Contacts of the strand formed by residues 129 - 137 (chain B) in PDB entry 4IYM


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 129 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    437A  VAL*     5.1     2.0    -      -       +      -
    124B  GLY*     3.0    19.3    +      -       -      -
    125B  ALA*     3.0    16.7    +      -       +      -
    126B  GLY*     3.1    27.3    +      -       -      +
    127B  PRO*     3.6    23.1    -      -       +      +
    128B  GLY*     1.3    77.0    -      -       -      +
    130B  ASP*     1.3    68.6    -      -       -      +
    131B  MSE      5.2     1.1    -      -       +      -
    477B  THR*     3.5    31.9    -      -       +      -
    478B  SER      3.3     6.7    -      -       -      +
    479B  ARG*     3.7    38.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  PHE*     4.0    22.6    -      -       +      -
    122B  THR      3.5     7.6    -      -       -      +
    123B  GLU*     3.3    17.6    -      -       -      +
    124B  GLY*     3.0    22.0    +      -       -      -
    128B  GLY      5.0     3.9    -      -       -      +
    129B  ILE*     1.3    77.7    +      -       -      +
    131B  MSE      1.3    60.2    +      -       -      +
    132B  TYR*     4.4     6.7    -      -       +      -
    476B  ILE      3.8     0.5    -      -       -      +
    477B  THR*     3.5     2.4    -      -       -      -
    478B  SER*     2.9    41.8    +      -       -      +
    134C  ILE*     5.7     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with MSE 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441A  VAL      4.2     4.7    -      -       -      +
    442A  PRO*     4.1     6.3    -      -       +      -
    443A  LEU*     3.4    53.8    -      -       +      +
    446A  HIS*     3.6    31.3    -      -       +      +
    121B  PHE*     3.7     0.3    -      -       -      -
    122B  THR*     2.8    37.7    +      -       -      +
    125B  ALA*     3.9    16.8    -      -       +      +
    129B  ILE*     5.2     1.1    -      -       +      -
    130B  ASP*     1.3    74.5    -      -       -      +
    132B  TYR*     1.3    64.1    +      -       -      +
    475B  THR*     4.1    11.9    -      -       +      -
    476B  ILE      3.3     9.6    -      -       -      +
    477B  THR*     3.4    29.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    425A  ALA*     5.7     0.9    -      -       -      +
    435A  VAL*     5.5     1.7    -      -       -      +
    446A  HIS*     4.6     2.5    -      -       -      -
    120B  GLU      3.2    13.0    -      -       -      +
    121B  PHE*     3.5    31.0    -      +       +      -
    130B  ASP*     4.4     3.4    -      -       +      -
    131B  MSE      1.3    86.1    -      -       -      +
    133B  SER*     1.3    63.2    +      -       -      +
    134B  ILE*     4.6     0.2    -      -       +      -
    475B  THR*     3.4     4.4    -      -       -      -
    476B  ILE*     2.7    89.5    +      -       +      +
    478B  SER*     4.2    18.3    +      -       -      -
    121C  PHE*     3.4    38.8    -      +       +      -
    132C  TYR*     6.6     0.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446A  HIS*     4.7     5.6    +      -       -      -
    119B  SER*     2.5    26.4    +      -       -      -
    120B  GLU*     3.0    34.0    +      -       -      +
    132B  TYR*     1.3    77.2    -      -       -      +
    134B  ILE*     1.3    63.0    +      -       -      +
    135B  ARG*     5.7     0.4    -      -       -      +
    473B  THR*     3.8    19.7    -      -       -      +
    474B  LYS      2.9    12.8    -      -       -      -
    475B  THR*     3.8     9.2    -      -       -      +
    121C  PHE*     3.9     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    425A  ALA      5.2     1.6    -      -       -      +
    426A  SER*     5.4     1.6    -      -       -      -
    119B  SER*     3.4     4.5    -      -       -      +
    132B  TYR*     4.6     1.1    -      -       +      -
    133B  SER*     1.3    79.8    -      -       -      +
    135B  ARG*     1.3    69.0    +      -       -      +
    136B  GLN*     3.6    13.4    +      -       +      +
    472B  ARG      3.5     2.4    -      -       -      +
    473B  THR*     3.6     1.7    -      -       -      -
    474B  LYS*     2.7    47.0    +      -       +      +
    476B  ILE*     3.6    31.4    -      -       +      -
    121C  PHE*     3.7    25.6    -      -       +      -
    123C  GLU*     3.6    49.4    -      -       +      +
    130C  ASP*     5.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116B  LEU      2.9    26.1    +      -       -      -
    117B  GLN*     3.1    35.4    +      -       +      +
    118B  LYS      3.1    26.3    +      -       -      -
    119B  SER*     4.1    10.8    -      -       -      +
    133B  SER*     5.7     0.4    -      -       -      +
    134B  ILE*     1.3    79.5    -      -       -      +
    136B  GLN*     1.3    61.7    +      -       -      +
    464B  THR*     4.6     3.6    +      -       -      -
    467B  ILE*     3.5    25.6    -      -       -      +
    468B  LYS*     3.7    41.3    -      -       -      +
    471B  THR*     3.9    17.9    +      -       -      +
    472B  ARG      3.5     4.0    -      -       -      -
    473B  THR*     4.5    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426A  SER*     2.9    23.7    +      -       -      +
    428A  ILE      4.5     0.2    -      -       -      +
    451A  TRP*     3.2    22.7    -      -       +      -
    117B  GLN*     4.7     0.2    -      -       -      -
    134B  ILE*     3.9    14.6    -      -       +      +
    135B  ARG*     1.3    77.7    -      -       -      +
    137B  PRO*     1.3    75.1    -      -       +      +
    471B  THR*     3.2     8.3    -      -       -      -
    472B  ARG*     2.8    34.7    +      -       -      +
    474B  LYS*     2.8    31.0    +      -       +      +
    123C  GLU*     3.1    33.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  GLN*     3.7    11.4    -      -       -      +
     56B  ALA*     3.8    19.3    -      -       +      -
    117B  GLN*     5.0     2.0    -      -       -      +
    135B  ARG      4.9     0.2    -      -       -      +
    136B  GLN*     1.3    94.2    -      -       +      +
    138B  VAL*     1.3    60.2    +      -       -      +
    139B  GLY      3.5     1.1    +      -       -      +
    164B  CYS      3.5    22.4    -      -       -      +
    165B  GLY*     3.6    20.0    -      -       -      +
    166B  ASN*     3.2    16.2    -      -       -      +
    470B  TRP      4.1     4.0    -      -       -      +
    472B  ARG*     3.2    19.5    +      -       -      -
    123C  GLU*     6.1     0.2    -      -       -      +
----------------------------------------------------------
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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