Contacts of the strand formed by residues 280 - 285 (chain I) in PDB entry 5GJQ


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 SER 280 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245I  ALA*     3.9     6.5    -      -       -      +
    246I  THR*     2.2    39.0    -      -       -      -
    248I  LEU*     4.6     4.2    -      -       -      +
    274I  ALA*     3.0    37.8    +      -       -      +
    277I  HIS*     4.8     0.7    -      -       -      -
    278I  ALA      3.0     1.9    +      -       -      -
    279I  PRO*     1.3    71.3    -      -       -      +
    281I  ILE*     1.3    62.9    +      -       -      +
    282I  VAL      3.7     0.9    +      -       -      -
    324I  ASP      3.3     4.6    +      -       -      +
    325I  VAL*     3.9     2.4    -      -       -      +
    326I  LYS*     3.3    25.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 281 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201I  VAL*     5.0     7.9    -      -       +      -
    205I  LEU*     6.1     2.0    -      -       +      -
    239I  VAL*     4.4    17.3    -      -       +      -
    243I  THR*     3.9    22.2    -      -       -      +
    245I  ALA*     4.7     8.7    -      -       +      +
    246I  THR      2.7    10.2    +      -       -      +
    247I  PHE*     3.1    44.1    -      -       +      -
    248I  LEU*     2.7    29.3    +      -       -      +
    280I  SER*     1.3    73.8    -      -       -      +
    282I  VAL*     1.3    68.9    +      -       -      +
    283I  PHE*     3.5     0.6    +      -       +      +
    326I  LYS*     3.8    17.9    -      -       +      +
    328I  ILE*     3.8    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 282 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248I  LEU*     3.7    10.8    -      -       +      -
    270I  LEU*     4.2    22.9    -      -       +      +
    271I  PHE*     4.7    13.9    -      -       +      -
    274I  ALA*     3.4    24.9    -      -       +      -
    280I  SER*     3.7     1.2    +      -       -      +
    281I  ILE*     1.3    73.9    -      -       -      +
    283I  PHE*     1.3    61.6    +      -       -      +
    284I  ILE*     4.2    23.1    -      -       +      -
    325I  VAL*     3.4    27.8    -      -       +      -
    326I  LYS      2.9    15.7    +      -       -      +
    327I  VAL*     3.3     6.3    -      -       +      +
    328I  ILE      2.9    23.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 283 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224I  LEU*     5.4     0.7    -      -       +      -
    232I  LYS      4.7     5.4    -      -       -      -
    233I  THR*     5.0     4.0    -      -       +      -
    236I  ALA*     3.3    32.5    -      -       +      -
    247I  PHE*     4.0    19.5    -      +       +      -
    248I  LEU      2.9    15.3    +      -       -      +
    249I  ARG*     4.2    18.4    -      -       +      -
    250I  VAL*     3.0    29.6    +      -       -      +
    281I  ILE*     3.5     0.6    +      -       +      -
    282I  VAL*     1.3    74.5    -      -       -      +
    284I  ILE*     1.3    64.7    +      -       -      +
    285I  ASP*     3.3    31.2    -      -       +      -
    328I  ILE*     2.5    54.7    -      -       +      -
    330I  ALA*     3.6    23.6    -      -       +      -
    283J  PHE*     5.0     3.1    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 284 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250I  VAL*     3.3    14.4    -      -       +      +
    252I  GLY*     4.7     9.0    -      -       -      +
    255I  LEU*     6.3     1.8    -      -       +      -
    270I  LEU*     4.7     9.9    -      -       +      -
    271I  PHE*     5.1     3.6    -      -       +      -
    282I  VAL*     4.2    20.4    -      -       +      -
    283I  PHE*     1.3    74.2    -      -       -      +
    285I  ASP*     1.3    55.2    +      -       -      +
    286I  GLU      3.7     0.3    +      -       -      -
    287I  ILE*     2.7    43.7    -      -       +      +
    290I  ILE*     5.7     1.6    -      -       +      -
    312I  LEU*     3.7    36.1    -      -       +      -
    316I  LEU*     5.4     0.2    -      -       +      -
    327I  VAL*     5.0     5.2    -      -       +      -
    328I  ILE      2.4    24.0    +      -       -      +
    329I  MET*     3.0    15.6    -      -       -      +
    330I  ALA      2.7    26.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 285 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233I  THR*     3.3    28.4    +      -       -      +
    249I  ARG*     4.8    12.4    +      -       +      +
    250I  VAL      3.8     5.1    +      -       -      -
    251I  VAL*     3.9    27.2    -      -       +      +
    252I  GLY      3.9     4.0    +      -       -      -
    283I  PHE*     3.3    19.7    -      -       +      -
    284I  ILE*     1.3    71.2    -      -       -      +
    286I  GLU*     1.3    97.3    +      -       -      +
    330I  ALA*     2.4    39.2    -      -       -      +
    501I  ADP      5.1     3.2    +      -       -      -
    278J  ASN*     5.0     4.9    +      -       -      +
----------------------------------------------------------
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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