Contacts of the strand formed by residues 291 - 302 (chain D) in PDB entry 2J2M


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 291 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216D  ARG*     3.2    38.8    -      -       +      -
    218D  VAL*     4.7    12.3    -      -       +      -
    261D  PHE*     3.7    41.6    -      +       +      -
    262D  VAL      3.9     3.6    -      -       -      -
    263D  GLN*     3.5    37.0    -      -       +      -
    286D  GLU*     3.6    52.9    +      -       +      +
    290D  PRO*     1.3    75.5    -      -       -      +
    292D  GLN*     1.3    60.8    +      -       -      +
    293D  HIS      4.3     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 292 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72D  MET*     5.3     5.3    -      -       +      +
     74D  LYS*     4.8     2.8    +      -       -      -
     75D  TYR*     3.1    37.6    +      -       -      -
    261D  PHE*     3.2     3.2    -      -       -      -
    262D  VAL*     2.7    54.9    +      -       +      +
    264D  VAL*     3.6    25.0    -      -       -      +
    290D  PRO*     4.0    13.3    +      -       +      +
    291D  PHE*     1.3    78.4    -      -       -      +
    293D  HIS*     1.3    65.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 293 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69D  LYS*     3.6    26.2    -      -       +      +
     70D  ASN*     2.7    45.8    +      -       -      +
     72D  MET*     3.5    10.0    -      -       -      +
    259D  ASP*     3.2    26.2    +      -       +      -
    260D  LEU      3.8     8.7    -      -       -      -
    261D  PHE*     3.6    38.1    -      +       +      -
    291D  PHE      4.3     0.2    +      -       -      -
    292D  GLN*     1.3    72.2    -      -       -      +
    294D  VAL*     1.3    57.8    +      -       -      +
    295D  GLY*     3.7    19.8    +      -       -      -
    296D  THR*     4.3     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 294 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66D  PHE*     4.2     5.2    -      -       +      -
     68D  VAL*     3.7     3.1    -      -       -      -
     69D  LYS      2.8    20.4    +      -       -      -
     70D  ASN*     3.1    17.4    +      -       -      +
     72D  MET*     4.1    16.4    -      -       +      -
     81D  LEU*     3.9    29.2    -      -       +      -
    203D  TRP*     5.0     4.5    -      -       +      -
    215D  LEU*     5.4     0.2    -      -       +      -
    260D  LEU*     2.8    38.7    +      -       +      +
    261D  PHE      4.3     1.1    -      -       -      -
    262D  VAL*     3.8    28.9    -      -       +      +
    292D  GLN      3.8    11.0    -      -       -      +
    293D  HIS*     1.3    79.2    -      -       -      +
    295D  GLY*     1.3    56.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 295 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66D  PHE*     3.5    11.6    -      -       -      -
     67D  LYS      3.1    14.8    -      -       -      -
     69D  LYS*     3.7     5.4    -      -       -      -
    259D  ASP*     3.5     1.2    -      -       -      -
    260D  LEU      2.7    25.5    +      -       -      +
    293D  HIS*     3.7    10.4    +      -       -      -
    294D  VAL*     1.3    83.8    -      -       -      +
    296D  THR*     1.3    68.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 296 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65D  VAL*     3.9     0.9    -      -       -      +
     66D  PHE*     3.5     4.5    -      -       -      -
     67D  LYS*     2.9    40.7    +      -       -      +
     69D  LYS*     5.6     2.5    -      -       +      -
    257D  GLU*     5.2     8.5    +      -       -      -
    258D  TRP      3.3     8.7    -      -       -      -
    259D  ASP*     2.6    30.3    -      -       -      +
    293D  HIS*     4.1     8.1    -      -       +      +
    295D  GLY*     1.3    77.5    -      -       -      -
    297D  MET*     1.3    62.7    +      -       -      +
    298D  THR*     4.1     8.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 297 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65D  VAL      3.4     9.4    -      -       -      +
     66D  PHE*     3.9     8.6    -      -       +      -
     90D  VAL*     4.1     7.4    -      -       +      -
     92D  ALA*     4.6     2.2    -      -       +      -
     94D  PHE*     4.5     5.4    -      -       +      -
    113D  PHE*     3.8    27.1    -      -       +      -
    115D  VAL*     3.9    32.8    -      -       +      -
    217D  TRP*     3.5    25.1    -      -       +      -
    256D  PRO      4.0     0.3    -      -       -      +
    257D  GLU*     3.1     7.1    -      -       -      +
    258D  TRP*     2.8    61.7    +      -       +      +
    296D  THR*     1.3    74.5    -      -       -      +
    298D  THR*     1.3    62.6    +      -       -      +
    299D  LEU*     3.7    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 298 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64D  GLY*     3.1     3.3    -      -       -      -
     65D  VAL*     2.9    47.6    +      -       -      +
    255D  PHE*     3.7    34.1    -      -       +      -
    256D  PRO      3.6     2.5    -      -       -      -
    257D  GLU*     3.7    27.3    +      -       +      +
    296D  THR*     4.1     8.5    +      -       -      -
    297D  MET*     1.3    75.6    -      -       -      +
    299D  LEU*     1.3    66.3    +      -       -      +
    300D  ASN*     3.7     5.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 299 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62D  ALA*     4.3    16.8    -      -       +      +
     63D  HIS      3.6    10.3    -      -       -      +
     64D  GLY*     4.1    11.4    -      -       -      +
     90D  VAL*     4.2     5.2    -      -       +      -
     92D  ALA*     4.2    11.2    -      -       +      -
     94D  PHE*     3.6    33.0    -      -       +      -
    246D  THR*     5.9     1.6    -      -       +      -
    250D  ILE*     3.8    15.6    -      -       +      +
    255D  PHE*     3.5    20.5    -      -       -      +
    256D  PRO*     2.9    27.5    +      -       +      +
    258D  TRP*     3.7    18.8    -      -       +      -
    297D  MET*     3.7    27.1    -      -       +      -
    298D  THR*     1.3    76.0    -      -       -      +
    300D  ASN*     1.3    60.2    +      -       -      +
    301D  LYS      3.7     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 300 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63D  HIS*     3.1     1.5    +      -       -      +
     64D  GLY*     3.5    18.5    -      -       -      -
     65D  VAL*     4.6    15.0    -      -       -      +
    250D  ILE*     3.7     9.2    -      -       -      +
    255D  PHE*     3.7    40.9    -      -       +      -
    298D  THR*     4.6     7.7    -      -       +      +
    299D  LEU*     1.3    74.5    -      -       -      +
    301D  LYS*     1.3    69.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 301 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154C  ARG*     6.1     1.2    -      -       -      +
     62D  ALA*     3.6     2.8    -      -       -      +
     63D  HIS*     2.7    51.0    +      -       +      +
    250D  ILE*     3.7     6.0    -      -       -      +
    299D  LEU      3.7     1.4    -      -       -      -
    300D  ASN*     1.3    87.3    +      -       -      +
    302D  ASN*     1.3    72.9    +      -       -      +
    304D  ASP*     4.5    19.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 302 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154C  ARG*     3.9    11.4    +      -       -      +
     60D  PHE*     3.8    10.4    -      -       -      -
     61D  GLY      5.0     0.3    -      -       -      +
     62D  ALA*     4.4     3.3    -      -       -      +
     63D  HIS*     4.4     3.6    -      -       -      -
    247D  PHE*     3.1    58.2    +      -       +      -
    250D  ILE*     3.5    29.0    -      -       -      +
    251D  GLU*     2.7    30.7    +      -       -      +
    301D  LYS*     1.3    94.6    +      -       -      +
    303D  VAL*     1.3    65.2    +      -       -      +
    304D  ASP*     3.8     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