Contacts of the strand formed by residues 171 - 184 (chain B) 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 PHE 171 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  ILE*     3.6    38.1    -      -       +      -
     39B  LEU      4.8     2.0    -      -       -      -
     41B  VAL*     3.4    35.9    -      -       +      -
    128B  VAL*     3.9    12.3    -      -       +      -
    165B  PHE*     3.4    14.5    -      -       -      -
    166B  SER      4.8     0.5    -      -       -      +
    169B  SER*     2.9    11.5    +      -       -      +
    170B  ARG*     1.3   118.1    -      -       +      +
    172B  GLU*     1.3    62.8    +      -       -      +
    201B  PHE*     3.9    20.9    -      +       +      -
    202B  ARG      3.3    21.5    -      -       -      +
    203B  LYS*     4.0    20.6    -      -       +      -
    204B  LYS*     3.4    15.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  PHE*     4.1     6.7    -      -       -      -
    171B  PHE*     1.3    77.7    -      -       -      +
    173B  ILE*     1.3    65.3    +      -       -      +
    174B  LEU*     3.7     6.6    +      -       +      +
    201B  PHE*     3.2     6.8    -      -       -      +
    202B  ARG*     2.6    75.7    +      -       +      +
    203B  LYS      4.1     4.0    -      -       -      +
    204B  LYS*     3.8    26.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  PHE*     3.7    21.5    -      -       +      +
     38B  ILE*     4.7     3.8    -      -       +      -
    162B  SER*     3.4    32.1    +      -       -      +
    165B  PHE*     3.4    46.9    -      -       +      -
    172B  GLU*     1.3    76.2    -      -       -      +
    174B  LEU*     1.3    67.6    +      -       -      +
    175B  ASP*     3.7    14.6    -      -       -      +
    176B  VAL*     3.8    22.2    -      -       +      -
    199B  LEU*     4.0    15.7    -      -       +      -
    200B  ASN      3.7     4.5    -      -       -      +
    201B  PHE*     4.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131B  GLU      3.9     9.6    -      -       -      +
    132B  SER*     3.4    33.9    -      -       -      +
    133B  GLY*     4.2     2.7    -      -       -      +
    172B  GLU*     4.5     7.0    -      -       +      -
    173B  ILE*     1.3    79.2    -      -       -      +
    175B  ASP*     1.3    62.8    +      -       +      +
    200B  ASN*     2.6    33.2    +      -       -      +
    201B  PHE*     4.3     4.9    -      -       -      -
    202B  ARG*     3.7    42.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173B  ILE*     3.6     4.1    -      -       -      +
    174B  LEU*     1.3    83.1    -      -       +      +
    176B  VAL*     1.3    78.4    +      -       -      +
    177B  THR*     3.6    21.5    -      -       +      +
    198B  SER      3.6     0.8    -      -       -      +
    200B  ASN*     2.9    42.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 176 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU      5.2     3.1    -      -       -      +
     35B  PHE*     4.1    15.5    -      -       +      -
    162B  SER      6.0     2.5    -      -       -      +
    173B  ILE*     3.8    19.3    -      -       +      -
    175B  ASP*     1.3    87.6    +      -       -      +
    177B  THR*     1.3    68.4    +      -       -      +
    178B  GLN*     4.5    11.1    -      -       +      +
    197B  VAL*     3.7    28.7    -      -       +      -
    198B  SER      3.3     5.2    -      -       -      +
    199B  LEU*     4.0    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  ASP*     3.6    20.8    -      -       -      +
    176B  VAL*     1.3    76.9    -      -       -      +
    178B  GLN*     1.3    65.7    +      -       -      +
    196B  GLU      3.6     1.1    -      -       -      +
    197B  VAL*     3.4     3.8    -      -       -      +
    198B  SER*     2.7    54.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 178 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  VAL      3.6     8.7    -      -       -      +
     32B  SER*     4.1     8.7    +      -       -      +
     33B  LEU      3.8    27.1    +      -       -      +
    154B  PRO*     3.1    43.1    -      -       +      +
    155B  THR      4.1     2.8    +      -       -      -
    176B  VAL*     4.5     8.3    -      -       +      +
    177B  THR*     1.3    82.9    -      -       -      +
    179B  LYS*     1.3    60.7    +      -       -      +
    195B  VAL*     4.5     4.3    -      -       +      +
    196B  GLU      3.4     4.5    -      -       -      +
    197B  VAL*     3.8    25.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  PRO*     4.7     0.4    -      -       -      -
    178B  GLN*     1.3    74.9    -      -       -      +
    180B  LYS*     1.3    67.3    +      -       -      +
    181B  ASN*     3.1    26.1    +      -       -      +
    195B  VAL*     3.3     4.4    -      -       -      -
    196B  GLU*     2.5    60.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  SER*     4.5     0.4    -      -       -      -
    152B  VAL      2.7    21.2    +      -       -      +
    153B  ASP*     2.9    31.9    +      -       -      +
    154B  PRO*     4.0    18.2    -      -       +      +
    179B  LYS*     1.3    78.9    -      -       -      +
    181B  ASN*     1.3    75.6    +      -       -      +
    182B  SER*     6.4     0.7    -      -       -      -
    193B  GLU*     2.3    44.3    +      -       -      +
    194B  ASP      3.4     7.4    -      -       -      +
    195B  VAL*     4.3     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179B  LYS*     3.1    37.2    +      -       -      +
    180B  LYS*     1.3    81.2    -      -       -      +
    182B  SER*     1.3    61.7    +      -       -      +
    183B  VAL*     4.2     8.3    -      -       +      -
    193B  GLU*     3.1     8.2    -      -       -      +
    194B  ASP*     2.6    64.1    +      -       -      +
    196B  GLU*     3.3    30.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  SER*     4.7     2.6    -      -       -      -
    180B  LYS*     6.4     0.7    -      -       -      -
    181B  ASN*     1.3    74.6    -      -       -      +
    183B  VAL*     1.3    62.7    +      -       -      +
    184B  THR      4.4     0.3    +      -       -      -
    191B  ALA*     3.4    23.8    -      -       -      +
    192B  TYR      3.6     4.3    +      -       -      -
    193B  GLU*     4.0    18.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139B  LYS*     4.6     7.0    -      -       -      +
    181B  ASN*     4.3     8.1    -      -       +      -
    182B  SER*     1.3    79.6    +      -       -      +
    184B  THR*     1.3    72.7    +      -       -      +
    185B  TYR*     3.3    39.8    -      -       +      +
    191B  ALA*     3.6     1.7    -      -       -      -
    192B  TYR      2.8    31.9    +      -       -      +
    194B  ASP*     3.4    22.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183B  VAL*     1.3    81.6    -      -       -      +
    185B  TYR*     1.3    65.8    +      -       -      +
    188B  CYS      3.9    16.2    -      -       -      +
    189B  PRO*     4.1    10.0    +      -       +      +
    190B  GLU      4.0     9.8    -      -       -      +
    191B  ALA*     4.2    12.1    -      -       -      +
    163C  GLU*     5.1     3.1    -      -       -      +
    164C  TYR*     5.7     0.7    -      -       -      -
----------------------------------------------------------
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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