Contacts of the strand formed by residues 140 - 148 (chain B) in PDB entry 1I3R


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 LEU 140 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129B  PRO*     3.5     7.4    -      -       -      +
    130B  THR*     3.4    37.3    +      -       -      +
    131B  LYS*     5.4    11.4    -      -       +      +
    139B  ASN*     1.3    88.9    +      -       +      +
    141B  LEU*     1.3    60.6    +      -       -      +
    142B  VAL*     4.0     0.9    -      -       +      -
    169B  VAL*     5.7     3.4    -      -       +      -
    186B  MET*     3.5    40.8    -      -       +      -
    187B  LEU      3.4    10.1    -      -       -      +
    188B  GLU*     3.6    33.9    -      -       +      +
    191B  PRO*     5.0     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  VAL*     4.3     2.5    -      -       +      -
    128B  TYR      3.9     4.0    -      -       -      -
    129B  PRO*     4.0    20.0    -      -       +      -
    140B  LEU*     1.3    75.2    -      -       -      +
    142B  VAL*     1.3    58.7    +      -       -      +
    157B  TRP*     3.0    40.7    -      -       +      -
    186B  MET*     3.4     1.4    -      -       -      -
    187B  LEU*     3.0    31.2    +      -       +      +
    189B  THR*     4.8     4.7    -      -       -      +
    191B  PRO*     5.3     4.0    -      -       +      -
    197B  TYR*     3.2    50.5    -      -       +      -
    214B  TRP*     3.7    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  THR      3.7     0.2    -      -       -      +
    127B  VAL*     3.4     4.3    -      -       -      -
    128B  TYR*     2.7    63.1    +      -       +      +
    130B  THR*     3.4    38.6    -      -       +      +
    141B  LEU*     1.3    69.7    -      -       -      +
    143B  CYS*     1.3    64.9    +      -       -      +
    144B  SER      3.6     1.1    +      -       -      +
    157B  TRP*     4.1     1.8    -      -       -      -
    184B  LEU*     4.1    24.7    -      -       +      -
    186B  MET*     3.9    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  VAL*     4.0    17.7    -      -       -      -
    126B  THR      3.6     4.0    -      -       -      -
    127B  VAL*     4.5     1.6    -      -       -      -
    141B  LEU      3.5     1.2    +      -       -      -
    142B  VAL*     1.3    73.9    -      -       -      +
    144B  SER*     1.3    58.2    +      -       -      +
    145B  VAL*     3.9     8.6    +      -       -      +
    155B  VAL*     4.2     5.4    -      -       -      -
    157B  TRP*     3.3    14.6    -      -       +      +
    183B  THR      4.0     0.3    -      -       -      +
    184B  LEU*     3.5     2.4    -      -       -      -
    185B  VAL*     2.7    50.9    +      -       +      +
    199B  CYS*     2.0    49.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  PRO*     3.3    27.6    -      -       -      +
    124B  THR      3.5     2.1    +      -       -      +
    125B  VAL*     3.3     6.1    -      -       -      +
    126B  THR*     2.8    43.8    +      -       -      -
    128B  TYR*     4.2    19.7    -      -       -      -
    142B  VAL*     3.6     1.4    +      -       -      -
    143B  CYS*     1.3    72.9    -      -       -      +
    145B  VAL*     1.3    65.5    +      -       -      +
    146B  SER*     4.1     1.6    +      -       -      -
    183B  THR      3.9     3.8    -      -       -      -
    184B  LEU*     3.7    20.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  PRO*     3.6    20.9    -      -       +      -
    124B  THR      3.8     2.5    -      -       -      -
    125B  VAL*     4.3     4.5    -      -       +      +
    143B  CYS*     4.2    11.9    -      -       -      +
    144B  SER*     1.3    79.4    +      -       -      +
    146B  SER*     1.3    60.9    -      -       -      +
    148B  PHE*     3.6     3.4    -      -       +      -
    153B  ILE*     3.2    31.0    -      -       +      -
    155B  VAL*     4.0    16.4    -      -       +      -
    182B  GLN*     3.3     1.9    -      -       -      -
    183B  THR*     2.8    47.6    +      -       +      +
    185B  VAL*     5.6     0.2    -      -       +      -
    201B  VAL*     3.8    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ARG      4.8     0.2    -      -       -      -
     95A  SER*     4.3     7.9    -      -       -      -
     96A  PRO*     3.1    36.9    -      -       -      +
    123B  PRO*     3.3     2.9    -      -       -      +
    124B  THR*     3.0    39.9    +      -       -      +
    144B  SER*     4.5     1.1    +      -       -      -
    145B  VAL*     1.3    76.7    -      -       -      +
    147B  ASP*     1.3    73.5    +      -       -      +
    148B  PHE*     3.5     3.8    -      -       -      -
    181B  PHE      3.6     4.5    -      -       -      -
    182B  GLN*     3.9    13.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ARG*     2.9    43.6    +      -       -      +
     95A  SER*     5.6     6.2    -      -       -      -
    121B  VAL*     3.6    16.6    -      -       -      +
    122B  GLU      3.1    16.6    -      -       -      +
    124B  THR*     4.7     8.7    -      -       -      +
    146B  SER*     1.3    81.3    -      -       -      +
    148B  PHE*     1.3    56.3    +      -       -      +
    176B  ASN*     5.2     1.7    -      -       -      +
    180B  THR*     3.8    15.7    +      -       -      +
    181B  PHE      2.9    13.5    +      -       -      -
    182B  GLN*     4.5     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 148 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  VAL*     3.2    15.7    -      -       -      +
    123B  PRO*     3.6    18.2    -      -       +      -
    145B  VAL*     3.6    34.8    -      -       +      -
    146B  SER      3.9     5.8    -      -       -      -
    147B  ASP*     1.3    75.1    -      -       -      +
    149B  TYR*     1.3    62.5    -      -       -      +
    150B  PRO      3.3    18.8    -      -       -      -
    151B  GLY      4.0     1.1    -      -       -      -
    153B  ILE*     3.7    35.9    -      -       +      -
    173B  LEU*     3.7    18.6    -      -       +      -
    180B  THR*     3.6     2.5    -      -       -      -
    181B  PHE*     2.9    58.6    +      -       +      +
    182B  GLN*     3.8     4.9    -      -       -      -
    183B  THR*     4.3     4.3    -      -       +      -
    203B  HIS*     3.5    10.1    -      +       -      +
----------------------------------------------------------
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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