A  ILE      2.7    32.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273A  MET*     3.7    44.0    -      -       +      -
    274A  LEU      2.8    51.0    +      -       -      +
    275A  TRP*     3.1    50.5    -      +       +      -
    276A  ILE      3.1    21.5    +      -       -      -
    296A  LEU*     3.9    17.7    -      -       +      -
    304A  VAL*     5.2     1.3    -      -       +      -
    355A  THR*     4.1     2.9    -      -       +      +
    356A  LEU*     1.3    75.2    -      -       -      +
    358A  GLY*     1.3    57.7    +      -       -      +
    366A  VAL*     3.8     4.5    -      -       -      +
    383A  ILE*     3.2    29.4    -      -       +      -
    385A  GLN*     4.4     4.7    -      -       -      +
    607A  VAL*     5.1     5.2    -      -       +      -
    608A  PHE*     3.9    12.6    -      +       -      -
    633A  TRP*     4.2    14.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275A  TRP*     3.6     9.3    -      -       -      -
    276A  ILE      3.2    16.4    -      -       -      -
    357A  PHE*     1.3    75.7    -      -       -      +
    359A  GLU*     1.3    59.2    +      -       -      -
    362A  GLY      3.8    10.3    -      -       -      -
    363A  ALA*     3.4    10.0    -      -       -      +
    366A  VAL*     3.6     3.4    -      -       -      +
    383A  ILE      3.3     5.3    +      -       -      -
    384A  LEU      3.9     0.2    -      -       -      -
    385A  GLN*     2.9    29.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 359 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275A  TRP*     3.6    23.4    -      -       +      -
    276A  ILE      4.0     1.0    +      -       -      -
    278A  GLY*     3.4    16.3    +      -       -      +
    358A  GLY*     1.3    73.7    -      -       -      -
    360A  SER*     1.3    83.7    +      -       -      +
    361A  ALA      3.2     0.2    +      -       -      -
    362A  GLY*     2.9    17.7    +      -       -      -
    363A  ALA      3.5     1.0    -      -       -      +
    385A  GLN*     3.2    28.3    -      -       +      +
    386A  SER*     3.8     5.9    +      -       -      -
    600A  HIS*     3.3    27.5    +      -       -      -
    601A  GLY*     3.4    17.6    +      -       -      -
    603A  GLU*     4.0     4.5    -      -       -      +
    604A  ILE*     3.6    25.6    -      -       +      +
----------------------------------------------------------
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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