Contacts of the strand formed by residues 119 - 126 (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 SER 119 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  GLN      3.5     0.5    +      -       -      -
    118B  LYS*     1.3    75.3    -      -       -      +
    120B  GLU*     1.3    68.4    +      -       -      +
    133B  SER*     2.5    38.7    +      -       -      -
    134B  ILE*     3.4    12.0    -      -       -      +
    135B  ARG*     4.1    15.7    +      -       -      +
    119C  SER      3.6     0.2    -      -       -      +
    120C  GLU*     3.4     9.0    -      -       -      +
    121C  PHE*     2.9    38.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445A  TYR      4.7     0.9    -      -       -      +
    446A  HIS*     4.1    16.5    +      -       +      -
    464A  THR*     4.4    14.8    +      -       -      +
    119B  SER*     1.3    84.0    -      -       -      +
    121B  PHE*     1.3    60.9    +      -       -      +
    132B  TYR*     3.2     5.2    -      -       -      +
    133B  SER*     3.0    35.2    +      -       -      +
    115C  HIS*     4.2     8.5    -      -       -      -
    118C  LYS*     3.1    49.7    +      -       +      +
    119C  SER      3.3     5.4    -      -       -      +
    121C  PHE*     4.7     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446A  HIS*     4.7     0.2    -      -       -      -
    120B  GLU*     1.3    76.1    -      -       -      +
    122B  THR*     1.3    65.8    +      -       -      +
    123B  GLU*     3.6    23.1    -      -       +      -
    130B  ASP*     4.0    23.6    -      -       +      -
    131B  MSE      3.8     1.6    -      -       -      -
    132B  TYR*     3.5    36.6    -      +       +      -
    117C  GLN      4.7     0.5    -      -       -      +
    118C  LYS*     3.4     8.6    -      -       -      -
    119C  SER*     2.7    47.4    +      -       -      +
    120C  GLU      4.5     6.3    -      -       -      +
    121C  PHE*     4.2     7.4    -      +       +      -
    132C  TYR*     3.4    37.7    -      +       -      -
    133C  SER      3.7    15.7    -      -       -      +
    134C  ILE*     3.7    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445A  TYR*     3.6    30.0    -      -       +      +
    446A  HIS*     2.8    30.6    +      -       -      -
    121B  PHE*     1.3    80.6    +      -       -      +
    123B  GLU*     1.3    70.9    +      -       -      +
    125B  ALA*     3.9    12.8    -      -       +      +
    130B  ASP*     3.5     2.8    -      -       -      -
    131B  MSE      2.8    40.1    +      -       -      -
     60C  PRO*     4.6     9.0    -      -       +      -
    114C  PRO      4.5     2.8    +      -       -      +
    117C  GLN      6.0     0.4    -      -       -      -
    118C  LYS*     4.0     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  PHE*     3.6    10.2    -      -       +      -
    122B  THR*     1.3    76.3    -      -       -      +
    124B  GLY*     1.3    69.4    +      -       -      +
    125B  ALA      3.5     0.3    +      -       -      -
    130B  ASP*     3.3    17.1    -      -       -      +
     60C  PRO*     4.8     6.2    -      -       -      +
    134C  ILE*     3.6    34.2    -      -       +      +
    135C  ARG      5.5     0.2    -      -       -      +
    136C  GLN*     2.9    35.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  GLU*     1.3    77.5    -      -       -      +
    125B  ALA*     1.3    66.8    +      -       -      +
    126B  GLY      3.0    14.3    +      -       -      +
    128B  GLY*     5.3     1.8    -      -       -      -
    129B  ILE      3.0     9.7    +      -       -      -
    130B  ASP*     3.0    13.9    +      -       -      -
     57C  ALA      5.6     0.7    -      -       -      +
     59C  ASN*     3.4    18.9    -      -       -      +
     60C  PRO*     3.6     6.1    -      -       -      +
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Residues in contact with ALA 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  LEU*     3.8    25.3    -      -       +      +
    445A  TYR*     3.7    23.3    +      -       -      +
    122B  THR*     3.9     7.1    +      -       +      +
    123B  GLU      3.3     4.0    +      -       -      -
    124B  GLY*     1.3    75.9    -      -       -      +
    126B  GLY*     1.3    57.7    +      -       -      +
    129B  ILE*     3.0     7.7    +      -       +      +
    131B  MSE      3.9    32.1    -      -       +      +
     59C  ASN*     3.4    19.1    +      -       -      +
     60C  PRO*     4.5     1.8    -      -       -      -
     61C  GLN*     4.8     1.2    -      -       -      +
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Residues in contact with GLY 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124B  GLY*     3.2    17.2    -      -       -      +
    125B  ALA*     1.3    77.8    -      -       -      +
    127B  PRO*     1.4    75.0    -      -       -      +
    128B  GLY      3.2     1.7    +      -       -      -
    129B  ILE*     3.1    30.3    +      -       -      +
     59C  ASN*     4.7     6.7    -      -       -      -
----------------------------------------------------------
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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