Contacts of the strand formed by residues 54 - 57 (chain Z) in PDB entry 1YI2


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 ILE 54 (chain Z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   16540    U      5.6     2.2    -      -       -      +
     45A  ILE*     3.6    38.4    -      -       +      +
     46A  GLU*     3.9    17.9    -      -       -      -
     47A  HIS*     4.1    11.7    -      -       +      +
     54A  PRO*     4.0     7.2    -      -       +      -
     49Z  ARG*     3.5     6.1    -      -       -      +
     50Z  GLN*     2.7    50.9    +      -       +      -
     51Z  GLY*     3.3    14.1    +      -       -      +
     52Z  THR      3.2     6.4    -      -       -      +
     53Z  GLY*     1.3    78.6    -      -       -      +
     55Z  TRP*     1.3    67.9    +      -       -      +
     63Z  LYS*     4.0    21.5    -      -       +      -
     64Z  PHE      3.8     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 55 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33Z  MET*     4.0    16.6    -      -       +      -
     37Z  HIS*     4.1    11.0    -      +       -      -
     47Z  VAL*     3.8    11.2    -      -       +      -
     48Z  ASP      3.5     7.0    -      -       -      -
     49Z  ARG*     3.4    48.2    -      -       +      -
     50Z  GLN*     4.5     1.3    -      -       -      -
     53Z  GLY      3.5     3.0    +      -       -      -
     54Z  ILE*     1.3    80.3    -      -       -      +
     56Z  GLN*     1.3    61.4    +      -       -      +
     63Z  LYS*     3.2     6.2    -      -       -      +
     64Z  PHE*     2.7    63.4    +      +       +      +
     65Z  THR      4.2     0.4    -      -       -      -
     66Z  GLY*     3.5    26.8    -      -       -      -
     67Z  GLY      3.1    21.6    +      -       -      -
     68Z  SER      4.2     0.2    -      -       -      -
     69Z  TYR*     3.5    26.0    -      -       -      -
     70Z  LYS      3.2    23.1    +      -       -      -
     71Z  PRO*     3.4    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 56 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46Z  ARG      3.4     1.0    -      -       -      +
     47Z  VAL*     3.3     6.3    -      -       -      +
     48Z  ASP*     2.8    37.7    +      -       -      +
     50Z  GLN*     3.7    32.9    +      -       +      +
     55Z  TRP*     1.3    77.9    -      -       -      +
     57Z  CYS*     1.3    68.1    +      -       -      +
     58Z  SER*     3.6     1.4    +      -       -      -
     61Z  ASP*     3.1    27.9    +      -       -      +
     62Z  TYR      2.9    13.9    -      -       -      +
     63Z  LYS*     3.7    26.7    -      -       +      +
     64Z  PHE*     4.7     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 57 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39Z  CYS*     3.7    23.1    -      -       +      -
     42Z  CYS*     4.1     1.8    -      -       -      -
     46Z  ARG*     3.0    15.3    -      -       -      -
     47Z  VAL*     4.2     2.6    -      -       +      +
     56Z  GLN*     1.3    73.9    -      -       -      +
     58Z  SER*     1.3    57.1    +      -       -      +
     59Z  TYR*     3.0    31.0    -      -       -      -
     60Z  CYS*     3.2     9.9    -      -       -      -
     61Z  ASP*     2.8    31.2    +      -       -      +
     62Z  TYR*     2.8    12.8    +      -       +      +
     64Z  PHE*     5.1     0.4    -      -       -      -
   8703Z   CD      2.5    31.0    -      -       -      -
----------------------------------------------------------
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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