Contacts of the strand formed by residues 305 - 310 (chain K) 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 VAL 305 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200K  ARG*     3.5    22.2    +      -       -      +
    254K  ALA*     3.8    31.0    -      -       +      +
    255K  LYS*     4.7     0.2    -      -       -      -
    258K  ALA      4.7     1.3    -      -       -      +
    260K  ALA      3.5     9.4    -      -       -      +
    262K  ILE*     3.7    32.8    -      -       +      -
    299K  PHE*     3.8    21.6    -      -       +      -
    303K  VAL*     2.5    40.5    +      -       +      +
    304K  ASN*     1.3    76.8    -      -       -      +
    306K  LYS*     1.3    67.3    +      -       -      +
    307K  VAL*     4.5     3.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 306 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180K  ALA      4.2    12.9    +      -       -      +
    181K  VAL*     3.8    27.4    -      -       +      -
    184K  PRO*     4.4     6.5    +      -       -      +
    185K  LEU*     3.7    46.9    -      -       +      +
    188K  PHE*     5.2     7.0    -      -       -      -
    198K  PRO*     3.8    24.4    -      -       -      +
    199K  PRO*     3.3    30.0    +      -       +      +
    200K  ARG*     3.4     3.5    -      -       -      +
    201K  GLY*     5.8     0.4    -      -       -      -
    260K  ALA      3.2     7.8    +      -       -      +
    261K  ILE*     3.8     6.4    -      -       +      -
    262K  ILE*     3.0    29.3    +      -       -      +
    304K  ASN*     5.3     2.8    -      -       -      +
    305K  VAL*     1.3    79.7    -      -       -      +
    307K  VAL*     1.3    62.2    +      -       -      +
    308K  ILE*     5.5     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 307 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181K  VAL*     5.7     0.5    -      -       -      +
    200K  ARG*     2.8    18.0    +      -       +      +
    201K  GLY*     3.7     7.4    -      -       -      -
    202K  VAL*     2.4    36.3    +      -       -      +
    251K  PHE*     5.4     4.0    -      -       +      -
    262K  ILE*     3.3    22.0    -      -       +      +
    264K  ILE*     4.4    11.4    -      -       +      -
    292K  LEU*     5.6     1.3    -      -       +      -
    296K  MET*     3.7    28.0    -      -       +      -
    299K  PHE*     5.6     4.9    -      -       +      -
    305K  VAL*     4.5     4.9    -      -       +      +
    306K  LYS*     1.3    77.6    -      -       -      +
    308K  ILE*     1.3    63.1    +      -       -      +
    309K  MET*     4.1    30.1    -      -       +      -
    327K  LEU*     4.7     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 308 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177K  VAL*     4.7    13.7    -      -       +      -
    181K  VAL*     4.4    20.2    -      -       +      -
    202K  VAL*     3.5    16.2    -      -       +      -
    204K  MET*     3.4    28.0    -      -       +      -
    216K  ALA*     6.0     0.7    -      -       +      -
    219K  VAL*     5.0     4.7    -      -       +      -
    227K  PHE*     4.4     7.9    -      -       +      -
    261K  ILE*     3.5    29.2    -      -       +      -
    262K  ILE      2.8    11.4    +      -       -      +
    263K  PHE*     3.1    26.7    -      -       +      -
    264K  ILE      2.6    34.0    +      -       -      +
    306K  LYS      5.4     0.2    -      -       -      -
    307K  VAL*     1.3    78.9    -      -       -      +
    309K  MET*     1.3    57.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 309 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202K  VAL      2.9     7.4    +      -       -      +
    203K  LEU*     2.8     9.9    -      -       +      +
    204K  MET*     2.6    33.9    +      -       -      +
    264K  ILE*     3.2    20.0    -      -       +      -
    267K  ILE*     2.9    46.0    -      -       +      -
    292K  LEU*     3.7    32.1    -      -       +      -
    296K  MET*     5.1     2.2    -      -       -      -
    307K  VAL*     4.1    10.8    -      -       +      -
    308K  ILE*     1.3    79.7    -      -       -      +
    310K  ALA*     1.3    56.9    +      -       -      +
    321K  LEU*     3.9    12.8    -      -       +      -
    327K  LEU*     3.0    39.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 310 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204K  MET*     3.0    14.6    -      -       +      +
    212K  LYS*     4.6    17.5    -      -       +      +
    213K  THR*     5.4     1.6    -      -       -      +
    263K  PHE*     4.3    15.5    -      -       +      -
    264K  ILE      3.0     6.9    +      -       -      -
    265K  ASP*     3.9    22.0    -      -       -      +
    266K  GLU*     2.5    31.5    +      -       -      +
    308K  ILE*     5.6     0.2    -      -       +      -
    309K  MET*     1.3    74.2    -      -       -      +
    311K  THR*     1.3    67.1    +      -       -      +
    501K  ADP      6.0     0.4    -      -       -      +
----------------------------------------------------------
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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