Contacts of the strand formed by residues 192 - 202 (chain B) in PDB entry 2HA5


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 192 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  PRO*     4.6     3.5    -      -       -      +
    112B  THR      3.4     9.0    -      -       -      -
    114B  VAL*     3.8    12.6    -      -       -      -
    145B  VAL*     3.9    10.8    -      -       -      +
    187B  ILE*     3.1    18.1    +      -       -      -
    188B  ALA*     3.3    20.3    -      -       -      +
    190B  PHE      3.4     2.6    +      -       -      -
    191B  GLY*     1.3    81.7    -      -       -      +
    193B  ASP*     1.3    58.9    +      -       -      -
    194B  PRO*     3.4     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  PRO*     3.9    18.9    -      -       -      +
    112B  THR      2.7    32.6    +      -       -      +
    113B  PRO*     4.2     2.6    -      -       -      +
    114B  VAL*     3.7     5.7    -      -       -      +
    187B  ILE*     4.3     2.2    -      -       -      -
    192B  GLY*     1.3    71.2    -      -       -      -
    194B  PRO*     1.3    69.3    -      -       -      +
    195B  MET*     3.1    29.6    +      -       -      +
    196B  SER*     3.0    36.8    +      -       -      +
    197B  VAL*     3.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  PRO*     5.8     0.9    -      -       +      -
    184B  GLN*     2.7    62.8    +      -       -      +
    187B  ILE*     3.9    17.2    -      -       +      -
    188B  ALA*     4.4    15.0    -      -       +      -
    192B  GLY      3.4    11.0    -      -       -      +
    193B  ASP*     1.3    86.1    -      -       -      +
    195B  MET*     1.3    62.1    +      -       +      +
    196B  SER      3.2     1.5    +      -       -      -
    197B  VAL*     3.6     4.5    -      -       +      +
    223B  HIS*     3.2    10.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  ASP*     3.1    17.2    +      -       -      +
    194B  PRO*     1.3    83.4    -      -       +      +
    196B  SER*     1.3    59.6    +      -       -      +
    223B  HIS*     3.2    27.2    +      -       +      -
    224B  ARG*     5.1     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  PRO*     3.8    17.7    -      -       -      +
    114B  VAL      3.0    23.7    +      -       -      +
    193B  ASP*     3.0    28.2    +      -       -      +
    194B  PRO      3.2     0.2    -      -       -      -
    195B  MET*     1.3    81.5    -      -       -      +
    197B  VAL*     1.3    59.0    +      -       -      +
    198B  THR*     5.1     0.6    +      -       -      -
    223B  HIS*     3.8     2.7    -      -       -      -
    224B  ARG*     2.9    25.2    +      -       -      +
    484B  ALA      3.6     8.5    +      -       -      -
    485B  ARG      4.7     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  VAL*     3.5    13.0    -      -       +      +
    116B  ILE*     3.4    35.4    -      -       +      -
    183B  VAL*     4.4     9.4    -      -       +      -
    184B  GLN*     3.7    11.7    -      -       -      +
    193B  ASP      3.9     7.0    -      -       -      +
    194B  PRO*     3.6    21.5    -      -       +      +
    196B  SER*     1.3    78.9    -      -       -      +
    198B  THR*     1.3    63.1    +      -       -      +
    199B  LEU*     4.3     2.9    -      -       +      -
    221B  LEU      3.9    15.3    -      -       -      +
    222B  PHE*     3.7     8.3    -      -       +      +
    223B  HIS*     3.0    38.9    +      -       +      +
    224B  ARG*     3.4     5.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  VAL      2.9     8.6    +      -       -      -
    115B  LEU*     3.3    27.5    -      -       +      +
    116B  ILE      2.8    26.3    +      -       -      -
    196B  SER      5.1     0.5    -      -       -      -
    197B  VAL*     1.3    74.8    -      -       -      +
    199B  LEU*     1.3    73.2    +      -       -      +
    200B  PHE      3.8     0.2    +      -       -      -
    224B  ARG*     3.5    27.1    +      -       +      +
    226B  VAL*     4.2    15.3    -      -       +      -
    483B  PHE*     4.2     9.0    -      -       +      -
    484B  ALA*     3.3    27.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116B  ILE*     3.5    37.5    -      -       +      +
    118B  ILE*     4.7     4.5    -      -       +      -
    180B  LEU*     4.0    18.8    -      -       +      -
    197B  VAL*     4.1     0.4    -      -       +      -
    198B  THR*     1.3    76.1    -      -       -      +
    200B  PHE*     1.3    62.2    +      -       -      +
    209B  VAL*     4.0    24.9    -      -       +      -
    212B  HIS*     4.1    19.7    -      -       +      -
    222B  PHE*     3.7    51.1    -      -       +      -
    224B  ARG      3.0     9.6    +      -       -      +
    225B  ALA*     3.3     1.6    -      -       -      -
    226B  VAL      2.8    24.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115B  LEU*     3.7    35.7    -      -       +      -
    116B  ILE      2.9    19.8    +      -       -      +
    117B  TRP*     3.3    50.6    -      +       +      -
    118B  ILE*     2.9    24.6    +      -       -      +
    138B  LEU*     4.5     3.8    -      -       +      -
    146B  LEU*     3.9    15.0    -      -       +      -
    199B  LEU*     1.3    76.9    -      -       -      +
    201B  GLY*     1.3    58.8    +      -       -      +
    209B  VAL*     4.0     4.7    -      -       -      -
    226B  VAL*     3.4    28.7    -      -       +      -
    228B  GLN*     3.7    11.2    -      -       -      -
    454B  ILE*     4.4     8.5    -      -       +      -
    455B  PHE*     3.7    22.0    -      +       -      -
    480B  TRP*     3.9    18.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  TRP*     3.5    11.8    -      -       -      -
    118B  ILE      3.2    16.2    -      -       -      -
    200B  PHE*     1.3    77.2    -      -       -      +
    202B  GLU*     1.3    60.4    +      -       -      -
    205B  GLY      4.0     8.3    -      -       -      -
    206B  ALA*     3.4     9.1    -      -       -      +
    209B  VAL*     4.0     1.2    -      -       -      +
    226B  VAL      3.2     7.3    +      -       -      +
    228B  GLN*     3.0    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  TRP*     3.5    22.3    -      -       +      -
    118B  ILE      3.7     2.8    +      -       -      -
    120B  GLY*     3.3    10.7    +      -       -      -
    133B  TYR*     5.2     0.2    +      -       -      -
    201B  GLY*     1.3    73.5    -      -       -      +
    203B  ALA*     1.3    76.3    +      -       -      +
    205B  GLY      2.9    17.2    +      -       -      -
    206B  ALA      3.6     1.5    -      -       -      +
    228B  GLN*     3.1    13.9    -      -       +      +
    229B  SER*     4.1     2.4    -      -       -      -
    447B  HIS*     3.5    19.8    +      -       -      -
    448B  GLY*     3.4    23.6    +      -       -      -
    450B  GLU*     3.3    23.1    -      -       -      +
    451B  ILE*     3.7    23.0    -      -       +      +
   1951B  AT3      3.8    15.5    -      -       -      -
----------------------------------------------------------
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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