Contacts of the strand formed by residues 281 - 290 (chain B) in PDB entry 3M9M


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 PRO 281 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273B  TYR*     4.3     8.3    -      -       +      +
    276B  LEU*     3.9    13.0    -      -       +      -
    279B  ARG      3.6     8.7    -      -       -      +
    280B  ILE*     1.3    89.3    -      -       +      +
    282B  LYS*     1.3    60.5    +      -       -      +
    283B  ALA      3.4     1.3    -      -       -      +
    306B  ILE*     2.8    39.3    +      -       +      +
    337B  PHE*     3.5    45.3    -      -       +      -
    338B  SER      3.4    18.2    -      -       -      +
    339B  LYS      3.9     0.7    -      -       -      +
    340B  PHE*     3.8     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 282 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281B  PRO*     1.3    74.0    -      -       -      +
    283B  ALA*     1.3    55.7    +      -       -      +
    301B  THR*     3.4     3.5    -      -       +      +
    302B  PHE*     2.5    50.2    +      -       -      +
    303B  PRO*     5.0     3.1    -      -       +      -
    304B  HIS*     3.5    31.6    -      -       -      +
    305B  GLY      4.3     1.6    -      -       -      +
    306B  ILE*     3.6     5.4    -      -       -      -
    338B  SER      3.2     0.2    +      -       -      -
    339B  LYS*     3.0    33.1    +      -       +      +
    340B  PHE      3.8     9.4    +      -       -      -
    341B  ILE*     4.3    24.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 283 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281B  PRO*     3.4     1.3    -      -       -      +
    282B  LYS*     1.3    80.8    -      -       -      +
    284B  ILE*     1.3    61.0    +      -       -      +
    285B  HIS*     4.5     6.3    -      -       +      -
    300B  ARG      3.6     6.1    -      -       -      +
    301B  THR*     3.8    17.3    -      -       -      +
    306B  ILE*     3.7     3.4    -      -       -      -
    336B  ARG      3.6     0.2    -      -       -      +
    337B  PHE*     3.3     7.1    -      -       -      +
    338B  SER*     2.7    36.9    +      -       -      +
    339B  LYS*     3.2    33.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 284 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269B  ILE*     5.0     0.4    -      -       +      -
    283B  ALA*     1.3    74.1    -      -       -      +
    285B  HIS*     1.3    69.8    +      -       -      +
    286B  VAL*     5.0     0.4    -      -       +      -
    299B  GLY*     3.5     1.0    -      -       -      -
    300B  ARG      3.2    30.5    +      -       -      +
    302B  PHE*     4.2    11.9    -      -       +      -
    306B  ILE*     3.7    20.4    -      -       +      -
    311B  ALA*     3.8    15.9    -      -       +      +
    314B  GLU*     4.3     6.3    -      -       +      -
    315B  SER*     3.8    29.6    -      -       -      +
    318B  LEU*     3.8    15.2    -      -       +      +
    335B  VAL*     3.5    27.6    -      -       +      -
    336B  ARG      3.3     3.1    -      -       -      -
    337B  PHE*     3.8    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 285 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283B  ALA*     4.5     8.5    -      -       +      +
    284B  ILE*     1.3    86.4    +      -       -      +
    286B  VAL*     1.3    64.1    +      -       -      +
    287B  VAL*     3.8     7.3    +      -       +      +
    297B  SER*     4.8    10.4    +      -       -      -
    298B  ARG      3.6     5.7    -      -       -      +
    299B  GLY*     3.7    21.0    +      -       -      -
    300B  ARG      4.8     2.0    +      -       -      -
    301B  THR*     5.2     2.2    +      -       -      -
    335B  VAL*     3.2     5.7    -      -       -      +
    336B  ARG*     2.8    46.3    +      -       +      +
    338B  SER*     3.9    21.2    +      -       -      -
    339B  LYS*     5.1     7.1    +      -       -      -
      6P    A      4.9     8.5    -      -       +      -
      7P    A      4.0    18.3    +      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 286 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265B  LEU*     3.7    17.7    -      -       +      -
    284B  ILE*     5.0     2.0    -      -       +      -
    285B  HIS*     1.3    73.3    -      -       -      +
    287B  VAL*     1.3    62.6    +      -       -      +
    297B  SER*     3.1    24.3    -      -       -      -
    298B  ARG      2.9    12.5    +      -       -      +
    315B  SER*     3.5    23.1    -      -       -      +
    318B  LEU*     3.3    38.8    -      -       +      -
    319B  LEU*     4.1    11.4    -      -       +      +
    322B  ILE*     3.7    19.2    -      -       +      +
    333B  ILE*     4.3     7.0    -      -       +      -
    334B  GLY      3.5    11.7    -      -       -      +
    335B  VAL*     4.4     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 287 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  ILE*     3.5    27.9    -      -       +      +
    285B  HIS*     4.1    15.3    -      -       +      +
    286B  VAL*     1.3    77.0    -      -       -      +
    288B  ALA*     1.3    65.7    +      -       -      +
    289B  VAL*     4.9     1.1    -      -       +      -
    295B  ILE*     3.9    27.4    -      -       +      -
    296B  VAL      3.7     3.8    -      -       -      +
    297B  SER*     4.0    12.1    -      -       -      -
    333B  ILE*     3.5     3.9    -      -       -      +
    334B  GLY      2.7    38.1    +      -       -      +
    335B  VAL      4.9     2.7    -      -       -      +
    336B  ARG*     4.8    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 288 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  ILE*     5.0     0.2    -      -       -      -
    286B  VAL      4.3     0.2    -      -       -      -
    287B  VAL*     1.3    75.2    -      -       -      +
    289B  VAL*     1.3    65.5    -      -       -      +
    290B  THR*     3.9     2.2    +      -       +      +
    295B  ILE*     4.0     0.3    -      -       -      -
    296B  VAL*     3.0    37.5    +      -       +      +
    322B  ILE*     4.5    12.3    -      -       +      +
    330B  ILE*     3.5    28.9    -      -       +      -
    332B  ARG      3.1    14.6    -      -       -      +
    333B  ILE*     3.6    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 289 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  ILE*     4.6    11.2    -      -       +      -
    288B  ALA*     1.3    75.6    -      -       -      +
    290B  THR*     1.3    65.0    +      -       -      +
    293B  LEU*     3.3    44.2    -      -       +      +
    294B  ASP      3.4     2.2    -      -       -      -
    295B  ILE*     3.9    25.1    -      -       +      -
    330B  ILE*     4.9     1.1    -      -       -      -
    331B  ARG*     3.2    24.7    +      -       +      +
    332B  ARG*     3.1    47.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 290 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  ALA*     3.9     2.5    -      -       +      +
    289B  VAL*     1.3    78.3    -      -       -      +
    291B  GLU*     1.3    55.5    +      -       -      +
    292B  ASP*     2.6    22.8    +      -       -      -
    293B  LEU*     2.5    27.5    +      -       -      -
    294B  ASP*     3.2    20.2    +      -       -      +
    296B  VAL*     4.0    14.6    -      -       +      -
    326B  ASP*     4.0     6.3    -      -       -      +
    328B  ARG*     3.3    44.4    +      -       +      +
    329B  LYS      3.1    12.1    -      -       -      +
    330B  ILE*     4.5     6.7    -      -       +      +
    331B  ARG*     4.1     1.6    -      -       -      -
----------------------------------------------------------
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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