Contacts of the strand formed by residues 501 - 510 (chain K) in PDB entry 6KC4


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 GLN 501 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    496K  VAL      3.6     0.3    -      -       -      +
    497K  TYR*     3.5     7.3    -      -       -      -
    498K  SER      2.9    29.9    +      -       -      +
    499K  ASP      4.3     3.6    +      -       -      -
    500K  GLY*     1.3    85.4    -      -       -      +
    502K  ARG*     1.3    69.6    +      -       -      +
    503K  ARG*     3.4    38.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 502 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471K  GLN*     3.0    53.5    +      -       +      +
    472K  GLU*     5.3     0.8    -      -       -      +
    474K  LEU*     2.8    42.6    +      -       +      -
    475K  LYS*     4.3     9.5    +      -       -      +
    496K  VAL      3.3     5.2    -      -       -      +
    497K  TYR*     3.8    26.1    +      -       +      +
    500K  GLY      5.5     2.4    +      -       -      -
    501K  GLN*     1.3    75.3    -      -       -      +
    503K  ARG*     1.3    62.9    +      -       -      +
    504K  HIS*     4.1    13.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 503 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494K  LEU      3.7     1.2    -      -       -      +
    495K  SER*     3.3     3.1    -      -       -      -
    496K  VAL*     2.7    39.4    +      -       +      +
    498K  SER*     2.9    33.8    +      -       -      -
    499K  ASP*     3.4    16.1    +      -       -      +
    501K  GLN*     3.4    41.9    +      -       +      +
    502K  ARG*     1.3    79.6    -      -       -      +
    504K  HIS*     1.3    65.3    +      -       -      +
    505K  PHE*     4.0    11.7    -      -       +      -
    542K  SER*     5.6     2.5    -      -       -      -
    544K  VAL*     4.1    21.1    -      -       +      -
      4L  GLU*     3.8    33.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 504 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467K  ARG*     3.5    30.5    -      -       +      +
    470K  ALA*     4.8     2.7    -      -       +      -
    471K  GLN*     3.1    38.6    +      -       +      -
    474K  LEU*     5.1     1.6    -      -       +      -
    483K  ARG*     3.1    16.9    +      -       -      -
    493K  VAL*     3.9     5.8    -      -       +      -
    494K  LEU      3.5     3.8    -      -       -      -
    495K  SER*     2.7    32.0    +      -       -      -
    502K  ARG*     4.1    12.0    -      -       +      +
    503K  ARG*     1.3    81.0    -      -       -      +
    505K  PHE*     1.3    59.4    +      -       -      +
      2L  GLU      4.5     3.3    +      -       -      +
      3L  PTR      3.4    24.8    -      -       +      -
      4L  GLU*     2.7    34.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 505 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493K  VAL*     3.3     5.9    -      -       -      -
    494K  LEU*     2.8    54.7    +      -       +      +
    496K  VAL*     4.6     4.0    -      -       +      -
    503K  ARG*     4.0    20.9    -      -       +      -
    504K  HIS*     1.3    74.4    -      -       -      +
    506K  ILE*     1.3    63.2    +      -       -      +
    516K  PHE*     3.9    18.6    -      -       +      -
    538K  ILE*     3.9    20.2    -      -       +      -
    539K  THR*     4.1    11.4    -      -       +      -
    542K  SER*     3.5    35.2    -      -       -      -
    544K  VAL*     3.8    23.6    -      -       +      -
      3L  PTR      4.6     0.2    -      -       -      -
      4L  GLU*     3.7    26.2    -      -       +      -
      5L  ASN*     3.3    20.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 506 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488K  LYS*     4.1    16.6    -      -       +      -
    491K  GLU*     3.9    37.5    -      -       +      +
    492K  TYR      3.6     2.5    -      -       -      +
    493K  VAL*     4.0     9.9    -      -       +      -
    504K  HIS      4.2     0.8    +      -       -      -
    505K  PHE*     1.3    70.7    -      -       -      +
    507K  ILE*     1.3    73.3    +      -       -      +
    508K  GLN*     3.3    26.9    +      -       -      +
    516K  PHE*     3.8     5.8    -      -       -      -
      3L  PTR      3.8    40.4    -      -       +      -
      5L  ASN*     2.7    33.9    +      -       -      +
      6L  VAL*     3.9    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 507 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    482K  VAL*     4.2    13.5    -      -       +      -
    491K  GLU*     3.9     6.8    -      -       -      +
    492K  TYR*     2.9    39.1    +      -       +      +
    494K  LEU*     4.1    19.5    -      -       +      +
    506K  ILE*     1.3    75.8    -      -       -      +
    508K  GLN*     1.3    66.2    +      -       -      +
    509K  TYR*     3.4     4.5    +      -       -      +
    514K  TYR*     3.9    26.1    -      -       +      -
    515K  ARG      4.0     2.2    -      -       -      -
    516K  PHE*     3.7    21.1    -      -       +      -
    524K  ILE*     4.0    26.0    -      -       +      -
    527K  LEU*     3.6    24.7    -      -       +      -
    528K  ILE*     4.7     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 508 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491K  GLU*     5.1     2.6    +      -       -      -
    506K  ILE*     3.6    30.6    -      -       -      +
    507K  ILE*     1.3    72.0    -      -       -      +
    509K  TYR*     1.3    60.8    +      -       -      +
    510K  VAL*     4.0     8.1    -      -       +      -
    513K  MET      3.5     0.7    -      -       -      +
    514K  TYR*     3.2     6.8    -      -       -      +
    515K  ARG*     2.9    55.6    +      -       +      +
    516K  PHE      4.1    12.6    -      -       -      +
      5L  ASN*     3.7    19.6    +      -       -      +
      6L  VAL*     4.6     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 509 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467I  ARG*     4.8     5.9    -      -       +      +
    468I  ILE*     6.1     2.0    -      -       +      +
      1J  ASP*     2.4    43.6    +      -       -      -
      3J  PTR      5.9     1.3    -      -       -      -
    491K  GLU*     4.8     8.6    +      -       -      +
    507K  ILE      3.4     4.3    +      -       -      +
    508K  GLN*     1.3    74.0    -      -       -      +
    510K  VAL*     1.3    61.1    +      -       -      +
    512K  ASN*     3.5    36.1    +      -       -      +
    513K  MET      3.3    11.0    -      -       -      -
    514K  TYR*     3.5    45.5    -      +       +      -
    522K  SER      5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 510 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    508K  GLN*     4.8     6.7    -      -       +      -
    509K  TYR*     1.3    76.4    -      -       -      +
    511K  ASP*     1.3    79.7    +      -       +      +
    512K  ASN      3.2     2.5    -      -       -      +
    513K  MET*     2.9    22.9    +      -       +      +
    515K  ARG*     3.6    37.2    -      -       +      +
----------------------------------------------------------
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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