Contacts of the strand formed by residues 711 - 728 (chain C) in PDB entry 6VSB


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 SER 711 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    895A  GLN*     3.2    23.2    +      -       -      +
    897A  PRO*     3.3    14.2    -      -       -      +
    706C  ALA      5.3     0.6    +      -       -      -
    708C  SER*     3.6    27.3    -      -       -      +
    710C  ASN*     1.3    82.1    -      -       -      +
    712C  ILE*     1.3    61.4    +      -       -      +
   1074C  ASN*     4.5    15.1    +      -       -      +
   1075C  PHE      3.0    14.7    +      -       -      -
   1076C  THR*     4.9     1.8    -      -       -      -
   1077C  THR*     3.4     2.5    +      -       -      -
      1Q  NAG      5.2     0.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 712 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    894A  LEU*     5.7     1.1    -      -       +      -
    895A  GLN*     3.1    11.7    -      -       -      +
    896A  ILE*     3.8    31.6    -      -       +      -
    897A  PRO*     4.5     3.1    -      -       +      -
    900A  MET*     5.2     1.6    -      -       +      -
    711C  SER*     1.3    74.0    -      -       -      +
    713C  ALA*     1.3    70.6    +      -       -      +
    714C  ILE*     3.8    25.6    -      -       +      -
   1073C  LYS      3.9     0.2    -      -       -      +
   1074C  ASN*     4.3     0.8    -      -       -      -
   1075C  PHE*     2.7    39.3    +      -       +      +
   1077C  THR*     3.3    28.8    +      -       +      +
   1094C  VAL*     4.1    22.2    -      -       +      -
   1096C  VAL*     3.9     4.0    -      -       +      -
   1107C  ARG*     5.1     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 713 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    894A  LEU*     3.5    44.5    -      -       +      +
    895A  GLN*     3.2    21.9    +      -       -      +
    712C  ILE*     1.3    78.4    -      -       -      +
    714C  ILE*     1.3    63.8    +      -       -      +
   1072C  GLU*     4.2     0.2    -      -       +      -
   1073C  LYS      3.4     8.1    -      -       -      +
   1107C  ARG      5.6     0.2    -      -       -      +
      1Q  NAG      3.5    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 714 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    712C  ILE*     3.8    18.7    +      -       +      -
    713C  ALA*     1.3    80.4    -      -       -      +
    715C  PRO*     1.3    85.1    -      -       +      +
    716C  THR*     3.5     6.2    +      -       -      +
   1072C  GLU*     3.2    16.7    -      -       -      +
   1073C  LYS      3.3    11.9    +      -       -      -
   1075C  PHE*     4.1    16.1    -      -       +      -
   1094C  VAL*     4.2     8.5    -      -       +      -
   1096C  VAL*     3.4    33.7    -      -       +      -
   1105C  THR*     4.0    13.2    -      -       +      -
   1106C  GLN      4.2     4.5    -      -       -      +
   1107C  ARG*     4.1    15.0    -      -       -      +
   1109C  PHE      4.2     2.2    -      -       -      -
   1110C  TYR*     3.7    20.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 715 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    894A  LEU*     3.7    23.6    -      -       +      -
    714C  ILE*     1.3    88.3    -      -       +      +
    716C  THR*     1.3    54.9    +      -       -      +
    717C  ASN      3.5    11.7    -      -       -      +
   1069C  PRO*     3.5    28.9    -      -       +      -
   1070C  ALA      3.9     4.5    -      -       -      +
   1072C  GLU*     3.5    13.4    -      -       +      -
   1107C  ARG      4.2     5.6    -      -       -      +
   1108C  ASN      3.1    29.4    -      -       -      +
   1109C  PHE*     3.5     1.9    -      -       -      -
   1110C  TYR*     2.8    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 716 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    714C  ILE      3.5     9.4    -      -       -      +
    715C  PRO*     1.3    73.0    -      -       -      +
    717C  ASN*     1.3    62.7    +      -       -      +
   1071C  GLN*     2.3    35.9    +      -       -      +
   1073C  LYS*     3.8    28.2    -      -       +      +
   1075C  PHE*     4.6     0.4    -      -       +      -
   1109C  PHE*     3.7    14.9    -      -       -      -
   1110C  TYR*     3.5    38.1    -      -       +      -
      1S  NAG      4.7    10.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 717 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    715C  PRO*     3.8     9.2    -      -       -      +
    716C  THR*     1.3    78.4    -      -       -      +
    718C  PHE*     1.3    92.6    +      -       -      +
    719C  THR*     5.6     0.9    -      -       -      -
    922C  LEU*     4.6     5.4    -      -       -      +
   1067C  TYR*     4.6     0.2    +      -       -      -
   1069C  PRO*     4.0     0.3    -      -       -      +
   1070C  ALA*     2.8    29.2    +      -       +      +
   1071C  GLN*     3.1    23.4    +      -       +      +
   1109C  PHE*     3.4    13.6    -      -       -      -
      1S  NAG      1.4    63.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 718 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    717C  ASN*     1.3    95.3    +      -       -      +
    719C  THR*     1.3    64.9    +      -       -      +
    720C  ILE*     4.0    17.3    -      -       +      -
    906C  PHE*     4.1     4.3    -      +       -      -
    915C  VAL*     4.0    21.8    -      -       +      -
    919C  ASN*     4.7    11.4    -      -       +      -
    922C  LEU*     5.2     6.5    -      -       +      +
    923C  ILE*     3.3    43.3    -      -       +      -
    926C  GLN*     3.4    16.4    +      -       -      +
   1067C  TYR*     3.3    45.3    -      +       +      -
   1068C  VAL      3.4    11.2    -      -       -      +
   1069C  PRO*     4.4     0.2    -      -       +      -
   1070C  ALA      4.1     2.9    -      -       -      +
   1109C  PHE*     3.8    20.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 719 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    717C  ASN*     5.6     0.4    -      -       -      -
    718C  PHE*     1.3    77.9    -      -       -      +
    720C  ILE*     1.3    64.7    +      -       -      +
    721C  SER*     3.8     3.5    +      -       -      -
    926C  GLN*     3.2    15.0    -      -       -      +
   1068C  VAL*     2.9    40.7    +      -       -      +
   1070C  ALA*     4.4    17.8    -      -       +      +
      1S  NAG      4.9    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 720 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    718C  PHE*     4.0    26.2    -      -       +      -
    719C  THR*     1.3    76.4    -      -       -      +
    721C  SER*     1.3    59.6    +      -       -      +
    722C  VAL*     5.7     0.9    -      -       +      -
    800C  PHE*     5.0     1.3    -      -       +      -
    902C  MET*     5.1     4.5    -      -       +      -
    906C  PHE*     4.8     2.0    -      -       +      -
    923C  ILE*     3.9    22.4    -      -       +      -
    926C  GLN*     3.2    22.6    +      -       +      +
    927C  PHE*     3.6    50.5    -      -       +      +
    930C  ALA*     4.5     3.1    -      -       -      +
   1049C  LEU*     4.7     9.0    -      -       +      -
   1065C  VAL*     4.2    11.7    -      -       +      -
   1066C  THR      3.2    16.2    -      -       -      +
   1067C  TYR*     4.5     7.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 721 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    719C  THR*     3.8     5.5    +      -       -      -
    720C  ILE*     1.3    75.8    -      -       -      +
    722C  VAL*     1.3    63.8    +      -       -      +
    723C  THR*     3.4    14.0    +      -       -      +
    930C  ALA*     4.6     4.5    -      -       -      -
   1045C  LYS      5.4     0.2    +      -       -      -
   1064C  HIS      3.4     3.3    -      -       -      +
   1066C  THR*     3.3    34.5    +      -       -      -
   1068C  VAL*     4.2    10.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 722 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    720C  ILE      5.5     0.9    -      -       -      +
    721C  SER*     1.3    71.8    -      -       -      +
    723C  THR*     1.3    61.6    +      -       -      +
    724C  THR*     4.4     0.3    -      -       -      +
    927C  PHE*     4.5     9.0    -      -       +      +
    930C  ALA*     3.6    26.5    -      -       +      +
    931C  ILE*     4.0    16.4    -      -       +      -
    934C  ILE*     3.3    36.9    -      -       +      +
   1063C  LEU*     3.7    24.9    -      -       +      -
   1064C  HIS      3.3     4.3    -      -       -      +
   1065C  VAL*     3.6    34.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 723 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    721C  SER*     4.3    17.7    -      -       -      +
    722C  VAL*     1.3    77.8    -      -       -      +
    724C  THR*     1.3    61.2    +      -       -      +
   1044C  GLY*     3.7    14.2    -      -       -      -
   1045C  LYS*     4.9    18.2    -      -       +      +
   1063C  LEU*     3.4     4.2    -      -       -      -
   1064C  HIS*     2.7    51.5    +      -       -      +
   1066C  THR*     5.3     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 724 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    722C  VAL      4.4     0.2    -      -       -      +
    723C  THR*     1.3    85.0    +      -       -      +
    725C  GLU*     1.3    63.2    +      -       -      +
    726C  ILE*     5.4     7.4    -      -       -      +
    934C  ILE*     3.8    39.3    -      -       +      -
    938C  LEU*     5.6     9.4    -      -       +      +
   1061C  VAL*     4.9    10.1    -      -       +      -
   1062C  PHE      3.2    10.1    -      -       -      +
   1063C  LEU*     4.8     5.4    -      -       +      -
   1064C  HIS*     4.7     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 725 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    724C  THR*     1.3    77.8    -      -       -      +
    726C  ILE*     1.3    72.3    +      -       -      +
    727C  LEU*     4.2    16.1    -      -       +      +
    947C  LYS*     5.7     1.5    +      -       -      +
   1024C  LEU*     5.4     0.3    -      -       -      +
   1028C  LYS*     2.9    43.8    +      -       -      +
   1042C  PHE      4.2     0.9    -      -       -      +
   1044C  GLY      4.9     0.9    +      -       -      -
   1060C  VAL      3.9     0.7    -      -       -      +
   1061C  VAL*     3.3     5.9    -      -       -      +
   1062C  PHE*     2.8    34.8    +      -       +      +
   1064C  HIS*     2.8    34.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 726 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    724C  THR*     5.4     7.0    -      -       -      +
    725C  GLU*     1.3    82.8    -      -       -      +
    727C  LEU*     1.3    69.0    +      -       -      +
    938C  LEU*     5.7     3.1    -      -       +      -
    944C  ALA      3.2    27.8    -      -       -      +
    945C  LEU*     3.5    19.1    -      -       +      -
    946C  GLY      5.3     0.7    -      -       -      +
    947C  LYS*     3.0    46.7    +      -       +      +
    948C  LEU*     3.6    36.6    -      -       +      +
   1060C  VAL      3.8     2.9    -      -       -      +
   1061C  VAL*     4.1    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 727 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    725C  GLU*     4.2    15.5    -      -       +      +
    726C  ILE*     1.3    83.9    -      -       -      +
    728C  PRO*     1.3    66.8    -      -       +      +
    947C  LYS*     4.0    12.3    -      -       -      +
    948C  LEU*     4.1     3.3    -      -       -      +
   1021C  SER*     4.2    12.8    -      -       -      +
   1024C  LEU*     4.2    20.0    -      -       +      -
   1025C  ALA*     3.8    37.0    -      -       +      +
   1028C  LYS*     3.8    22.2    -      -       +      -
   1059C  GLY*     3.2     1.5    -      -       -      -
   1060C  VAL*     2.7    40.2    +      -       +      +
   1062C  PHE*     4.1    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 728 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    726C  ILE      4.6     2.2    -      -       -      +
    727C  LEU*     1.3    85.2    -      -       +      +
    729C  VAL*     1.3    66.9    +      -       -      +
    730C  SER      3.8     4.3    -      -       -      +
    947C  LYS*     4.7    19.3    -      -       +      +
    948C  LEU*     4.0    10.1    -      -       +      -
    951C  VAL*     3.8    30.1    -      -       +      -
   1017C  GLU*     5.5     3.4    -      -       -      +
   1018C  ILE*     4.5     9.3    -      -       +      +
   1021C  SER*     2.9    40.2    +      -       -      +
   1022C  ALA      3.9     0.5    +      -       -      -
   1058C  HIS      3.4    14.6    -      -       -      +
   1059C  GLY*     3.8     0.9    -      -       -      -
----------------------------------------------------------
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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