Contacts of the strand formed by residues 87 - 95 (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 GLU 87 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65D  VAL*     3.1    29.5    -      -       +      +
     66D  PHE      3.1     4.7    -      -       -      -
     67D  LYS*     3.2    41.1    +      -       +      +
     85D  GLY      3.4     1.5    +      -       -      +
     86D  THR*     1.3    76.9    +      -       -      +
     88D  VAL*     1.3    65.1    +      -       -      +
     89D  PRO*     4.3     3.9    -      -       -      +
    120D  GLU*     5.2     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 88 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65D  VAL*     3.5     4.6    -      -       -      -
     66D  PHE*     2.7    47.1    +      -       +      +
     80D  PHE*     3.6    39.3    -      -       +      -
     86D  THR*     4.1     6.7    -      -       -      +
     87D  GLU*     1.3    79.0    -      -       -      +
     89D  PRO*     1.4    77.6    -      -       +      +
     90D  VAL*     4.0     2.0    -      -       +      -
    117D  PHE*     3.5    37.7    -      -       +      -
    118D  TYR      4.3     8.1    -      -       -      +
    119D  THR*     4.6     2.7    -      -       -      +
    120D  GLU*     4.4     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64D  GLY      3.7     8.7    -      -       -      +
     65D  VAL*     4.6     2.5    -      -       +      -
     87D  GLU      4.3     3.8    -      -       -      +
     88D  VAL*     1.4    85.3    -      -       -      +
     90D  VAL*     1.3    62.3    +      -       -      +
    118D  TYR*     3.0    59.1    +      -       +      +
    360D  PHE*     5.5     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63D  HIS*     3.6     7.4    +      -       -      +
     64D  GLY*     2.9    53.9    +      -       -      +
     65D  VAL*     3.5     8.1    -      -       -      +
     66D  PHE*     4.0     9.4    -      -       +      -
     88D  VAL      3.8     7.4    -      -       -      +
     89D  PRO*     1.3    79.1    -      -       -      +
     91D  PHE*     1.3    61.2    +      -       -      +
    115D  VAL*     3.8    13.9    -      -       +      -
    116D  LYS      3.1    12.8    -      -       -      +
    117D  PHE*     3.8    26.2    -      -       +      -
    118D  TYR*     4.0     4.9    -      -       -      -
    297D  MET*     4.1    18.8    -      -       -      -
    299D  LEU*     4.2     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 91 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61D  GLY*     3.9     8.1    -      -       -      -
     62D  ALA      3.3    28.0    -      -       -      -
     63D  HIS*     3.5    26.7    -      +       -      +
     90D  VAL*     1.3    75.0    -      -       -      +
     92D  ALA*     1.3    66.5    +      -       -      +
     93D  ARG*     4.9     1.1    -      -       +      -
    115D  VAL*     3.5     1.1    -      -       -      -
    116D  LYS*     2.8    36.9    +      -       +      -
    118D  TYR*     3.6    21.6    -      -       +      +
    303D  VAL*     3.7    15.9    -      -       +      -
    309D  GLU*     3.8    17.7    -      -       +      -
    310D  THR*     3.6    31.9    -      -       -      -
    313D  VAL*     4.0    22.4    -      -       +      -
    315D  PHE*     3.6     8.5    -      +       -      -
    356D  ILE*     3.8    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 92 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  PHE      4.5     0.2    -      -       -      -
     61D  GLY*     3.0     3.5    -      -       -      -
     62D  ALA      2.9    36.3    +      -       -      +
     90D  VAL*     4.3     0.4    -      -       +      -
     91D  PHE*     1.3    79.2    -      -       -      +
     93D  ARG*     1.3    61.5    +      -       -      +
     94D  PHE*     4.2    21.7    -      -       +      -
    114D  SER      3.0    12.3    -      -       -      +
    115D  VAL*     4.1    13.7    -      -       +      -
    297D  MET*     4.6     2.7    -      -       -      -
    299D  LEU*     4.2    19.0    -      -       +      +
    315D  PHE*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 93 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  ARG*     3.5    26.4    -      -       -      +
     56D  HIS      2.9    22.0    +      -       -      -
     57D  ALA      2.8    29.5    +      -       -      -
     59D  GLY*     3.8    13.4    -      -       -      +
     60D  PHE      3.1    15.5    -      -       -      +
     61D  GLY*     4.4     2.0    -      -       -      -
     91D  PHE*     4.9     1.1    -      -       +      -
     92D  ALA*     1.3    76.1    -      -       -      +
     94D  PHE*     1.3    67.7    +      -       -      +
     95D  SER*     3.7    11.9    +      -       -      -
    112D  GLY      4.1     1.0    -      -       -      +
    113D  PHE*     4.0     0.9    +      -       -      -
    114D  SER*     2.9    34.3    +      -       -      -
    306D  TYR*     4.8     3.8    +      -       -      -
    310D  THR*     3.5    34.6    +      -       +      +
    311D  GLU*     4.8     1.8    +      -       -      -
    313D  VAL*     4.2     4.9    -      -       +      -
    315D  PHE*     3.8    13.4    -      -       +      -
    501D  HEM      2.8    42.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59D  GLY*     2.9     3.6    -      -       -      -
     60D  PHE*     2.7    51.6    +      +       -      +
     61D  GLY*     5.7     0.2    -      -       -      -
     62D  ALA      5.9     0.4    -      -       -      -
     92D  ALA*     4.2    15.9    -      -       +      -
     93D  ARG*     1.3    77.1    -      -       -      +
     95D  SER*     1.3    61.2    +      -       -      +
    112D  GLY      3.4     8.3    -      -       -      +
    113D  PHE*     3.6    37.5    -      +       -      -
    114D  SER      5.1     0.2    -      -       -      -
    190D  TYR*     3.6    38.9    -      -       +      -
    193D  MET*     3.4    18.8    -      -       +      -
    246D  THR*     5.3     2.7    -      -       +      -
    258D  TRP*     3.6    26.9    -      +       -      -
    297D  MET*     4.5     1.6    -      -       +      -
    299D  LEU*     3.6    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56D  HIS*     2.7    30.2    +      -       -      +
     58D  ARG      2.9    20.6    -      -       -      -
     59D  GLY*     4.0     1.6    -      -       -      -
     93D  ARG*     3.7    17.8    +      -       -      -
     94D  PHE*     1.3    76.0    -      -       -      +
     96D  THR*     1.3    63.4    +      -       -      +
    111D  ARG*     3.1    13.3    -      -       -      +
    112D  GLY*     2.7    36.9    +      -       -      -
    190D  TYR*     3.9     7.1    -      -       -      -
    501D  HEM      4.2     4.6    +      -       -      +
----------------------------------------------------------
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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