Contacts of the strand formed by residues 64 - 75 (chain A) in PDB entry 5X1X


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 VAL 64 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  LYS*     3.4    40.6    -      -       -      +
     50A  LEU*     5.0     4.3    -      -       +      -
     51A  ILE*     5.5     2.9    -      -       +      +
     54A  ILE*     4.9    12.3    -      -       +      -
     62A  LEU      4.1     5.8    +      -       -      +
     63A  ILE*     1.3    91.5    -      -       -      +
     65A  GLY*     1.3    70.9    +      -       -      +
     85A  TYR*     3.7    24.5    -      -       +      -
     86A  LYS      3.4    10.3    -      -       -      +
     87A  CYS*     4.6    12.1    -      -       -      -
     88A  THR*     4.8     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  VAL*     1.3    79.6    -      -       -      +
     66A  ASP*     1.3    69.7    +      -       -      +
     86A  LYS*     2.7    20.2    +      -       -      -
     88A  THR*     5.0     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  VAL*     4.4     0.4    -      -       -      +
     65A  GLY*     1.3    81.3    -      -       -      +
     67A  LYS*     1.3    71.1    +      -       -      +
     68A  VAL*     3.4     0.9    +      -       -      +
     85A  TYR*     3.7    10.1    -      -       -      -
     86A  LYS*     3.4    29.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  GLU*     3.5    18.4    +      -       -      -
     66A  ASP*     1.3    82.0    +      -       -      +
     68A  VAL*     1.3    65.8    -      -       -      +
     69A  ILE*     4.1     9.2    -      -       -      +
     70A  THR*     2.9    26.9    +      -       -      +
     83A  THR*     2.9    23.8    -      -       -      +
     85A  TYR*     3.2    47.6    +      -       +      +
    125A  LYS*     3.9     7.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ILE*     3.5    16.8    -      -       +      -
     67A  LYS*     1.3    74.9    -      -       -      +
     69A  ILE*     1.3    62.5    +      -       +      +
     84A  THR*     3.0    43.3    +      -       -      +
     86A  LYS*     3.5    31.2    -      -       +      +
    122A  ALA*     3.4    28.0    -      -       +      +
    125A  LYS*     2.9    42.1    +      -       +      +
    126A  ILE*     5.5     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  LYS*     3.8     5.7    -      -       -      +
     68A  VAL*     1.3    84.5    -      -       +      +
     70A  THR*     1.3    77.7    +      -       -      +
     71A  THR*     4.0    12.5    +      -       -      +
     83A  THR*     3.0    27.2    +      -       -      -
     84A  THR*     3.8     1.3    +      -       -      +
    121A  PRO*     4.4    19.5    -      -       +      +
    122A  ALA*     3.2    38.4    -      -       +      +
    125A  LYS*     5.1     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  GLU*     5.7     4.9    -      -       -      +
     67A  LYS*     2.9    31.7    +      -       -      +
     69A  ILE*     1.3    82.8    -      -       -      +
     71A  THR*     1.3    66.4    +      -       -      +
     72A  GLU*     3.6    27.1    -      -       +      +
     81A  ARG*     5.8     2.9    -      -       +      -
     82A  LEU      4.4     1.3    -      -       -      +
     83A  THR*     4.5     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ILE*     4.0    12.1    -      -       -      +
     70A  THR*     1.3    76.8    -      -       -      +
     72A  GLU*     1.3    66.7    +      -       -      +
     73A  HIS*     3.6    13.9    -      -       +      +
     81A  ARG*     3.1     6.1    -      -       -      +
     82A  LEU      2.9    39.3    +      -       -      +
    117A  PRO      4.3     0.9    -      -       -      +
    118A  ALA*     2.7    45.6    +      -       -      +
    121A  PRO*     4.3    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  THR*     3.6    22.0    -      -       +      +
     71A  THR*     1.3    84.7    -      -       -      +
     73A  HIS*     1.3    73.5    +      -       -      +
     79A  ILE*     4.3     5.9    -      -       +      +
     80A  VAL      3.4     7.2    -      -       -      +
     81A  ARG*     3.5    52.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  THR*     3.6    20.2    -      -       +      +
     72A  GLU*     1.3    98.8    +      -       -      +
     74A  GLU*     1.3    61.8    +      -       -      +
     75A  TYR*     3.5     8.7    +      +       +      -
     79A  ILE*     3.4    10.8    -      -       -      +
     80A  VAL*     3.0    48.9    +      -       +      -
    117A  PRO*     4.0    31.5    -      -       +      +
    118A  ALA*     3.6    22.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  LYS*     3.3    25.9    +      -       -      +
     73A  HIS*     1.3    72.0    -      -       -      +
     75A  TYR*     1.3    71.5    +      -       -      +
     76A  ASP*     5.6     0.3    -      -       -      +
     79A  ILE*     3.1    32.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  LYS*     3.6    11.6    +      -       -      -
      5A  ILE*     6.0     3.1    -      -       +      -
     28A  SER*     5.2    10.9    +      -       -      -
     73A  HIS*     3.5     8.2    +      -       +      -
     74A  GLU*     1.3    90.8    -      -       -      +
     76A  ASP*     1.3    65.6    +      -       -      +
     77A  PHE*     4.1    10.1    -      +       +      +
     78A  GLY      2.6    37.3    +      -       -      +
     79A  ILE      4.9     0.2    -      -       -      -
     80A  VAL*     3.6    40.3    -      -       +      +
----------------------------------------------------------
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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