Contacts of the strand formed by residues 198 - 208 (chain B) in PDB entry 2YXT


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 TYR 198 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  LEU      4.6     6.4    -      -       -      +
    192B  SER*     3.6    26.5    +      -       -      +
    194B  GLN*     3.3    56.7    +      -       +      -
    195B  GLY      3.4     5.1    +      -       -      +
    196B  SER*     3.1     2.5    -      -       -      +
    197B  ASN*     1.3    98.7    -      -       +      +
    199B  LEU*     1.3    59.8    -      -       -      +
    222B  ASP      3.8    11.9    -      -       -      -
    223B  ILE      3.2    26.0    -      -       -      +
    224B  ARG*     3.3    41.7    +      -       +      -
    225B  LYS*     3.2    16.0    +      -       -      -
   1335B  PO4      3.9     6.1    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    186B  THR      4.2     4.7    -      -       -      +
    187B  SER*     4.2    16.4    -      -       -      +
    188B  SER      4.1    12.6    -      -       -      +
    190B  LEU      5.3     0.9    -      -       -      -
    198B  TYR*     1.3    73.4    -      -       -      +
    200B  ILE*     1.3    73.2    +      -       -      +
    201B  VAL*     4.0    11.4    -      -       +      -
    221B  MET      3.6     1.6    -      -       -      +
    222B  ASP*     3.6     2.1    -      -       -      -
    223B  ILE*     2.7    47.6    +      -       +      +
    225B  LYS*     4.0    27.5    -      -       +      +
   1023B  MPD      3.9    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  ILE      4.1     1.2    -      -       -      +
    187B  SER*     3.6     6.9    -      -       -      -
    188B  SER*     3.4    37.3    +      -       -      +
    190B  LEU*     3.5    30.3    -      -       +      +
    191B  PRO      3.9     4.0    -      -       -      +
    192B  SER*     3.9     7.2    -      -       -      -
    199B  LEU*     1.3    77.4    -      -       -      +
    201B  VAL*     1.3    67.2    +      -       -      +
    202B  LEU*     3.7    32.8    -      -       +      -
    220B  ARG*     2.9    32.8    -      -       +      +
    221B  MET      3.4     1.1    -      -       -      -
    222B  ASP*     2.8    33.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184B  VAL*     4.0    19.7    -      -       +      -
    185B  ILE      3.5     7.4    -      -       -      +
    186B  THR*     3.4    23.3    -      -       -      +
    199B  LEU*     4.0     4.3    -      -       +      -
    200B  ILE*     1.3    75.3    -      -       -      +
    202B  LEU*     1.3    69.5    +      -       -      +
    219B  ILE*     4.0     1.9    -      -       +      +
    220B  ARG*     3.2     5.0    -      -       -      -
    221B  MET*     2.8    55.9    +      -       +      -
    223B  ILE*     3.2    31.9    -      -       +      -
    237B  PHE*     5.1     4.3    -      -       +      -
    256B  CYS*     5.7     0.7    -      -       -      -
    260B  VAL*     5.0     5.8    -      -       +      -
   1023B  MPD      4.1     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  GLN*     4.3    14.1    -      -       +      +
    168B  ALA*     3.5    33.0    -      -       +      -
    169B  LEU*     4.8     0.4    -      -       +      -
    172B  MET*     3.4    24.1    -      -       +      +
    183B  VAL      4.0     0.3    -      -       -      +
    184B  VAL*     3.1     4.7    -      -       -      +
    185B  ILE*     2.7    48.5    +      -       +      +
    188B  SER*     5.5     0.9    -      -       -      +
    190B  LEU*     4.2    15.5    -      -       +      -
    200B  ILE*     3.7     8.3    -      -       +      -
    201B  VAL*     1.3    83.6    -      -       -      +
    203B  GLY*     1.3    58.8    +      -       -      +
    219B  ILE      3.5    12.8    -      -       -      +
    220B  ARG*     3.7    21.1    -      -       +      -
    312B  LEU*     3.9    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  LEU*     5.7     0.5    -      -       -      +
    172B  MET*     4.6     2.7    -      -       -      +
    183B  VAL      3.5     5.6    -      -       -      -
    184B  VAL*     3.9    11.7    -      -       -      -
    202B  LEU*     1.3    75.2    -      -       -      +
    204B  SER*     1.3    62.3    +      -       -      -
    218B  ARG*     3.2     4.7    -      -       -      +
    219B  ILE*     2.7    52.6    +      -       -      +
    252B  LEU*     3.5     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172B  MET*     4.1    22.2    -      -       -      +
    173B  ASP*     5.0     0.3    +      -       -      -
    176B  HIS*     2.6    31.7    +      -       -      -
    182B  THR*     3.5     3.1    -      -       -      +
    183B  VAL      2.8    34.0    +      -       -      +
    184B  VAL*     4.9     0.2    -      -       -      +
    203B  GLY*     1.3    75.9    -      -       -      -
    205B  GLN*     1.3    61.3    +      -       -      +
    216B  MET*     3.7    17.2    -      -       -      +
    217B  GLU      3.3     6.1    -      -       -      -
    218B  ARG*     3.9    12.3    +      -       -      +
    252B  LEU*     3.6     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176B  HIS*     4.3     0.2    -      -       -      -
    181B  ASP      3.4     4.3    -      -       -      +
    182B  THR*     3.2    26.1    +      -       -      +
    204B  SER*     1.3    75.4    +      -       -      +
    206B  ARG*     1.3    72.6    +      -       -      +
    207B  ARG*     2.8    36.0    +      -       +      +
    215B  VAL      3.6     0.9    -      -       -      +
    216B  MET*     3.1     5.0    -      -       -      -
    217B  GLU*     2.8    39.8    +      -       -      +
    245B  THR*     4.4     8.3    -      -       -      +
    248B  HIS      5.7     0.6    +      -       -      -
    249B  PRO      3.5    15.5    +      -       -      +
    251B  ASN      4.4     0.2    +      -       -      -
    252B  LEU*     3.7    38.7    +      -       +      +
   1053B  MPD      3.4    21.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176B  HIS*     3.5    32.5    +      -       +      +
    181B  ASP*     2.9    36.8    +      -       -      +
    205B  GLN*     1.3    77.1    -      -       -      +
    207B  ARG*     1.3    66.3    +      -       -      +
    214B  VAL*     3.7    21.9    -      -       +      +
    215B  VAL      3.2     7.2    +      -       -      +
    216B  MET*     3.3    38.6    -      -       +      +
   1027B  MPD      3.7    39.6    -      -       +      +
   1041B  MPD      3.5    36.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  GLN*     2.8    40.7    +      -       +      +
    206B  ARG*     1.3    76.2    -      -       -      +
    208B  ARG*     1.3    63.0    +      -       -      +
    209B  ASN*     5.7     0.9    -      -       -      -
    214B  VAL*     3.3     3.1    -      -       -      -
    215B  VAL*     2.7    56.6    +      -       +      +
    217B  GLU*     2.7    45.1    +      -       -      +
    249B  PRO      4.2     2.7    -      -       -      -
    250B  ASN*     3.1    52.5    +      -       -      +
   1027B  MPD      4.1    12.9    -      -       -      +
   1053B  MPD      6.4     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207B  ARG*     1.3    79.3    -      -       -      +
    209B  ASN*     1.3    62.6    +      -       -      +
    210B  PRO*     4.9     0.2    -      -       -      +
    212B  GLY*     2.7    54.0    +      -       -      +
    213B  SER      3.2     4.5    -      -       -      +
    214B  VAL*     3.6    23.3    -      -       +      +
    250B  ASN*     5.0     4.9    -      -       -      +
   1027B  MPD      3.8    35.6    +      -       +      +
----------------------------------------------------------
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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