Contacts of the strand formed by residues 122 - 129 (chain S) in PDB entry 5IY8


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 122 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    546B  GLU*     3.1    22.4    +      -       +      +
    547B  GLU*     5.6     2.5    -      -       -      -
    119S  THR*     2.4    34.3    +      -       -      +
    121S  ASN*     1.3    90.1    -      -       +      +
    123S  SER*     1.3    62.0    +      -       -      +
    124S  TYR*     4.8     0.9    -      -       -      -
     22T  LYS*     3.1    40.3    -      -       +      +
     23T  VAL      3.2    11.0    -      -       -      -
     24T  PRO*     3.9    20.0    -      -       +      -
     25T  LYS*     3.8     4.2    -      -       -      -
    115T  GLU*     6.0     2.0    -      -       +      -
    116T  CYS      5.9     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 123 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119S  THR*     4.1     4.8    +      -       -      -
    122S  THR*     1.3    77.6    +      -       -      +
    124S  TYR*     1.3    65.4    +      -       -      +
    125S  TYR*     3.5    28.9    +      -       -      -
     23T  VAL*     2.5    37.7    +      -       -      +
     25T  LYS*     3.4    22.7    -      -       -      +
     28T  SER*     4.4     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 124 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552B  ASN*     4.9     3.7    -      -       -      +
    555B  GLU*     2.2    39.7    +      -       +      -
    115S  LYS*     4.7    13.7    -      -       -      -
    119S  THR*     4.2    23.4    +      -       +      +
    122S  THR*     4.8     0.4    -      -       -      -
    123S  SER*     1.3    71.7    -      -       -      +
    125S  TYR*     1.3    71.8    +      -       -      +
    140S  VAL*     3.2    31.8    +      -       +      +
    143S  TRP*     4.9    19.1    -      +       +      -
     20T  LEU*     3.7    23.3    -      -       +      -
     21T  VAL      3.5     3.4    -      -       -      -
     22T  LYS*     3.4    53.9    +      -       +      +
     86T  GLN*     6.0     0.4    -      -       -      -
    113T  ARG*     4.6     7.8    +      -       -      -
    114T  ALA      5.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 125 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18S  VAL*     6.1     5.6    -      -       +      -
    123S  SER*     4.0    16.9    -      -       -      -
    124S  TYR*     1.3    84.7    -      -       -      +
    126S  ILE*     1.3    63.4    +      -       -      +
    127S  PHE*     3.9    17.8    +      +       +      -
    137S  ALA*     5.0     4.0    -      -       +      -
    138S  PHE      3.4    17.9    -      -       -      +
    139S  PRO*     3.5    24.4    -      -       +      +
    140S  VAL      4.4     0.7    -      -       -      -
     19T  TRP      3.5     0.7    -      -       -      +
     20T  LEU*     3.5     5.9    -      -       -      -
     21T  VAL*     2.9    35.7    +      -       -      +
     23T  VAL*     3.5    25.4    -      -       +      -
     28T  SER*     3.4    34.6    +      -       -      -
     31T  TRP*     4.0    17.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 126 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26S  TYR*     5.7     4.5    -      -       +      -
     28S  ILE*     4.1     7.0    -      -       +      -
    125S  TYR*     1.3    72.2    -      -       -      +
    127S  PHE*     1.3    64.4    +      -       -      +
    128S  THR      4.8     0.2    -      -       -      +
    136S  GLU      3.4     1.6    -      -       -      +
    137S  ALA*     3.1     2.3    -      -       -      -
    138S  PHE*     2.5    62.7    +      -       +      +
    140S  VAL*     4.3    14.3    -      -       +      +
     18T  VAL*     3.8    26.9    -      -       +      -
     19T  TRP      3.2    10.8    -      -       -      +
     20T  LEU*     4.1    16.8    -      -       +      -
     95T  VAL*     3.8    34.1    -      -       +      -
    110T  VAL*     4.0    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 127 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16S  VAL*     3.6    32.1    -      -       +      -
    125S  TYR*     4.0    15.3    -      +       +      -
    126S  ILE*     1.3    79.1    -      -       -      +
    128S  THR*     1.3    60.0    +      -       -      +
    135S  PHE*     4.2    30.1    -      +       +      -
    136S  GLU      3.2     3.8    -      -       -      -
    137S  ALA*     3.9    21.1    -      -       +      -
     18T  VAL*     3.5     3.1    -      -       -      -
     19T  TRP*     2.6    59.5    +      -       +      +
     21T  VAL*     3.4    36.3    -      -       +      -
     23T  VAL*     5.4     1.1    -      -       +      -
     31T  TRP*     4.7    16.2    -      +       -      -
     43T  LEU*     5.5     4.5    -      -       +      -
     56T  PHE*     5.8     1.8    -      +       -      -
     83T  PHE*     5.0    12.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 128 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126S  ILE*     4.0     0.6    +      -       -      -
    127S  PHE*     1.3    74.1    -      -       -      +
    129S  GLN*     1.3    67.0    +      -       -      +
    130S  CYS*     3.8     7.8    +      -       -      -
    135S  PHE*     3.6     6.9    -      -       -      -
    136S  GLU*     2.5    61.5    +      -       +      +
    138S  PHE*     4.1    23.3    -      -       +      -
     16T  THR*     5.3     4.9    -      -       -      +
     17T  GLY      4.4     3.9    +      -       -      -
     18T  VAL*     3.9    21.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 129 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14S  TYR*     4.6    22.0    +      -       -      -
    128S  THR*     1.3    81.4    +      -       -      +
    130S  CYS*     1.3    72.7    +      -       -      +
    131S  PRO*     4.3     3.5    -      -       -      +
    133S  GLY*     5.6     4.8    -      -       -      -
    134S  ALA      4.2     4.5    -      -       -      +
    135S  PHE*     3.7    25.8    -      -       +      -
     17T  GLY      5.1     3.6    +      -       -      -
     19T  TRP*     6.2     1.0    -      -       -      -
----------------------------------------------------------
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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