Contacts of the strand formed by residues 27 - 42 (chain C) in PDB entry 3U8M


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 VAL 27 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  ILE*     3.5    30.5    -      -       +      -
     20C  PRO*     3.6    33.4    -      -       +      +
     21C  THR*     3.9     4.5    -      -       -      +
     22C  GLN      6.1     0.2    -      -       -      +
     25C  ARG      3.7     0.2    +      -       -      -
     26C  PRO*     1.3    70.0    -      -       -      +
     28C  ALA*     1.3    61.5    +      -       -      +
     29C  VAL*     3.3     8.3    +      -       +      +
     58C  TRP*     4.2    19.3    -      -       +      -
     59C  SER*     4.3     8.1    -      -       -      +
     82C  TRP*     4.1    24.7    -      -       +      -
    149C  GLU      2.7    11.0    +      -       -      +
    150C  ILE*     3.5     5.1    -      -       +      -
    151C  SER      3.0    21.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 28 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  PRO      3.3     6.3    +      -       -      +
     27C  VAL*     1.3    71.1    -      -       -      +
     29C  VAL*     1.3    62.6    +      -       -      +
     30C  SER*     4.0     0.9    +      -       -      -
     57C  THR*     3.7     8.0    -      -       -      +
     58C  TRP*     3.8    12.3    -      -       -      +
     59C  SER      4.7     1.2    +      -       -      -
    151C  SER*     3.5    15.9    -      -       -      +
    153C  ASP*     5.8     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 29 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  VAL*     3.9    14.8    -      -       +      +
     28C  ALA*     1.3    74.6    -      -       -      +
     30C  SER*     1.3    66.5    +      -       -      +
     31C  VAL*     4.1    11.0    -      -       +      -
     56C  THR*     3.8    26.7    -      -       +      -
     57C  THR      3.4     6.1    -      -       -      +
     58C  TRP*     4.5     3.1    -      -       +      -
     82C  TRP*     4.8     0.2    -      -       +      -
     84C  PRO*     3.9    26.5    -      -       +      -
     86C  LEU*     4.2     6.1    -      -       +      -
    150C  ILE*     3.8    23.8    -      -       +      -
    151C  SER      2.7    11.9    +      -       -      +
    152C  VAL*     3.1    10.0    -      -       +      -
    153C  ASP*     2.8    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 30 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28C  ALA      4.0     1.1    +      -       -      -
     29C  VAL*     1.3    72.6    +      -       -      +
     31C  VAL*     1.3    62.2    +      -       -      +
     55C  GLN*     3.4     3.1    -      -       -      +
     56C  THR*     3.3     7.8    -      -       -      +
     57C  THR*     2.8    56.2    +      -       -      +
    153C  ASP*     3.1    15.0    +      -       -      +
    154C  PRO      4.1     6.6    +      -       -      -
    155C  THR*     4.5    13.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 31 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  VAL*     4.1     7.4    -      -       +      -
     30C  SER*     1.3    79.3    -      -       -      +
     32C  SER*     1.3    68.3    +      -       -      +
     33C  LEU*     4.7     0.9    -      -       +      -
     54C  GLN*     4.4    16.8    -      -       +      -
     55C  GLN      3.4     7.0    -      -       -      +
     56C  THR*     4.8     0.9    -      -       -      +
     86C  LEU*     3.6    33.2    -      -       +      -
    140C  ILE*     4.4    24.0    -      -       +      -
    152C  VAL*     4.3    19.3    -      -       +      -
    153C  ASP      2.9     6.8    +      -       -      +
    154C  PRO*     3.4    21.3    -      -       -      +
    155C  THR*     4.7     0.9    -      -       -      -
    178C  GLN*     3.8     3.8    -      -       -      +
    195C  VAL*     4.9    16.0    -      -       +      +
    197C  VAL*     6.5     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 32 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31C  VAL*     1.3    78.8    -      -       -      +
     33C  LEU*     1.3    67.6    +      -       -      +
     34C  LYS*     3.6    20.8    +      -       -      +
     53C  TRP      3.6     0.2    -      -       -      +
     54C  GLN      3.8     0.2    -      -       -      -
     55C  GLN*     2.9    57.2    +      -       -      +
    155C  THR*     3.7    14.5    +      -       -      -
    178C  GLN*     4.2    15.1    +      -       -      +
    197C  VAL*     6.0     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31C  VAL*     4.7     2.7    -      -       +      -
     32C  SER*     1.3    80.7    +      -       -      +
     34C  LYS*     1.3    65.3    +      -       -      +
     35C  PHE*     3.7    37.0    +      -       +      -
     52C  PHE*     3.6    38.1    -      -       +      -
     53C  TRP      3.6     1.3    -      -       -      -
     54C  GLN*     3.9    12.3    -      -       +      -
    138C  ILE*     4.3    15.5    -      -       +      -
    140C  ILE*     3.8    26.9    -      -       +      -
    176C  VAL*     5.3     2.9    -      -       -      +
    178C  GLN*     3.9    11.0    +      -       -      +
    197C  VAL*     3.9    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 34 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  SER*     5.3    11.2    -      -       -      -
    187B  CYS*     5.8     1.3    -      -       -      -
     32C  SER*     3.6    21.9    +      -       -      +
     33C  LEU*     1.3    76.7    -      -       -      +
     35C  PHE*     1.3    64.4    +      -       -      +
     36C  ILE*     3.5     3.7    -      -       -      +
     52C  PHE*     4.1     1.1    -      -       -      -
     53C  TRP*     2.8    59.3    +      -       +      +
     55C  GLN*     3.4    29.6    +      -       -      +
    114C  MET*     4.6     6.7    -      -       -      -
    155C  THR*     5.6     4.8    -      -       -      +
    161C  ASP      5.6     1.8    -      -       -      -
    164C  TYR*     4.0    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 35 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33C  LEU*     4.0    28.3    -      -       +      -
     34C  LYS*     1.3    72.0    -      -       -      +
     36C  ILE*     1.3    64.1    +      -       -      +
     37C  ASN      5.4     0.2    -      -       -      -
     38C  ILE*     5.6     0.9    -      -       +      -
     50C  VAL*     3.5    32.8    -      -       +      -
     51C  VAL      3.9     1.6    -      -       -      -
     52C  PHE*     4.1     9.9    -      +       +      -
    138C  ILE*     4.2    14.4    -      -       +      -
    161C  ASP      4.4    10.8    +      -       -      +
    164C  TYR*     3.7     4.7    -      -       -      +
    165C  PHE*     3.7    22.3    +      -       +      +
    173C  ILE*     3.7    19.1    -      -       +      -
    176C  VAL*     4.2    16.8    -      -       +      -
    197C  VAL*     4.0    22.0    -      -       +      -
    199C  LEU*     3.9    45.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 36 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89B  TYR      4.7    14.6    -      -       -      +
     90B  ASN*     6.0     1.1    -      -       -      -
     34C  LYS      3.5    16.4    -      -       -      +
     35C  PHE*     1.3    74.3    -      -       -      +
     37C  ASN*     1.3    65.3    +      -       +      +
     51C  VAL*     2.8    27.4    +      -       +      +
     52C  PHE*     3.9     1.1    -      -       -      -
     53C  TRP*     3.5    45.1    -      -       +      +
    116C  SER*     5.5     0.2    -      -       -      +
    164C  TYR*     3.6    36.3    -      -       +      +
    165C  PHE*     3.6     3.8    -      -       -      -
    166C  SER*     2.7    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 37 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  ILE*     4.7     3.2    -      -       +      +
    122B  SER*     2.9    38.0    +      -       -      -
     35C  PHE*     5.4     0.3    -      -       -      -
     36C  ILE*     1.3    81.3    -      -       +      +
     38C  ILE*     1.3    82.7    +      -       -      +
     39C  LEU*     3.6    19.6    -      -       +      +
     50C  VAL*     3.6     3.3    -      -       -      +
     51C  VAL*     3.0    39.4    +      -       +      +
    165C  PHE*     3.6     7.9    -      -       -      -
    166C  SER*     3.3    17.1    +      -       -      -
    169C  SER*     3.1    21.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 38 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  PHE*     5.6     0.7    -      -       +      -
     37C  ASN*     1.3    85.4    +      -       -      +
     39C  LEU*     1.3    64.2    +      -       -      +
     40C  GLU      4.8     0.2    -      -       -      +
     41C  VAL*     3.8    28.7    -      -       +      -
     48C  VAL*     5.2     1.6    -      -       +      -
     49C  ASP      3.7    10.1    -      -       -      +
     50C  VAL*     4.7    11.2    -      -       +      +
    165C  PHE*     3.6    22.6    -      -       +      -
    169C  SER*     3.0    22.6    +      -       -      +
    170C  ARG      4.7     0.7    +      -       -      -
    171C  PHE*     3.6    20.9    -      -       +      -
    173C  ILE*     4.7     2.7    -      -       +      -
    199C  LEU*     3.9    25.6    -      -       +      -
    201C  PHE*     3.7    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 39 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  THR*     5.1     2.3    -      -       -      +
     47B  GLU*     3.8    28.1    -      -       +      +
     92B  ILE*     3.8    26.7    -      -       +      -
    122B  SER*     5.0     2.2    -      -       -      -
     37C  ASN*     3.6    34.8    -      -       +      +
     38C  ILE*     1.3    76.2    -      -       -      +
     40C  GLU*     1.3    62.4    +      -       +      +
     49C  ASP*     2.9    15.3    +      -       +      +
     51C  VAL*     3.9    12.1    -      -       +      -
    118C  ARG*     3.2    52.5    -      -       -      +
    170C  ARG*     3.3    17.6    +      -       -      -
    171C  PHE*     4.8     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 40 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  LEU*     1.3    82.2    -      -       +      +
     41C  VAL*     1.3    76.9    +      -       -      +
     42C  ASN*     4.8    12.0    +      -       -      +
     47C  GLU      4.8     0.2    -      -       -      -
     48C  VAL*     3.4     2.3    -      -       -      -
     49C  ASP*     2.7    47.7    +      -       +      +
    118C  ARG*     5.8     1.7    +      -       -      +
    120C  ARG*     6.1     0.5    -      -       -      -
    170C  ARG*     4.1     9.9    -      -       -      +
    171C  PHE*     5.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 41 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  ILE*     3.8    10.1    -      -       +      -
     40C  GLU*     1.3    90.4    -      -       -      +
     42C  ASN*     1.3    66.7    +      -       -      +
     43C  GLU      4.3     0.9    -      -       -      +
     47C  GLU      3.7     4.3    -      -       -      -
     48C  VAL*     4.0     6.7    -      -       +      -
    125C  VAL*     3.2    28.7    -      -       +      -
    128C  VAL*     4.1    16.6    -      -       +      -
    170C  ARG*     4.7     1.7    +      -       -      +
    171C  PHE*     3.5    35.1    -      -       +      -
    201C  PHE*     3.6    19.1    -      -       +      -
    203C  LYS*     4.9     6.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 42 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40C  GLU*     4.8    11.8    +      -       -      +
     41C  VAL*     1.3    76.5    -      -       -      +
     43C  GLU*     1.3    57.7    +      -       -      +
     44C  ILE*     2.8    26.2    +      -       -      +
     45C  THR*     2.9    36.3    +      -       -      +
     46C  ASN*     2.8    30.8    +      -       -      -
     47C  GLU*     3.0    15.7    +      -       +      +
    125C  VAL*     3.9     3.9    -      -       -      +
----------------------------------------------------------
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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