Contacts of the strand formed by residues 145 - 149 (chain B) in PDB entry 5I75


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 145 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  PRO      3.7     4.4    +      -       -      -
    144B  PRO*     1.3    72.3    -      -       -      +
    146B  VAL*     1.3    62.2    +      -       -      +
    147B  TYR*     3.7    32.9    +      -       -      -
    166B  LEU      3.6     1.0    -      -       -      +
    167B  VAL*     3.5     3.8    -      -       -      -
    168B  LYS*     2.9    54.0    +      -       -      +
    169B  GLY      4.8     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  PRO*     3.7    11.1    +      -       +      +
    145B  SER*     1.3    72.8    -      -       -      +
    147B  TYR*     1.3    74.8    +      -       -      +
    148B  PRO*     4.1     0.2    -      -       -      +
    165B  CYS*     5.3     1.1    -      -       +      -
    166B  LEU      3.5     7.0    -      -       -      +
    167B  VAL*     4.8     1.3    -      -       +      -
    220B  CYS*     4.9     7.0    -      -       -      -
    222B  VAL*     3.6    48.9    -      -       +      -
    231B  VAL*     3.8    31.6    -      -       +      +
    233B  LYS*     3.8    27.4    -      -       +      +
    143C  GLU*     3.7    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  SER*     3.8    31.4    +      -       -      -
    146B  VAL*     1.3    89.4    -      -       -      +
    148B  PRO*     1.3    69.3    -      -       +      +
    149B  LEU*     5.7     0.4    -      -       +      -
    165B  CYS*     5.1     0.4    -      -       -      -
    166B  LEU*     2.9    50.5    +      -       +      +
    168B  LYS*     4.8    15.9    +      -       +      +
    141C  SER*     4.1     2.7    -      -       -      +
    143C  GLU*     3.7    19.3    -      -       +      -
    144C  GLN*     3.5    55.9    -      -       +      +
    147C  SER*     2.9    28.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 148 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  VAL      4.1     1.1    -      -       -      +
    147B  TYR*     1.3    86.2    -      -       -      +
    149B  LEU*     1.3    65.2    +      -       -      +
    150B  ALA*     3.8     3.4    -      -       +      +
    165B  CYS*     4.5    11.7    -      -       -      -
    233B  LYS*     4.8    11.6    -      -       +      -
    234B  LYS      4.8    12.6    -      -       -      +
    235B  LEU*     4.6    12.1    -      -       +      -
    236B  GLU      6.0     0.7    -      -       -      +
    141C  SER*     2.9    45.0    +      -       -      +
    143C  GLU*     3.2    38.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 149 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  TYR*     3.7     1.1    +      -       +      +
    148B  PRO*     1.3    81.0    -      -       -      +
    150B  ALA*     1.3    61.7    +      -       -      +
    151B  PRO*     3.9     2.9    -      -       -      +
    164B  GLY*     2.9    35.9    +      -       -      +
    165B  CYS      4.1    10.5    -      -       -      +
    166B  LEU*     3.7    39.3    -      -       +      +
    203B  SER*     5.0     1.1    -      -       -      -
    235B  LEU*     3.4     6.0    -      -       -      +
    138C  PHE*     4.1    18.6    -      -       +      -
    139C  PRO      4.7    13.0    -      -       -      +
    140C  PRO*     5.4     0.4    -      -       +      -
    141C  SER      5.2     2.7    -      -       -      +
    144C  GLN*     5.3     3.8    -      -       -      +
    151C  SER      5.1     4.0    -      -       -      +
    153C  VAL*     3.9    31.4    -      -       +      -
    155C  PHE*     4.4    20.6    -      -       +      -
----------------------------------------------------------
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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