Contacts of the strand formed by residues 303 - 314 (chain K) in PDB entry 6X5A


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 GLU 303 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210K  ASN*     3.3    26.2    +      -       +      +
    297K  LEU*     3.2    30.8    -      -       -      +
    298K  ILE      3.2     2.2    -      -       -      -
    299K  ARG*     2.3    46.5    +      -       -      +
    302K  GLU*     1.3   100.0    +      -       -      +
    304K  ILE*     1.3    96.3    +      -       -      +
    305K  SER*     3.2     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 304 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167K  ALA*     4.2    14.8    -      -       +      +
    170K  THR*     3.5    22.7    -      -       +      -
    171K  VAL*     3.7    33.7    -      -       +      -
    209K  PRO      5.6     2.5    -      -       -      +
    210K  ASN*     4.4     8.3    -      -       -      +
    212K  PHE*     5.4     3.6    -      -       +      +
    296K  LEU      3.0     5.9    -      -       -      +
    298K  ILE*     2.7    48.8    +      -       +      +
    300K  ASN      3.1    28.3    -      -       -      +
    301K  PRO*     4.2     5.6    -      -       +      -
    302K  GLU*     3.3     9.4    -      -       +      +
    303K  GLU*     1.3    81.8    +      -       -      +
    305K  SER*     1.3    66.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 305 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210K  ASN      3.4    17.1    +      -       -      -
    211K  GLU*     3.2     8.0    -      -       -      -
    212K  PHE*     2.7    32.4    +      -       -      -
    295K  THR*     2.4    29.5    +      -       -      -
    296K  LEU      3.1     5.8    -      -       -      -
    297K  LEU*     4.1     7.8    -      -       -      +
    303K  GLU*     3.2     8.4    +      -       -      -
    304K  ILE*     1.3    78.2    -      -       -      +
    306K  VAL*     1.3    55.1    +      -       -      +
    307K  ASP      4.2     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 306 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171K  VAL*     3.9    25.6    -      -       +      -
    175K  VAL*     4.4    18.8    -      -       +      -
    212K  PHE*     3.3    20.9    -      -       +      +
    213K  ASP*     4.6     0.4    -      -       -      -
    214K  VAL*     4.1    26.0    -      -       +      -
    294K  VAL      3.4     4.3    -      -       -      +
    295K  THR*     4.3     2.2    -      -       -      -
    296K  LEU*     3.3    31.6    +      -       +      +
    298K  ILE*     4.8     5.4    -      -       +      -
    305K  SER*     1.3    76.7    +      -       -      +
    307K  ASP*     1.3    66.1    +      -       -      +
    308K  ILE*     3.4    17.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 307 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211K  GLU*     5.1     3.4    -      -       -      +
    212K  PHE      2.9    16.7    +      -       -      +
    213K  ASP*     2.7    50.2    -      -       -      +
    214K  VAL      3.7     5.9    +      -       -      +
    293K  ALA*     4.0    19.4    -      -       +      +
    294K  VAL      3.9     5.2    -      -       -      -
    295K  THR*     4.4     9.8    -      -       -      +
    305K  SER*     4.2     1.4    +      -       -      -
    306K  VAL*     1.3    72.2    -      -       -      +
    308K  ILE*     1.3    61.9    +      -       -      +
    309K  ILE*     3.7     9.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 308 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175K  VAL*     5.5     3.4    -      -       +      -
    178K  LEU*     5.5     1.8    -      -       +      -
    214K  VAL*     4.5     5.2    -      -       +      -
    216K  PHE*     3.3    48.0    -      -       +      -
    266K  PHE*     4.2    19.5    -      -       +      -
    270K  ILE*     3.7    22.0    -      -       +      -
    292K  PRO      4.5     1.0    -      -       -      +
    293K  ALA*     3.8     5.5    -      -       -      -
    294K  VAL*     3.0    50.6    +      -       +      +
    296K  LEU*     4.2    17.5    -      -       +      -
    306K  VAL*     3.4    25.1    -      -       +      +
    307K  ASP*     1.3    71.9    -      -       -      +
    309K  ILE*     1.3    63.1    +      -       -      +
    310K  LEU*     3.9     2.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 309 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213K  ASP*     3.9    12.3    -      -       -      +
    214K  VAL      3.5    15.4    +      -       -      +
    215K  MET*     3.6    38.4    -      -       +      -
    216K  PHE*     3.1    21.5    +      -       -      +
    292K  PRO      5.0     5.8    -      -       -      +
    293K  ALA*     4.7     9.2    -      -       +      -
    307K  ASP*     3.7    23.7    +      -       -      +
    308K  ILE*     1.3    76.4    -      -       -      +
    310K  LEU*     1.3    65.8    +      -       -      +
    311K  ALA*     4.7     1.4    -      -       +      +
    348K  VAL*     4.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 310 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189K  PHE*     5.8     1.3    -      -       +      -
    192K  VAL*     5.5     2.9    -      -       +      -
    216K  PHE*     3.7    12.3    -      -       +      +
    218K  LEU*     6.3     5.6    -      -       +      -
    262K  MET*     5.3     4.3    -      -       +      +
    263K  LEU*     3.5    30.1    -      -       +      +
    266K  PHE*     3.3    62.8    -      -       +      -
    292K  PRO      5.2     3.4    +      -       -      +
    308K  ILE*     3.9     3.1    +      -       +      +
    309K  ILE*     1.3    77.0    -      -       -      +
    311K  ALA*     1.3    59.5    -      -       -      +
    312K  LEU*     5.8     4.9    -      -       +      -
    348K  VAL*     3.6     9.1    -      -       -      +
    349K  PRO*     3.0    37.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 311 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195K  LEU*     3.8    23.8    -      -       +      -
    215K  MET*     5.3     4.0    -      -       +      -
    216K  PHE      2.9    14.0    +      -       -      +
    217K  LYS*     3.4     1.9    -      -       -      -
    218K  LEU*     3.1    27.5    +      -       -      +
    309K  ILE*     4.7     2.9    -      -       +      +
    310K  LEU*     1.3    75.3    -      -       -      +
    312K  LEU*     1.3    62.5    +      -       -      +
    346K  TYR*     4.1    12.1    -      -       +      -
    347K  LEU      3.2     5.2    -      -       -      +
    348K  VAL*     3.9    15.7    -      -       +      -
    366K  SER*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 312 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218K  LEU*     3.7    12.3    -      -       +      +
    220K  VAL*     3.7    24.9    -      -       +      -
    223K  ILE*     6.0     2.5    -      -       +      -
    237K  VAL*     4.6     6.3    -      -       +      -
    257K  LEU*     5.1    10.1    -      -       +      -
    262K  MET*     5.6     7.0    -      -       +      -
    310K  LEU*     5.8     4.7    -      -       +      -
    311K  ALA*     1.3    75.9    -      -       -      +
    313K  GLU*     1.3    60.2    +      -       -      +
    314K  SER      4.0     0.2    -      -       -      -
    345K  PHE      3.6     0.7    -      -       -      +
    346K  TYR*     3.2    14.0    -      -       -      -
    347K  LEU*     2.6    67.9    +      -       +      +
    363K  TRP*     3.4    42.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 313 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217K  LYS*     3.1    26.8    +      -       +      -
    218K  LEU      2.8    22.9    +      -       -      +
    219K  GLU*     2.7    55.0    -      -       +      +
    220K  VAL*     3.0    17.2    +      -       -      +
    311K  ALA      3.7     0.2    +      -       -      -
    312K  LEU*     1.3    73.1    -      -       -      +
    314K  SER*     1.3    55.7    +      -       -      +
    315K  LYS*     5.4     0.9    -      -       -      +
    344K  PRO*     3.0    36.9    -      -       -      +
    345K  PHE      4.1     0.6    -      -       -      +
    346K  TYR*     2.8    33.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 314 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219K  GLU*     4.1     3.1    -      -       -      -
    220K  VAL      5.1     2.2    -      -       -      -
    223K  ILE*     4.7    22.7    +      -       -      +
    312K  LEU*     3.9     0.6    +      -       -      -
    313K  GLU*     1.3    74.4    -      -       -      +
    315K  LYS*     1.3    60.8    +      -       -      +
    316K  GLY*     3.3     8.4    +      -       -      -
    344K  PRO*     3.1    20.2    -      -       -      +
    345K  PHE*     3.1    53.5    +      -       -      -
    347K  LEU*     5.2     6.3    -      -       -      -
----------------------------------------------------------
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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