Contacts of the strand formed by residues 486 - 493 (chain M) in PDB entry 4K4I


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 HIS 486 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379M  HIS*     3.4    30.3    +      +       +      +
    382M  ASP*     3.1    39.2    +      -       +      +
    383M  PHE*     3.7     5.4    -      -       +      -
    458M  THR*     3.4    44.2    +      -       +      +
    476M  VAL*     3.9     9.9    -      -       +      -
    477M  CYS      3.4     4.9    -      -       -      -
    478M  ARG*     3.4    40.6    +      -       +      -
    484M  ARG      5.2     0.8    +      -       -      -
    485M  ARG*     1.3    73.2    -      -       -      +
    487M  ARG*     1.3    67.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 487 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382M  ASP      4.0     4.7    +      -       -      -
    383M  PHE*     3.9     7.0    -      -       -      -
    385M  GLU*     2.8    51.6    +      -       -      +
    387M  MET*     3.5    42.0    -      -       +      +
    388M  PRO*     4.1     2.6    -      -       -      +
    391M  GLU*     2.6    44.7    +      -       -      +
    395M  ILE*     4.0    10.5    -      -       +      -
    476M  VAL*     3.2     5.0    -      -       -      -
    477M  CYS*     2.8    47.9    +      -       -      +
    478M  ARG*     5.9     0.2    -      -       -      -
    479M  LEU      6.2     0.2    -      -       -      +
    485M  ARG*     3.7    26.0    -      -       -      +
    486M  HIS*     1.3    81.8    -      -       -      +
    488M  ARG*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 488 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342M  TRP*     3.4    37.0    -      -       +      +
    383M  PHE*     3.9    30.3    -      -       +      -
    387M  MET*     5.3     0.2    -      -       -      +
    426M  GLY      5.0     3.9    +      -       -      +
    427M  ASP*     3.4    25.5    +      -       +      +
    428M  VAL*     3.1    25.6    +      -       -      +
    461M  LEU*     3.3    18.6    -      -       -      +
    474M  LEU*     3.7     4.8    -      -       -      +
    475M  GLY      2.8    24.8    +      -       -      +
    477M  CYS*     5.3     0.2    -      -       -      -
    487M  ARG*     1.3    76.2    -      -       -      +
    489M  LEU*     1.3    80.7    +      -       -      +
    490M  ASP*     2.5    34.6    +      -       -      -
      6O    C      3.0    24.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 489 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395M  ILE*     4.1     7.9    -      -       +      -
    399M  VAL*     4.1    11.9    -      -       +      -
    428M  VAL*     3.3    17.7    -      -       +      +
    430M  VAL*     4.1    16.8    -      -       +      -
    456M  PHE*     4.1    16.2    -      -       +      -
    457M  LEU*     4.1    14.1    -      -       +      -
    473M  TYR*     4.1     4.3    -      -       +      -
    474M  LEU*     3.9     0.2    -      -       -      -
    475M  GLY      2.9    23.6    +      -       -      +
    476M  VAL      4.9     0.2    -      -       -      +
    477M  CYS*     4.1    22.7    -      -       +      +
    487M  ARG      3.5     0.4    +      -       -      -
    488M  ARG*     1.3    96.6    +      -       -      +
    490M  ASP*     1.3    79.8    +      -       -      +
    491M  ILE*     3.8    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 490 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427M  ASP*     5.5     0.7    -      -       -      -
    428M  VAL      2.8     6.6    +      -       -      +
    429M  ASP*     2.9    30.3    -      -       +      +
    430M  VAL      2.8    24.2    +      -       -      -
    472M  LYS*     5.2     0.9    -      -       +      -
    473M  TYR      3.2     6.7    -      -       -      +
    474M  LEU*     3.3    23.7    -      -       +      +
    488M  ARG*     2.5    43.6    +      -       -      -
    489M  LEU*     1.3    80.8    -      -       -      +
    491M  ILE*     1.3    63.0    +      -       -      +
    492M  ILE*     4.5     9.9    -      -       +      -
    604M   CA      3.9     4.3    -      -       -      -
      6O    C      4.0    17.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 491 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399M  VAL*     4.0    15.3    -      -       +      -
    430M  VAL*     3.3     5.6    -      -       +      +
    432M  ILE*     3.9    26.5    -      -       +      -
    444M  PHE*     4.0     7.3    -      -       +      -
    447M  LEU*     4.1     8.1    -      -       +      -
    448M  LEU*     4.1    17.5    -      -       +      -
    451M  LEU*     4.0    24.0    -      -       +      -
    457M  LEU*     5.3     0.2    -      -       +      -
    471M  GLN      3.9     0.5    -      -       -      +
    472M  LYS*     3.4     2.8    -      -       -      -
    473M  TYR*     2.7    48.5    +      -       +      +
    489M  LEU*     3.8    26.7    -      -       +      -
    490M  ASP*     1.3    79.4    -      -       -      +
    492M  ILE*     1.3    66.8    +      -       -      +
    493M  VAL*     4.6     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 492 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429M  ASP*     4.5     9.9    -      -       +      -
    430M  VAL      2.9    27.1    +      -       -      +
    431M  LEU*     3.4    20.4    -      -       +      +
    432M  ILE*     2.7    33.8    +      -       -      +
    470M  GLN*     4.1     7.2    -      -       +      +
    471M  GLN      3.3    11.4    -      -       -      +
    472M  LYS*     3.9    22.7    -      -       +      -
    490M  ASP*     4.5     7.0    -      -       +      -
    491M  ILE*     1.3    79.1    -      -       -      +
    493M  VAL*     1.3    60.4    +      -       -      +
    494M  VAL*     3.9    12.8    -      -       +      -
    506M  PHE*     4.0    41.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 493 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    432M  ILE*     3.3    26.5    -      -       +      +
    440M  HIS*     3.7    40.7    -      -       +      +
    443M  ILE*     5.2     2.5    -      -       +      -
    444M  PHE*     3.7    41.1    -      -       +      +
    447M  LEU*     5.5     0.4    -      -       +      -
    469M  GLN      4.1     1.2    -      -       -      +
    470M  GLN*     3.4     4.7    -      -       -      -
    471M  GLN*     2.8    47.1    +      -       -      +
    491M  ILE*     4.6     6.7    -      -       +      -
    492M  ILE*     1.3    74.1    -      -       -      +
    494M  VAL*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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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