Contacts of the strand formed by residues 53 - 58 (chain C) 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 VAL 53 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24C  MET*     4.6    12.8    -      -       +      -
     43C  CYS*     5.2     1.8    -      -       -      -
     49C  VAL*     4.0     6.3    -      -       +      -
     51C  THR      3.6     3.4    +      -       -      -
     52C  ALA*     1.3    81.9    -      -       -      +
     54C  ALA*     1.3    65.7    +      -       -      +
     55C  TRP*     3.7    30.8    +      -       +      +
     68C  ILE      4.4     0.2    -      -       -      +
     69C  TYR*     3.7     1.7    +      -       -      -
     70C  SER      3.1     9.0    +      -       -      -
     71C  ALA*     3.0    25.0    +      -       -      +
     91C  PHE*     3.5    52.5    -      -       +      -
    108C  CYS*     4.5     8.5    -      -       +      -
    109C  GLN      3.5     6.1    -      -       -      +
    111C  HIS*     3.6     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 54 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  TYR*     4.9     4.9    -      -       +      -
     53C  VAL*     1.3    73.7    -      -       -      +
     55C  TRP*     1.3    63.3    +      -       -      +
     56C  TYR*     3.6    28.6    -      -       +      +
     66C  LEU*     4.2     3.6    -      -       +      -
     68C  ILE      3.2    13.0    -      -       -      +
     69C  TYR*     4.3     4.5    -      -       -      +
    107C  TYR      3.7     0.5    -      -       -      +
    108C  CYS*     3.3     6.4    -      -       -      +
    109C  GLN*     2.9    43.2    +      -       -      +
    111C  HIS*     4.4     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 55 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  GLN*     5.4     1.8    -      -       -      -
     41C  ILE*     3.5    33.2    -      -       +      -
     42C  THR      4.2     0.9    -      -       -      -
     43C  CYS*     3.5    26.0    -      -       +      -
     53C  VAL*     3.7    16.5    -      -       +      +
     54C  ALA*     1.3    73.8    -      -       -      +
     56C  TYR*     1.3    55.7    +      -       -      +
     66C  LEU*     3.9     0.9    -      -       -      +
     67C  LEU*     2.8    32.9    +      -       +      +
     68C  ILE*     2.9    49.5    +      -       +      +
     71C  ALA*     4.4     8.4    +      -       -      +
     84C  GLY*     5.3     0.7    -      -       -      -
     85C  SER      5.2     0.6    +      -       -      -
     91C  PHE*     3.9    17.2    -      -       +      +
     92C  THR      3.8     9.9    +      -       -      -
     93C  PHE*     3.4    49.9    -      +       +      +
    106C  TYR*     5.2     7.6    -      -       +      -
    107C  TYR      3.4    12.8    -      -       -      -
    108C  CYS*     3.7    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 56 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  LEU*     5.4     1.1    -      -       +      -
    124B  TYR*     3.6     6.4    -      -       -      +
    125B  PHE*     2.7    56.1    +      +       +      +
    128B  TRP*     3.8    15.7    -      +       -      -
     54C  ALA*     3.6    24.5    -      -       +      +
     55C  TRP*     1.3    77.0    -      -       -      +
     57C  GLN*     1.3    60.0    +      -       -      +
     58C  GLN      4.2     0.2    -      -       -      -
     64C  PRO*     4.6    11.9    -      -       +      -
     65C  LYS      3.3     5.4    -      -       -      +
     66C  LEU*     3.6    29.4    -      -       +      -
     67C  LEU*     4.7     1.3    -      -       -      -
    105C  VAL      3.9     0.3    -      -       -      +
    106C  TYR*     3.4     9.7    -      -       -      +
    107C  TYR*     2.9    44.9    +      -       +      +
    109C  GLN*     3.3    35.5    +      -       +      -
    118C  PHE*     4.4     9.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 57 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56C  TYR*     1.3    71.9    -      -       -      +
     58C  GLN*     1.3    60.2    +      -       -      +
     59C  LYS*     3.3    34.1    +      -       +      +
     63C  SER      4.1     1.0    -      -       -      +
     64C  PRO*     3.4     0.6    -      -       -      -
     65C  LYS*     2.6    56.5    +      -       +      +
     67C  LEU*     3.5    39.7    -      -       +      +
     82C  PHE*     5.0     6.3    -      -       -      -
    101C  GLU      4.4     6.1    +      -       -      -
    102C  ASP*     4.6     5.5    +      -       -      +
    104C  ALA*     3.6    23.2    -      -       +      +
    105C  VAL      3.8     2.9    -      -       -      -
    106C  TYR*     4.1    19.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 58 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  GLN*     2.7    47.1    +      -       -      +
     64B  LEU*     4.2     0.9    -      -       -      +
    114B  TYR*     3.6     7.5    +      -       -      -
     56C  TYR      4.2     0.2    -      -       -      -
     57C  GLN*     1.3    72.5    -      -       -      +
     59C  LYS*     1.3    64.4    +      -       -      +
     60C  PRO*     3.8     1.0    -      -       -      +
     61C  GLY      6.0     0.8    -      -       -      +
     62C  GLN      3.4    26.7    +      -       -      +
     63C  SER      4.4     0.9    -      -       -      -
     64C  PRO*     3.9    25.8    -      -       +      +
    104C  ALA*     3.8     2.9    -      -       -      -
    105C  VAL*     2.9    41.7    +      -       +      +
    107C  TYR*     3.2    22.8    -      -       +      -
----------------------------------------------------------
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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