Contacts of the strand formed by residues 1073 - 1080 (chain C) in PDB entry 6P19


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 LYS1073 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678C  ARG*     3.8    18.2    -      -       -      +
    681C  MET*     3.5    34.1    -      -       -      +
    685C  MET*     3.6    33.4    -      -       -      +
    814C  ASP*     3.6    24.9    +      -       -      +
    816C  ILE*     4.9     0.6    -      -       -      +
   1065C  LYS*     3.4    18.6    -      -       -      +
   1066C  MET      3.4     6.3    -      -       -      +
   1067C  ALA*     3.8     4.0    -      -       +      -
   1071C  GLY      3.4     2.8    +      -       -      +
   1072C  ASN*     1.3    79.4    -      -       -      +
   1074C  GLY*     1.3    60.3    +      -       -      +
   1106C  ARG*     5.6     1.0    -      -       -      +
    462D  ASP*     3.8    26.7    +      -       +      +
     70R    A      3.2    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1074 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    814C  ASP      3.5    13.2    -      -       -      -
    816C  ILE*     3.8    17.3    -      -       -      -
   1065C  LYS*     3.4     8.3    -      -       -      +
   1066C  MET      2.6    37.0    +      -       -      -
   1072C  ASN      3.9     0.2    +      -       -      -
   1073C  LYS*     1.3    77.4    -      -       -      +
   1075C  VAL*     1.3    64.5    +      -       -      +
    461D  PHE      4.4     0.2    -      -       -      -
    462D  ASP*     4.4     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1075 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    814C  ASP      3.7     1.6    +      -       -      -
    815C  SER*     3.8     9.5    +      -       -      +
    816C  ILE*     3.3    15.9    +      -       -      +
   1063C  GLY*     3.8    25.4    -      -       -      +
   1064C  ASP      4.2     2.5    -      -       -      -
   1065C  LYS*     4.4    10.8    -      -       +      -
   1074C  GLY*     1.3    76.1    -      -       -      +
   1076C  ILE*     1.3    67.6    +      -       -      +
   1077C  SER*     3.3     2.4    +      -       -      -
    354D  VAL*     4.3     7.2    -      -       +      -
    355D  ILE      3.8    18.6    -      -       -      +
    356D  THR*     3.9    11.7    -      -       +      +
    461D  PHE      3.3    15.4    +      -       -      +
    462D  ASP      3.6     1.6    -      -       -      -
    463D  GLY*     3.3    35.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1076 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    816C  ILE*     3.3    11.2    -      -       +      +
    818C  VAL*     3.8    34.1    -      -       +      +
   1060C  ILE*     4.4    17.5    -      -       +      -
   1061C  GLN      4.2    12.8    -      -       -      +
   1062C  PRO*     3.2    21.2    -      -       +      +
   1063C  GLY      3.3     4.0    +      -       -      +
   1064C  ASP*     3.4    31.8    +      -       +      +
   1066C  MET*     3.6    34.3    -      -       +      -
   1075C  VAL*     1.3    72.5    -      -       -      +
   1077C  SER*     1.3    62.3    +      -       -      +
   1078C  LYS      4.5     6.5    -      -       -      +
   1079C  ILE*     4.9    10.5    -      -       +      -
    356D  THR*     3.6     5.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1077 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    810C  TYR*     3.2    45.1    +      -       -      -
    815C  SER*     4.5     6.1    -      -       -      -
    816C  ILE      2.7    12.4    +      -       -      -
   1062C  PRO*     4.3    12.0    -      -       -      +
   1075C  VAL      4.2     3.8    -      -       -      -
   1076C  ILE*     1.3    76.4    -      -       -      +
   1078C  LYS*     1.3    60.3    +      -       -      +
    356D  THR*     3.6    16.0    -      -       -      +
    357D  VAL*     3.7    13.7    +      -       -      +
    448D  GLN*     4.5    13.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS1078 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  ARG*     5.7     2.8    -      -       -      +
    810C  TYR*     3.5    48.0    -      -       +      -
    816C  ILE      4.3     1.2    +      -       -      -
    817C  LEU*     3.9    13.3    -      -       +      +
    818C  VAL      3.2    24.3    +      -       -      +
   1062C  PRO*     4.9     4.5    -      -       -      -
   1076C  ILE*     3.8     2.5    -      -       -      +
   1077C  SER*     1.3    80.9    -      -       -      +
   1079C  ILE*     1.3    74.3    +      -       -      +
   1080C  ASN*     3.2    28.6    +      -       -      +
   1081C  PRO*     4.7     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1079 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  ARG*     4.0    11.6    +      -       -      -
    818C  VAL*     3.4     6.5    -      -       +      +
    819C  SER      3.8    12.3    -      -       -      +
    820C  GLU*     3.5    23.5    -      -       -      +
    823C  VAL*     3.8    35.0    -      -       +      -
   1060C  ILE*     4.0    21.1    -      -       +      +
   1061C  GLN*     4.2    13.2    -      -       -      +
   1062C  PRO*     4.3    14.9    -      -       +      +
   1076C  ILE*     4.9     8.3    -      -       +      -
   1078C  LYS*     1.3    82.2    +      -       -      +
   1080C  ASN*     1.3    62.4    +      -       -      +
   1081C  PRO*     3.9     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN1080 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    807C  TRP*     3.1    34.6    -      -       -      +
    810C  TYR*     5.5     0.4    -      -       -      -
    817C  LEU*     3.3    23.4    -      -       +      +
    818C  VAL      3.3     7.2    +      -       -      +
    819C  SER*     4.0     0.2    -      -       -      -
    820C  GLU*     3.0    28.4    +      -       -      +
   1078C  LYS*     3.2    29.8    +      -       -      +
   1079C  ILE*     1.3    75.3    -      -       -      +
   1081C  PRO*     1.3    71.1    -      -       +      +
   1084C  ASP*     4.4     9.3    -      -       +      +
   1085C  MET*     3.7    21.7    -      -       -      -
   1216C  ARG*     4.7     5.9    +      -       -      +
----------------------------------------------------------
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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