Contacts of the strand formed by residues 345 - 349 (chain K) in PDB entry 7JOA


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 PHE 345 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223K  ILE*     4.7     3.8    -      -       +      -
    225K  LEU*     4.2    27.1    -      -       +      -
    313K  GLU*     3.7     1.0    -      -       -      +
    314K  SER*     3.0    65.0    +      -       -      +
    316K  GLY*     4.2    11.2    -      -       -      -
    317K  SER      3.5    21.8    -      -       -      -
    318K  TRP*     4.1    24.9    -      +       +      +
    319K  PRO*     4.6     9.6    -      -       +      -
    344K  PRO*     1.3    75.2    -      -       -      +
    346K  TYR*     1.3    79.9    +      -       -      +
    347K  LEU*     4.3    10.5    -      -       +      -
    365K  LEU*     4.2    11.2    -      -       +      -
    366K  SER      4.5     0.2    -      -       -      +
    367K  PHE*     4.3    19.3    -      -       +      -
    369K  HIS*     4.2     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 346 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195K  LEU*     4.0    34.0    -      -       +      +
    215K  MET*     5.0     0.9    -      -       -      -
    217K  LYS*     4.1    24.5    -      -       +      +
    311K  ALA*     4.8    10.3    -      -       +      -
    312K  LEU      3.3    15.5    -      -       -      +
    313K  GLU*     3.3    34.0    +      -       +      +
    344K  PRO*     4.4     7.6    -      -       +      +
    345K  PHE*     1.3    81.0    -      -       -      +
    347K  LEU*     1.3    63.8    +      -       -      +
    365K  LEU*     3.4     5.5    -      -       -      +
    366K  SER*     2.8    51.6    +      -       -      +
    368K  SER*     5.1     0.4    -      -       -      -
    369K  HIS*     3.3    38.0    -      +       +      +
----------------------------------------------------------
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Residues in contact with LEU 347 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223K  ILE*     3.7    30.5    -      -       +      -
    225K  LEU*     4.2    15.3    -      -       +      -
    235K  TYR*     5.2     3.6    -      -       +      -
    237K  VAL*     4.4    14.1    -      -       +      -
    311K  ALA*     3.4     4.7    -      -       -      -
    312K  LEU*     2.9    56.8    +      -       +      +
    314K  SER*     4.9     3.4    -      -       -      -
    345K  PHE*     4.3    10.1    -      -       +      -
    346K  TYR*     1.3    74.8    -      -       -      +
    348K  VAL*     1.3    61.1    +      -       -      +
    363K  TRP*     4.0    26.9    -      -       +      -
    364K  ARG      3.3     7.6    -      -       -      +
    365K  LEU*     3.6    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 348 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215K  MET*     3.8    20.2    -      -       +      -
    309K  ILE*     4.6    11.7    -      -       +      -
    311K  ALA*     3.8    21.5    -      -       +      -
    347K  LEU*     1.3    76.5    -      -       -      +
    349K  PRO*     1.3    72.4    -      -       +      +
    350K  LYS*     4.2     3.8    -      -       +      +
    363K  TRP*     3.5     3.3    -      -       -      -
    364K  ARG*     2.9    48.4    +      -       +      +
    365K  LEU      4.5     7.2    -      -       -      +
    366K  SER*     4.3    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 349 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259K  ALA*     4.4    11.4    -      -       +      -
    263K  LEU*     4.2    35.0    -      -       +      -
    292K  PRO*     4.1    21.7    -      -       +      +
    309K  ILE*     4.7     7.4    -      -       +      +
    310K  LEU*     3.2    23.8    -      -       +      +
    348K  VAL*     1.3    87.0    -      -       +      +
    350K  LYS*     1.3    61.6    +      -       -      +
    362K  THR      3.8     7.9    -      -       -      +
    363K  TRP*     3.5    24.9    -      -       +      -
----------------------------------------------------------
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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