Contacts of the strand formed by residues 110 - 122 (chain R) in PDB entry 1YIT


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 THR 110 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37R  GLY*     3.9    20.8    +      -       -      +
     38R  LYS      3.8     4.0    -      -       -      -
     39R  THR*     4.5     6.7    +      -       -      +
    108R  ALA      3.7     0.4    +      -       -      -
    109R  MET*     1.3    72.1    -      -       -      +
    111R  ILE*     1.3    72.2    +      -       -      +
    112R  LYS*     2.8    14.3    +      -       +      +
    147R  LEU*     3.4     2.7    -      -       -      -
    148R  GLU*     2.9    43.8    +      -       -      +
    150R  PRO*     4.3    16.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 111 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35R  ILE*     3.6    27.8    -      -       +      +
     36R  LYS*     4.0     5.6    -      -       -      +
     37R  GLY*     3.1    25.3    +      -       -      +
     38R  LYS      3.0    18.1    +      -       -      +
     40R  ALA*     4.2     4.9    -      -       -      +
     43R  ALA*     3.7    26.9    -      -       +      -
     92R  LEU*     4.1    11.4    -      -       +      -
    110R  THR*     1.3    69.1    -      -       -      +
    112R  LYS*     1.3    61.3    +      -       -      +
    113R  HIS      4.0     1.8    -      -       -      +
    114R  VAL*     3.8    22.7    -      -       +      -
    145R  LEU*     3.3    24.7    -      -       +      -
    146R  ILE      3.8     4.3    -      -       -      -
    147R  LEU*     4.0    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 112 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6R  VAL*     4.8    12.7    -      -       +      +
      7R  GLU      4.0    18.8    +      -       -      +
      8R  ALA*     5.2     3.8    -      -       +      +
      9R  ASP      5.6     1.6    -      -       -      +
     13R  THR*     5.2     2.2    +      -       -      +
     36R  LYS*     3.7    19.0    +      -       -      -
    110R  THR*     2.8    12.3    +      -       +      +
    111R  ILE*     1.3    72.3    -      -       -      +
    113R  HIS*     1.3    63.2    +      -       +      +
    146R  ILE*     2.8    23.8    +      -       +      +
    148R  GLU*     3.6    49.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 113 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    5250    G      3.5    26.0    +      -       -      +
      5R  SER*     3.4     3.0    +      -       -      -
      6R  VAL*     3.3    34.0    -      -       +      +
     36R  LYS*     4.6    11.2    -      -       -      +
    111R  ILE*     3.3     0.6    -      -       -      -
    112R  LYS*     1.3    87.0    -      -       +      +
    114R  VAL*     1.3    71.3    +      -       -      +
    115R  ALA*     3.7    10.1    -      -       +      +
    144R  GLU*     3.0    42.3    +      -       +      +
    145R  LEU*     3.0     7.8    -      -       -      +
    146R  ILE*     2.6    58.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 114 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    5250    G      4.8     6.2    -      -       -      +
     32R  ALA*     3.6    24.8    -      -       +      +
     35R  ILE*     4.2     8.3    -      -       +      -
     36R  LYS*     3.7    35.8    -      -       +      +
     88R  PHE*     4.0    27.8    -      -       +      -
     91R  LEU*     4.9     0.9    -      -       +      -
    111R  ILE*     3.8     9.9    -      -       +      -
    113R  HIS*     1.3    81.8    -      -       -      +
    115R  ALA*     1.3    63.8    +      -       -      +
    143R  VAL*     4.5     4.5    -      -       +      -
    144R  GLU      3.1    13.2    -      -       -      +
    145R  LEU*     3.7    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 115 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    5240    A      3.4    16.6    -      -       -      +
    5250    G      3.7    18.2    -      -       -      +
     32R  ALA*     4.4     4.9    -      -       -      -
    113R  HIS*     3.7    15.9    -      -       -      +
    114R  VAL*     1.3    76.9    -      -       -      +
    116R  ALA*     1.3    58.8    +      -       -      +
    117R  HIS*     3.4    18.8    +      -       +      +
    143R  VAL*     3.3     5.9    -      -       -      -
    144R  GLU*     3.0    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 116 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    5240    A      2.7    32.4    +      -       -      +
     25R  PHE*     3.5    14.4    -      -       +      -
     28R  SER*     3.6    39.5    -      -       -      +
     29R  LYS*     4.3     4.6    -      -       +      +
     32R  ALA*     4.6     3.6    -      -       +      +
     88R  PHE*     4.9     3.1    -      -       +      -
    115R  ALA*     1.3    71.4    -      -       -      +
    117R  HIS*     1.3    64.9    +      -       -      +
    141R  VAL*     4.2     3.4    -      -       +      -
    142R  ASP      3.4     8.7    -      -       -      +
    143R  VAL*     4.1     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 117 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     200    G      3.3    35.7    +      -       -      +
     210    G      4.5     7.0    -      -       -      +
    5230    C      5.6     1.3    -      -       -      +
    5240    A      3.5    28.1    +      -       -      -
      2R  ILE*     3.8    37.1    -      -       +      +
      5R  SER*     4.7     1.0    +      -       -      -
     25R  PHE*     3.6     6.5    -      -       -      -
    115R  ALA*     3.4    26.1    +      -       +      +
    116R  ALA*     1.3    74.3    -      -       -      +
    118R  LYS*     1.3    63.8    +      -       -      +
    119R  VAL*     3.1     2.8    +      -       -      +
    141R  VAL*     3.7     0.5    -      -       -      -
    142R  ASP      2.8    34.6    +      -       -      +
    144R  GLU*     3.0    32.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 118 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     210    G      4.0    16.6    +      -       -      +
     220    U      4.2     8.7    +      -       -      +
    5230    C      5.0     5.5    +      -       -      +
   13660    C      4.8    15.5    +      -       -      +
     25R  PHE*     3.3    35.9    -      -       +      -
    117R  HIS*     1.3    67.5    -      -       -      +
    119R  VAL*     1.3    61.8    +      -       -      +
    120R  GLY*     4.0    11.4    -      -       -      +
    121R  GLU*     3.7    37.3    +      -       -      +
    139R  PRO*     4.0    16.1    -      -       -      +
    140R  GLN      3.7     8.3    -      -       -      +
   8806R   CL      3.3    29.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     210    G      4.4     7.4    -      -       -      +
     220    U      3.2    45.6    -      -       -      +
     230    G      4.9     1.2    +      -       -      -
      1R  GLY*     4.0    14.6    -      -       -      +
      2R  ILE*     4.6     2.5    -      -       +      -
     20R  GLU*     4.9    15.5    -      -       +      +
    117R  HIS      3.3     5.8    -      -       -      +
    118R  LYS*     1.3    73.0    -      -       -      +
    120R  GLY*     1.3    56.6    +      -       -      +
    140R  GLN*     2.9    14.6    +      -       +      +
    141R  VAL      4.3     0.2    -      -       -      -
    142R  ASP*     3.1    49.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 120 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     220    U      5.0     6.3    -      -       -      -
     230    G      5.4     2.7    -      -       -      -
    118R  LYS*     3.4    10.2    +      -       -      +
    119R  VAL*     1.3    80.3    -      -       -      +
    121R  GLU*     1.3    64.5    +      -       -      +
    139R  PRO*     3.8     1.0    -      -       -      +
    140R  GLN*     2.8    39.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 121 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   20540    A      4.8     5.5    +      -       -      -
    118R  LYS*     3.7    27.9    +      -       -      -
    120R  GLY*     1.3    78.8    -      -       -      +
    122R  GLN*     1.3    61.8    +      -       -      +
    123R  GLN*     3.4    18.6    +      -       +      +
    137R  ASN*     3.2    40.1    +      -       +      +
    138R  SER      3.2    11.4    -      -       -      +
    139R  PRO*     4.6     2.3    -      -       +      +
    140R  GLN*     3.5    10.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 122 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   14270    A      4.3     0.7    -      -       -      +
   14280    C      2.8    37.6    +      -       -      +
   14290    U      3.8    23.8    +      -       -      +
     22R  GLN*     2.8    30.2    +      -       -      -
    121R  GLU*     1.3    71.0    -      -       -      +
    123R  GLN*     1.3    67.7    +      -       -      +
    136R  TRP      4.6     0.3    -      -       -      +
    137R  ASN*     3.4     1.4    -      -       -      -
    138R  SER*     2.8    50.1    +      -       -      +
    140R  GLN*     4.1    15.4    +      -       -      +
----------------------------------------------------------
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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