Contacts of the strand formed by residues 121 - 131 (chain B) in PDB entry 5IYB


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 121 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  PRO*     3.2    18.3    -      -       -      +
     97B  THR      3.5    11.4    +      -       -      +
    108B  MET*     4.5     1.6    -      -       -      +
    119B  THR*     2.8    23.5    +      -       -      +
    120B  TYR*     1.3    75.0    -      -       -      +
    122B  ALA*     1.3    60.0    +      -       -      +
    151B  LYS*     3.9    21.8    -      -       -      +
    152B  ILE      3.1    26.7    -      -       -      -
    153B  PRO*     3.6     6.7    -      -       -      -
    154B  ILE*     3.9     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  LEU*     4.0     9.1    -      -       +      +
     94B  SER      3.1    28.9    -      -       -      +
     96B  PRO*     3.5    14.4    -      -       +      -
    121B  SER*     1.3    74.8    -      -       -      +
    123B  PRO*     1.4    66.3    -      -       +      +
    124B  LEU      3.8     0.2    +      -       -      -
    151B  LYS*     4.3     4.5    -      -       -      -
    152B  ILE*     2.8    30.3    +      -       -      +
    154B  ILE*     3.7    18.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  LEU*     3.7     2.1    -      -       -      +
     94B  SER*     3.1    36.7    +      -       -      -
     95B  LYS      4.0    10.3    -      -       -      +
     97B  THR*     4.0    15.3    -      -       -      +
     99B  TRP*     3.7    23.8    -      -       +      -
    121B  SER      4.7     0.2    -      -       -      +
    122B  ALA*     1.4    88.7    -      -       +      +
    124B  LEU*     1.3    58.5    +      -       -      +
    125B  TYR*     3.3    32.8    -      -       +      +
    148B  PHE*     3.8    14.1    -      -       +      -
    150B  GLY      3.6     5.8    -      -       -      +
    151B  LYS*     4.2     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  ILE*     5.9     1.8    -      -       +      -
     55B  VAL*     4.8     6.1    -      -       +      -
     91B  ILE*     3.8    21.8    -      -       +      -
     92B  TYR      3.4    12.6    -      -       -      +
     93B  LEU*     4.1    22.2    -      -       +      -
    123B  PRO*     1.3    72.2    -      -       -      +
    125B  TYR*     1.3    64.6    +      -       -      +
    148B  PHE*     3.6     4.6    -      -       -      -
    149B  ILE*     3.0    51.2    +      -       +      +
    150B  GLY      2.8    16.7    +      -       -      +
    152B  ILE*     4.0    26.0    -      -       +      -
    404B  PHE*     4.1    24.5    -      -       +      -
    440B  ILE*     5.0     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ILE*     3.3     6.1    -      -       -      +
     92B  TYR*     2.5    50.4    +      -       +      +
     94B  SER*     3.0    25.3    +      -       -      -
     99B  TRP*     4.6     8.1    -      -       -      -
    123B  PRO*     3.3    38.2    -      -       +      +
    124B  LEU*     1.3    74.3    -      -       -      +
    126B  VAL*     1.3    61.4    +      -       -      +
    146B  LYS*     4.9     5.6    -      -       +      -
    147B  THR*     3.0    12.8    -      -       -      +
    148B  PHE*     3.6    36.3    -      +       +      -
    149B  ILE*     4.2     1.3    -      -       -      -
    145T  LEU*     3.3    27.8    -      -       +      -
    148T  VAL*     3.4    33.8    +      -       +      +
    151T  THR*     4.4     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  VAL*     4.8     7.0    -      -       +      -
     88B  PHE*     4.0    19.1    -      -       +      -
     89B  GLU      3.9    11.7    -      -       -      +
     90B  GLN      3.3    13.5    -      -       -      +
     91B  ILE*     4.2     8.7    -      -       +      -
     92B  TYR*     5.1     0.7    -      -       -      -
    125B  TYR*     1.3    74.7    -      -       -      +
    127B  ASP*     1.3    71.9    +      -       -      +
    128B  ILE*     3.5    23.3    +      -       +      +
    146B  LYS*     3.8     5.2    -      -       -      -
    147B  THR      2.9    30.5    +      -       -      +
    149B  ILE*     3.7    35.7    -      -       +      -
    408B  PHE*     6.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  LYS      4.2     0.2    -      -       -      +
     88B  PHE*     3.5     3.3    -      -       -      -
     89B  GLU*     2.8    47.0    +      -       +      +
     90B  GLN*     2.8    35.6    +      -       +      +
     92B  TYR*     4.9     3.5    +      -       -      -
    126B  VAL*     1.3    72.5    -      -       -      +
    128B  ILE*     1.3    65.6    +      -       -      +
    129B  THR*     4.3     4.9    -      -       -      +
    144B  HIS*     2.5    42.9    +      -       -      -
    145B  GLN      3.8     4.0    -      -       -      -
    146B  LYS*     3.7    12.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  LEU*     4.9     7.2    -      -       +      -
     87B  LYS      3.8     6.7    -      -       -      +
     88B  PHE*     3.9    25.8    -      -       +      -
    126B  VAL*     3.5    20.3    +      -       +      +
    127B  ASP*     1.3    80.1    +      -       -      +
    129B  THR*     1.3    73.6    +      -       -      +
    143B  GLN      3.8     2.1    -      -       -      +
    145B  GLN*     3.6    30.0    +      -       +      +
    147B  THR*     3.4    31.0    -      -       +      +
    431B  LEU*     3.6    29.8    -      -       +      -
    435B  ILE*     3.8    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  LEU      3.7     0.5    -      -       -      +
     86B  LEU*     3.4     9.9    -      -       -      +
     87B  LYS*     3.0    60.6    +      -       -      +
     89B  GLU*     4.6    10.0    +      -       -      +
    127B  ASP*     4.3    11.0    -      -       -      +
    128B  ILE*     1.3    81.9    -      -       -      +
    130B  LYS*     1.3    59.3    +      -       -      +
    131B  THR*     4.1    10.8    +      -       -      -
    142B  THR*     4.4     9.6    -      -       -      +
    143B  GLN      3.7    14.1    -      -       -      +
    144B  HIS*     4.8     5.6    -      -       +      -
    431B  LEU*     5.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  TYR*     4.7    18.0    -      -       +      -
     85B  LEU      3.5     3.4    -      -       -      +
     86B  LEU*     4.0    18.6    -      -       +      -
    129B  THR*     1.3    72.9    -      -       -      +
    131B  THR*     1.3    63.2    +      -       -      +
    132B  VAL*     4.1    11.7    -      -       +      -
    141B  GLN      3.9     3.6    -      -       -      +
    142B  THR*     3.3    25.5    +      -       -      -
    143B  GLN*     3.5    37.0    +      -       +      +
    145B  GLN*     5.5    10.4    -      -       -      +
    429B  PHE*     3.5    41.7    +      -       +      +
    430B  ASN*     6.1     0.4    -      -       -      +
    431B  LEU*     5.2    11.1    -      -       +      +
    159T  HIS*     5.8     5.9    -      -       -      -
    160T  GLN*     6.0     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  ARG      5.6     0.2    -      -       -      -
     84B  TYR*     4.4     1.3    -      -       -      -
     85B  LEU*     3.0    54.1    +      -       +      +
     87B  LYS*     5.3     7.8    -      -       -      +
    129B  THR*     4.1     9.7    +      -       -      -
    130B  LYS*     1.3    82.6    +      -       -      +
    132B  VAL*     1.3    60.6    +      -       -      +
    133B  ILE*     3.5    20.5    +      -       +      +
    139B  GLN      5.4     2.0    -      -       -      +
    140B  LEU*     5.7     3.8    -      -       +      -
    141B  GLN      4.5     0.7    -      -       -      -
    142B  THR*     3.9    19.5    +      -       -      +
----------------------------------------------------------
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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