Contacts of the strand formed by residues 139 - 151 (chain G) in PDB entry 6A3V


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 GLY 139 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138G  ALA*     1.3    78.3    -      -       -      +
    140G  VAL*     1.3    65.4    +      -       -      -
    141G  TYR*     3.4    18.4    -      -       -      -
    205G  HIS*     3.8     5.7    +      -       -      -
    206G  LEU      2.9    27.9    +      -       -      -
    239G  ARG*     4.0    11.4    -      -       -      -
    241G  THR*     4.5     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 140 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139G  GLY*     1.3    73.7    -      -       -      -
    141G  TYR*     1.3    62.3    +      -       -      +
    203G  LEU*     4.4    25.8    -      -       +      -
    204G  LEU      3.7     9.4    -      -       -      +
    205G  HIS*     4.1    20.2    -      -       +      +
    239G  ARG*     3.7     2.3    -      -       -      +
    240G  VAL*     2.8    35.7    +      -       +      -
    241G  THR*     3.2    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 141 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91G  MET*     3.6    30.0    -      -       +      +
    124G  LEU*     4.8     0.4    -      -       +      -
    135G  VAL*     3.3    21.3    -      -       +      +
    137G  LYS      2.8    20.4    +      -       -      -
    139G  GLY*     3.4    35.0    -      -       -      -
    140G  VAL*     1.3    74.8    -      -       -      +
    142G  TYR*     1.3    60.2    +      -       -      +
    143G  VAL*     3.8     3.0    +      -       +      -
    203G  LEU*     3.5     5.4    -      -       -      -
    204G  LEU*     2.8    37.3    +      -       -      +
    206G  LEU*     3.6    19.3    -      -       +      -
    237G  LEU*     3.4    41.1    -      -       +      -
    238G  PHE      3.3     4.9    -      -       -      +
    239G  ARG*     3.4    36.4    +      -       +      -
    240G  VAL*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 142 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141G  TYR*     1.3    70.7    -      -       -      +
    143G  VAL*     1.3    60.3    +      -       -      +
    144G  PHE*     3.8    24.2    +      +       +      -
    199G  PHE*     4.3    10.7    -      -       -      -
    201G  GLY*     4.2     9.9    +      -       -      -
    202G  ARG*     3.6    30.5    -      -       -      -
    203G  LEU*     3.7    21.8    -      -       +      -
    237G  LEU*     3.5     3.5    -      -       -      -
    238G  PHE*     2.7    72.9    +      +       +      +
    240G  VAL*     4.2     4.3    -      -       +      +
    142I  TYR*     3.8    20.4    +      +       -      -
    199I  PHE*     5.6     1.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 143 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141G  TYR*     4.3    11.0    -      -       +      +
    142G  TYR*     1.3    77.0    -      -       -      +
    144G  PHE*     1.3    62.5    +      -       -      +
    165G  LEU*     3.9    16.8    -      -       +      -
    179G  LEU*     4.1    11.6    -      -       +      +
    201G  GLY*     3.2    18.9    -      -       -      -
    202G  ARG      3.2    12.7    +      -       -      +
    204G  LEU*     4.1    26.0    -      -       +      -
    206G  LEU*     5.1     1.1    -      -       +      -
    212G  LEU*     4.4     8.1    -      -       +      -
    235G  LEU*     3.6    27.4    -      -       +      -
    236G  GLY      3.7     7.2    -      -       -      +
    237G  LEU*     3.7    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 144 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94G  GLN*     3.9     4.7    -      -       -      -
    142G  TYR*     3.8    27.4    -      +       +      -
    143G  VAL*     1.3    75.4    -      -       -      +
    145G  PHE*     1.3    62.6    +      -       -      +
    146G  GLN*     4.3     8.7    -      -       -      -
    179G  LEU*     5.1     0.2    -      -       -      -
    199G  PHE*     3.6    25.8    -      +       +      -
    200G  GLN      3.1     5.8    -      -       -      +
    201G  GLY*     4.2     1.6    -      -       -      -
    234G  VAL*     4.4     0.7    -      -       +      -
    235G  LEU*     3.6    11.2    -      -       -      +
    236G  GLY*     3.4    50.1    +      -       -      -
    237G  LEU      4.0     2.9    -      -       -      -
    238G  PHE*     4.2     7.9    -      +       -      -
    142I  TYR*     3.7    13.7    -      +       -      -
    201I  GLY      4.0    11.7    -      -       -      -
    202I  ARG*     3.8    18.4    -      -       -      -
    203I  LEU*     3.8    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 145 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109G  TRP*     5.5     1.3    -      +       -      -
    144G  PHE*     1.3    76.3    -      -       -      +
    146G  GLN*     1.3    61.9    +      -       -      +
    163G  LEU*     3.7    24.9    -      -       +      -
    164G  ALA      3.8    14.6    -      -       -      -
    165G  LEU*     3.6    27.4    -      -       +      -
    179G  LEU*     3.4    37.7    -      -       +      -
    180G  ALA*     4.0    15.3    -      -       -      -
    181G  LEU*     3.8    19.5    -      -       +      -
    199G  PHE*     3.2    26.9    -      -       -      -
    200G  GLN*     2.4    34.2    +      -       +      +
    214G  VAL*     3.8    27.8    -      -       +      -
    234G  VAL      3.8     3.4    -      -       -      -
    235G  LEU*     4.6     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 146 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144G  PHE*     4.3     3.0    -      -       -      -
    145G  PHE*     1.3    80.7    -      -       -      +
    147G  LEU*     1.3    60.3    +      -       -      +
    148G  GLU      4.3     0.4    -      -       -      -
    163G  LEU*     4.1     5.9    -      -       -      +
    197G  PHE*     4.2     4.7    -      -       +      -
    198G  GLY      4.0     2.9    -      -       -      -
    199G  PHE*     4.0     6.5    -      -       +      -
    232G  ALA*     3.7    13.5    -      -       -      +
    233G  THR*     3.3    22.7    -      -       -      +
    234G  VAL*     3.0    45.8    +      -       -      +
    200I  GLN*     2.7    44.4    +      -       -      +
    201I  GLY      3.4     5.5    +      -       -      -
    202I  ARG*     3.2    37.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 147 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146G  GLN*     1.3    74.0    -      -       -      +
    148G  GLU*     1.3    60.6    +      -       -      +
    149G  LEU*     3.7    18.8    -      -       +      -
    161G  VAL*     4.0    24.5    -      -       +      +
    163G  LEU*     3.7    37.9    -      -       +      +
    181G  LEU*     4.8     6.5    -      -       +      +
    183G  VAL*     3.7    32.1    -      -       +      +
    196G  ALA      3.9     0.3    -      -       -      +
    197G  PHE*     3.2     9.4    -      -       -      -
    198G  GLY      3.2    30.7    +      -       -      +
    228G  LEU*     3.6    30.7    -      -       +      -
    232G  ALA      4.9     0.2    -      -       -      -
    233G  THR*     4.1     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 148 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146G  GLN      4.3     0.4    -      -       -      -
    147G  LEU*     1.3    75.8    -      -       -      +
    149G  LEU*     1.3    68.5    +      -       -      +
    150G  ARG*     5.9     0.3    -      -       -      +
    195G  SER*     5.1     9.6    +      -       -      -
    196G  ALA      3.4    10.5    -      -       -      +
    197G  PHE*     4.3    17.7    -      -       +      -
    228G  LEU*     3.6     5.5    -      -       -      +
    229G  THR*     2.8    38.7    +      -       -      +
    232G  ALA*     3.1    35.5    +      -       +      +
    233G  THR*     3.8    10.6    +      -       -      -
    180I  ALA*     5.3    11.4    -      -       -      +
    200I  GLN*     5.2     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 149 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102G  LEU*     3.9    27.4    -      -       +      -
    147G  LEU*     3.7    31.6    -      -       +      -
    148G  GLU*     1.3    78.3    -      -       -      +
    150G  ARG*     1.3    59.3    +      -       -      +
    161G  VAL*     3.6    30.7    -      -       +      -
    183G  VAL*     3.9    22.7    -      -       +      -
    185G  LEU*     4.1     9.0    -      -       +      -
    195G  SER*     3.3     7.6    -      -       -      -
    196G  ALA      3.1    29.3    +      -       -      +
    226G  TRP*     3.5    18.0    -      -       +      -
    227G  GLN      3.3    10.8    -      -       -      +
    228G  LEU*     4.6     6.7    -      -       +      -
    229G  THR*     3.7     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 150 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100G  VAL*     5.4     0.2    -      -       -      +
    148G  GLU*     5.9     0.2    -      -       -      +
    149G  LEU*     1.3    73.0    -      -       -      +
    151G  ARG*     1.3    66.1    +      -       -      +
    152G  VAL*     3.3    18.1    +      -       +      +
    194G  ASN*     3.3     7.2    -      -       +      +
    195G  SER*     4.7     5.8    -      -       -      +
    226G  TRP*     3.7     3.1    -      -       -      -
    227G  GLN*     2.9    39.4    +      -       -      +
    228G  LEU      5.3     2.2    +      -       -      -
    229G  THR*     3.3    33.4    -      -       -      +
    230G  GLN*     4.9     8.0    -      -       -      +
     66H  ARG*     4.0    21.7    -      -       -      +
     72H  PHE*     3.9     7.7    -      -       -      -
     99H  CYS      3.8     5.7    +      -       -      -
    100H  SER*     2.5    47.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 151 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150G  ARG*     1.3    73.3    +      -       -      +
    152G  VAL*     1.3    58.3    +      -       -      +
    153G  VAL      3.2    27.4    -      -       -      +
    154G  ALA*     4.2     8.3    -      -       -      +
    155G  GLY      4.7     1.1    -      -       -      +
    156G  GLU      2.7    30.5    +      -       -      +
    157G  GLY      3.2    15.0    +      -       -      -
    186G  PRO      2.4    29.7    +      -       -      -
    187G  PRO      3.6     8.3    +      -       -      -
    188G  ALA*     3.8    16.1    -      -       -      +
    193G  ARG      2.9    25.5    +      -       -      +
    194G  ASN*     2.8    35.8    +      -       -      +
    225G  ALA      3.2    12.8    -      -       -      +
    226G  TRP*     3.2    23.0    -      -       +      +
    100H  SER      3.7     3.8    -      -       -      +
    101H  MET*     3.1    20.6    -      -       -      +
----------------------------------------------------------
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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