Contacts of the strand formed by residues 52 - 60 (chain K) 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 LYS 52 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1K  MET*     5.0    11.6    -      -       +      +
     34K  VAL*     4.1     0.9    -      -       -      +
     35K  HIS*     2.8    79.1    +      -       +      +
     50K  GLY      4.0     1.2    +      -       -      -
     51K  ASP*     1.3    71.4    -      -       -      +
     53K  ILE*     1.3    59.8    +      -       -      +
     70K  GLU*     3.9    32.2    +      -       +      +
     71K  ALA      3.4    14.8    -      -       -      +
     72K  VAL*     4.6     5.8    -      -       +      +
     98K  VAL*     5.4     4.3    -      -       +      -
    100K  GLU      5.6     2.8    +      -       -      -
    102K  GLU*     3.2    34.1    +      -       +      +
    121K  PHE*     4.5    14.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 53 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18K  ILE*     4.2    11.7    -      -       +      -
     31K  VAL*     3.7    24.9    -      -       +      -
     33K  SER      3.2    13.9    -      -       -      +
     34K  VAL*     4.4     2.7    -      -       +      -
     35K  HIS*     5.1     0.4    -      -       -      -
     47K  ALA*     3.8    28.5    -      -       +      -
     51K  ASP*     3.7     5.6    +      -       +      -
     52K  LYS*     1.3    77.3    -      -       -      +
     54K  THR*     1.3    60.7    +      -       -      +
     55K  VAL*     3.3    25.8    -      -       +      -
     70K  GLU*     3.7     5.7    -      -       -      +
     71K  ALA      3.0    37.9    +      -       -      +
     73K  VAL*     3.9    26.2    -      -       +      -
     95K  ALA*     4.7     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 54 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   25960    A      3.7    32.3    -      -       -      +
   25970    U      3.3    25.6    +      -       -      +
     31K  VAL*     3.9     1.0    -      -       -      -
     32K  ILE*     3.0    26.3    +      -       +      -
     33K  SER*     2.8    16.8    +      -       -      +
     35K  HIS*     5.2     3.1    +      -       -      +
     53K  ILE*     1.3    71.7    -      -       -      +
     55K  VAL*     1.3    73.6    +      -       -      +
     68K  VAL*     3.8    21.5    -      -       +      -
     69K  LEU      3.8     6.5    -      -       -      +
     70K  GLU*     4.5     9.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 55 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29K  LEU*     3.3    35.4    -      -       +      -
     30K  LYS      3.0    17.7    -      -       -      +
     31K  VAL*     4.4     1.3    -      -       -      +
     32K  ILE*     4.1     6.1    -      -       -      -
     53K  ILE*     3.3    34.8    -      -       +      +
     54K  THR*     1.3    84.0    -      -       -      +
     56K  SER*     1.3    84.1    +      -       -      +
     57K  VAL*     5.9     0.7    -      -       -      -
     68K  VAL*     3.1     7.6    -      -       -      +
     69K  LEU*     2.7    44.2    +      -       +      +
     71K  ALA*     4.2    11.9    -      -       +      -
     97K  ILE*     6.5     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 56 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      2.8    40.5    +      -       -      -
     29K  LEU*     3.7     0.3    -      -       -      -
     30K  LYS*     3.0    42.0    +      -       -      +
     32K  ILE*     3.5    17.5    -      -       -      +
     55K  VAL*     1.3    82.0    -      -       -      +
     57K  VAL*     1.3    61.5    +      -       -      +
     58K  THR*     3.5     1.0    +      -       -      -
     66K  ARG      5.1     0.7    -      -       -      -
     67K  GLN      3.1     9.4    -      -       -      -
     68K  VAL*     4.5     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 57 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      5.1     3.5    +      -       -      -
     26K  ALA*     4.0    19.1    -      -       +      -
     28K  GLU      3.9     4.3    -      -       -      +
     29K  LEU*     3.6    18.4    -      -       +      -
     55K  VAL      5.8     0.4    -      -       -      +
     56K  SER*     1.3    74.3    +      -       -      +
     58K  THR*     1.3    60.1    +      -       -      +
     59K  LYS      3.4    25.4    -      -       -      +
     64K  MET*     3.3    31.6    -      -       +      +
     65K  ARG*     3.7    10.9    -      -       -      +
     66K  ARG*     3.1    20.8    +      -       -      +
     67K  GLN      3.1    13.0    +      -       -      +
     69K  LEU*     4.2    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 58 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      5.0     1.6    +      -       -      -
     17K  LEU*     3.9     9.8    -      -       +      +
     28K  GLU*     2.9    40.3    +      -       -      +
     30K  LYS*     3.5    33.9    +      -       -      +
     56K  SER*     3.5     1.3    +      -       -      -
     57K  VAL*     1.3    74.4    -      -       -      +
     59K  LYS*     1.3    66.0    +      -       +      +
     65K  ARG*     4.0    12.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 59 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27K  ARG*     2.8    31.7    +      -       +      -
     28K  GLU*     3.3    49.8    +      -       +      +
     57K  VAL*     3.4    13.2    -      -       -      +
     58K  THR*     1.3    87.4    -      -       +      +
     60K  GLY*     1.3    60.2    +      -       -      +
     65K  ARG*     4.3     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 60 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25K  GLY      3.1    12.8    -      -       -      -
     26K  ALA*     4.4     0.7    -      -       -      -
     27K  ARG*     4.0    20.2    -      -       -      +
     57K  VAL*     5.0     1.3    -      -       -      -
     59K  LYS*     1.3    75.7    -      -       -      +
     61K  THR*     1.3    66.3    +      -       -      -
     62K  PRO*     3.6     1.9    -      -       -      +
     65K  ARG*     3.3    19.0    +      -       -      +
----------------------------------------------------------
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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