Contacts of the strand formed by residues 223 - 237 (chain A) in PDB entry 3SPJ


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 LEU 223 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  THR*     5.2     3.6    -      -       +      -
    194A  LEU*     3.5    41.1    -      -       +      -
    217A  ASN*     3.8    16.7    -      -       -      +
    221A  SER      4.0     0.2    +      -       -      -
    222A  HIS*     1.3    80.9    -      -       -      +
    224A  VAL*     1.3    66.2    +      -       -      +
    225A  GLU      3.6     1.7    +      -       -      -
    226A  ALA*     3.9    24.5    +      -       +      +
    262A  ILE      5.2     1.9    -      -       -      +
    263A  PHE*     6.1     0.7    -      -       -      -
    264A  LEU*     4.4    26.6    +      -       +      +
    299A  LEU*     4.4     7.6    -      -       +      -
    300A  GLU      5.1     2.7    -      -       -      +
    301A  GLY*     5.2     2.9    -      -       -      -
    302A  MET      3.6    15.9    -      -       -      +
    303A  VAL*     4.2    17.9    -      -       +      +
    310A  THR*     5.4     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  HIS*     5.3     2.9    -      -       +      -
    223A  LEU*     1.3    70.9    -      -       -      +
    225A  GLU*     1.3    89.1    +      -       +      +
    226A  ALA      3.5     0.2    +      -       -      -
    301A  GLY*     3.7     0.2    -      -       -      -
    302A  MET*     3.0    43.1    +      -       +      +
    303A  VAL      5.5     0.2    -      -       -      -
    304A  GLU*     4.4    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  LEU      3.6     1.6    +      -       -      -
    224A  VAL*     1.3    89.0    -      -       +      +
    226A  ALA*     1.3    60.3    +      -       -      +
    227A  HIS*     3.9    11.2    -      -       +      -
    301A  GLY*     3.3    11.4    -      -       -      -
    302A  MET*     4.9    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  LEU*     3.9    31.3    +      -       +      +
    225A  GLU*     1.3    75.7    -      -       -      +
    227A  HIS*     1.3    63.3    +      -       -      +
    261A  ARG*     3.7     5.2    -      -       -      +
    262A  ILE*     3.1    48.0    +      -       +      +
    264A  LEU*     5.6     2.9    -      -       +      +
    299A  LEU*     4.4     5.8    -      -       +      -
    300A  GLU      3.3    12.8    -      -       -      +
    301A  GLY*     4.0     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  GLU      3.9    15.9    -      -       -      -
    226A  ALA*     1.3    74.6    -      -       -      +
    228A  VAL*     1.3    65.3    +      -       -      +
    229A  ARG*     4.3    13.5    -      -       -      +
    260A  ASP*     3.2    27.2    +      -       -      +
    261A  ARG*     4.5     6.7    -      -       +      -
    262A  ILE*     4.8     0.9    -      -       -      +
    299A  LEU*     3.4     3.6    -      -       -      +
    300A  GLU*     2.9    74.0    +      -       +      +
    301A  GLY*     4.8     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  PHE*     6.2     0.2    -      -       +      -
    213A  TRP*     5.5     2.5    -      -       +      +
    215A  VAL*     5.4     0.4    -      -       +      -
    227A  HIS*     1.3    72.0    -      -       -      +
    229A  ARG*     1.3    72.0    +      -       -      +
    253A  VAL*     3.4    33.8    -      -       +      +
    260A  ASP*     3.1    28.2    +      -       -      +
    262A  ILE*     3.8    19.7    -      -       +      -
    270A  ILE*     4.2    31.2    -      -       +      -
    298A  ILE      3.4     9.2    -      -       -      +
    299A  LEU*     3.4    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 229 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  TRP*     4.8     2.3    -      -       -      -
    227A  HIS*     4.3    11.4    -      -       -      +
    228A  VAL*     1.3    82.9    -      -       -      +
    230A  ALA*     1.3    64.9    +      -       -      +
    231A  GLN*     3.8    24.4    +      -       -      +
    250A  ASP*     5.2     9.1    +      -       -      +
    253A  VAL*     4.3     8.3    -      -       -      -
    260A  ASP*     5.6     0.4    -      -       -      +
    297A  VAL*     3.7     2.4    -      -       -      +
    298A  ILE*     2.9    53.6    +      -       +      +
    300A  GLU*     3.3    33.7    +      -       -      +
    311A  GLN*     5.8     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213A  TRP*     4.0    27.8    -      -       +      -
    229A  ARG*     1.3    78.7    -      -       -      +
    231A  GLN*     1.3    65.0    +      -       -      +
    250A  ASP*     3.3     6.3    +      -       -      +
    251A  ILE*     2.7    53.4    +      -       +      +
    253A  VAL*     4.5     2.4    -      -       +      +
    295A  ILE*     4.8     1.1    -      -       +      -
    296A  VAL      3.3    12.1    -      -       -      +
    297A  VAL*     4.5     2.5    -      -       +      +
    298A  ILE*     5.4     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  ARG*     3.8    22.2    +      -       +      +
    230A  ALA*     1.3    81.0    -      -       -      +
    232A  LEU*     1.3    65.1    +      -       -      +
    233A  ILE*     3.7    11.0    +      -       +      +
    248A  GLN*     3.0    40.2    +      -       -      +
    249A  ILE      3.0    13.9    -      -       -      +
    250A  ASP*     4.2    10.8    +      -       -      +
    251A  ILE*     3.5     6.3    -      -       -      -
    295A  ILE*     3.4     2.6    -      -       -      +
    296A  VAL*     2.9    44.3    +      -       +      +
    298A  ILE*     5.1     9.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  GLN*     1.3    71.9    -      -       -      +
    233A  ILE*     1.3    70.1    +      -       -      +
    234A  LYS*     3.8    20.9    -      -       +      +
    247A  ASP      3.2     3.1    -      -       -      +
    248A  GLN*     3.7     0.9    -      -       -      -
    249A  ILE*     2.8    45.4    +      -       +      +
    251A  ILE*     3.3    18.4    -      -       +      +
    279A  PRO*     3.8    30.7    -      -       +      +
    280A  LEU*     3.9    22.4    -      -       +      -
    283A  ILE*     5.9     0.7    -      -       +      -
    293A  PHE*     3.5    42.0    -      -       +      -
    294A  GLU      3.7     2.7    -      -       -      +
    295A  ILE*     4.4     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  GLN*     4.4     7.6    -      -       +      +
    232A  LEU*     1.3    78.3    -      -       -      +
    234A  LYS*     1.3    69.4    +      -       -      +
    246A  LEU*     3.3    35.4    -      -       +      -
    247A  ASP      3.2     7.6    -      -       -      +
    248A  GLN*     4.2    28.0    -      -       +      +
    292A  ASP      4.9     0.3    -      -       -      +
    293A  PHE*     3.8     0.5    -      -       -      -
    294A  GLU*     2.7    51.5    +      -       -      +
    296A  VAL*     3.4    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  LEU*     3.8    21.7    -      -       +      +
    233A  ILE*     1.3    81.4    -      -       -      +
    235A  PRO*     1.3    81.9    -      -       +      +
    236A  ARG*     4.5    13.9    -      -       +      +
    246A  LEU*     3.7     7.0    -      -       -      -
    247A  ASP*     2.6    39.3    +      -       -      +
    249A  ILE*     4.8    14.9    -      -       +      +
    279A  PRO*     5.9     0.8    +      -       -      +
    292A  ASP*     5.0     1.8    -      -       +      +
    293A  PHE*     4.2    17.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  LYS*     1.3   100.2    -      -       +      +
    236A  ARG*     1.3    64.3    +      -       -      +
    243A  TYR*     3.5    21.8    -      -       +      +
    244A  ILE      3.4     2.5    -      -       -      +
    245A  PRO      2.9    23.5    -      -       -      +
    246A  LEU*     3.9     9.6    -      -       +      -
    292A  ASP*     5.3    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  LYS*     3.9    13.4    +      -       -      +
    235A  PRO*     1.3    77.4    -      -       -      +
    237A  ILE*     1.3    66.3    +      -       -      +
    238A  THR*     3.8    28.3    -      -       -      +
    239A  GLU      5.0     0.8    -      -       -      +
    242A  GLU      3.8     0.5    -      -       -      +
    243A  TYR*     3.8     4.9    -      -       -      -
    244A  ILE*     2.9    54.3    +      -       +      +
    247A  ASP*     3.0    34.0    +      -       +      +
    249A  ILE*     4.9     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  ARG*     1.3    85.4    +      -       -      +
    238A  THR*     1.3    75.4    +      -       -      +
    239A  GLU      3.9     0.2    +      -       -      -
    241A  GLY*     3.7    17.3    -      -       -      -
    242A  GLU      3.2     9.2    -      -       -      +
    243A  TYR*     3.7    24.5    -      -       +      -
----------------------------------------------------------
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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