Contacts of the strand formed by residues 122 - 129 (chain A) 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 GLY 122 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  THR*     2.7    44.5    +      -       -      +
    120A  GLU      3.5     1.2    -      -       -      -
    121A  GLU*     1.3    79.4    -      -       -      +
    123A  ASN*     1.3    66.8    +      -       -      -
    321A  VAL*     3.4     3.0    -      -       -      +
    359A  PRO*     4.9     0.4    -      -       -      -
    361A  ALA*     3.8     4.1    -      -       -      +
     12C  GLN      3.1    14.6    -      -       -      -
     13C  GLY*     3.3    13.3    +      -       -      -
     14C  VAL*     4.0     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  LYS*     3.8    23.8    -      -       +      +
    117A  PHE      3.3     7.4    -      -       -      +
    118A  TYR*     3.6    22.0    -      -       -      -
    122A  GLY*     1.3    73.3    -      -       -      -
    124A  TRP*     1.3    60.0    -      -       -      +
    125A  ASP*     4.7     1.8    -      -       -      +
    319A  VAL*     3.3    22.2    -      -       +      +
    320A  LEU      4.2     3.3    -      -       -      +
    321A  VAL*     3.9     7.3    -      -       -      +
    352A  GLN*     4.4     0.4    -      -       -      +
    357A  ASN      3.1    27.3    +      -       -      -
    359A  PRO*     3.2    28.3    -      -       -      +
    360A  PHE      4.0     0.5    +      -       -      -
     12C  GLN*     2.9    34.0    +      -       -      +
     14C  VAL*     4.6     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  PHE*     3.6    34.3    -      +       +      -
     81A  LEU*     5.6     0.7    -      -       +      -
    117A  PHE*     2.9    75.2    +      +       +      -
    119A  THR*     5.2     0.4    -      -       -      +
    122A  GLY      3.8     1.0    +      -       -      -
    123A  ASN*     1.3    72.3    -      -       -      +
    125A  ASP*     1.3    83.6    +      -       -      +
    126A  PHE*     4.2    15.7    -      +       +      +
    201A  PHE*     6.1     0.4    -      -       -      -
    203A  TRP*     5.2     2.7    -      +       -      -
    215A  LEU*     3.7    33.7    -      -       +      -
    217A  TRP*     5.9     0.2    -      +       -      -
    260A  LEU*     4.8    12.6    -      -       +      -
    319A  VAL      3.3    12.6    -      -       -      -
    320A  LEU*     3.4    23.3    -      -       +      +
    321A  VAL*     4.2    18.6    -      -       +      +
    324A  MET*     3.8    24.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  VAL      3.5     3.6    -      -       -      +
    116A  LYS*     2.7    45.6    +      -       -      +
    123A  ASN*     4.7     0.5    -      -       -      +
    124A  TRP*     1.3    88.1    +      -       -      +
    126A  PHE*     1.3    58.5    +      -       -      +
    127A  VAL*     3.9     8.5    +      -       +      -
    314A  GLY      4.0     0.3    -      -       -      +
    315A  PHE*     3.3    11.4    -      -       +      -
    316A  ASN      2.9    46.7    +      -       -      +
    317A  PRO*     3.9     9.2    -      -       -      +
    319A  VAL*     2.9    24.2    +      -       -      +
     12C  GLN*     5.4     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PHE*     3.2    30.7    -      +       +      -
    114A  SER*     3.2     3.3    -      -       -      -
    115A  VAL*     2.7    46.2    +      -       +      +
    117A  PHE*     4.2    14.6    -      -       +      -
    124A  TRP*     3.8    14.4    +      +       +      +
    125A  ASP*     1.3    72.5    -      -       -      +
    127A  VAL*     1.3    61.6    +      -       -      +
    128A  GLY*     3.5     9.4    -      -       -      -
    196A  SER*     3.5    25.4    -      -       -      -
    197A  SER*     3.7    13.7    -      -       -      -
    201A  PHE*     6.4     0.9    -      +       -      -
    215A  LEU*     3.7    41.3    -      -       +      -
    217A  TRP*     3.3    41.7    -      +       +      +
----------------------------------------------------------
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Residues in contact with VAL 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PHE      3.9     2.5    -      -       -      -
    114A  SER*     3.7    14.1    -      -       -      +
    125A  ASP*     3.9     6.1    +      -       +      -
    126A  PHE*     1.3    82.3    -      -       -      +
    128A  GLY*     1.3    57.2    +      -       -      +
    197A  SER*     4.7     4.0    -      -       -      +
    201A  PHE*     6.0     0.7    -      -       -      -
    315A  PHE*     3.3    30.7    -      -       +      -
    316A  ASN      3.8    11.4    -      -       -      +
    317A  PRO*     3.9    18.4    -      -       +      +
    335A  ARG*     2.8    45.5    +      -       -      +
    339A  TYR*     3.8    14.6    -      -       +      -
    501A  HEM      3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PHE*     2.8    38.9    +      -       -      -
    126A  PHE*     3.5     8.5    -      -       -      -
    127A  VAL*     1.3    75.1    -      -       -      +
    129A  ASN*     1.3    56.7    +      -       -      -
    196A  SER      3.2    16.8    -      -       -      -
    197A  SER*     4.7     2.2    -      -       -      -
    501A  HEM      3.1    22.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  HIS*     3.5    15.1    +      -       -      -
     97A  VAL*     5.2     0.6    -      -       -      +
    110A  PRO*     3.8    23.3    -      -       +      +
    111A  ARG      3.2     5.7    -      -       -      +
    112A  GLY*     3.3    16.6    +      -       -      -
    113A  PHE*     4.3     1.8    -      -       -      +
    128A  GLY*     1.3    78.1    -      -       -      +
    130A  ASN*     1.3    63.6    +      -       -      +
    131A  LEU*     3.9    15.5    -      -       +      +
    133A  VAL      5.8     0.4    -      -       -      +
    134A  PHE*     3.7    22.0    -      -       -      -
    176A  MET*     5.2     1.0    -      -       -      +
    195A  GLY*     4.4     2.7    -      -       -      -
    196A  SER*     2.8    32.1    +      -       -      -
    198A  VAL*     4.6     1.5    -      -       +      +
    501A  HEM      3.5    31.2    -      -       +      +
----------------------------------------------------------
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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