Contacts of the strand formed by residues 140 - 146 (chain E) in PDB entry 5A0Q


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 ALA 140 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31E  ILE*     4.0    21.5    -      -       +      +
     78E  MET*     3.5     1.2    -      -       -      -
     79E  SER*     3.0    37.0    +      -       -      +
    138E  GLY      3.8     1.8    +      -       -      -
    139E  VAL*     1.4    76.8    -      -       -      +
    141E  LEU*     1.3    60.3    +      -       -      +
    155E  HIS*     4.0    12.3    -      -       +      +
    156E  MET      3.5    11.2    -      -       -      +
    158E  PRO*     5.1     1.3    -      -       +      -
    170E  ILE*     3.7    23.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 141 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76E  CYS*     4.0    13.7    -      -       -      -
     77E  ALA      3.5    12.1    -      -       -      +
     78E  MET*     4.1     7.6    -      -       +      -
     85E  ALA*     4.7     1.8    -      -       +      +
     88E  LEU*     4.5    15.3    -      -       +      -
     89E  ILE*     4.5    11.2    -      -       +      -
    116E  VAL*     3.8    29.4    -      -       +      -
    139E  VAL*     3.6    24.9    -      -       +      +
    140E  ALA*     1.3    75.8    -      -       -      +
    142E  LEU*     1.3    62.1    +      -       -      +
    143E  PHE*     3.6    25.1    -      -       +      -
    155E  HIS*     3.4     8.3    -      -       -      -
    156E  MET*     2.9    46.0    +      -       +      +
    170E  ILE*     4.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 142 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  ALA*     4.1     6.5    -      -       +      +
     38E  ILE      4.0     9.6    -      -       -      +
     39E  GLY*     3.7    24.2    -      -       -      +
     48E  LEU*     3.4    20.2    -      -       +      +
     76E  CYS*     4.3     0.9    -      -       -      -
     77E  ALA*     3.0    39.7    +      -       +      -
    141E  LEU*     1.3    79.2    -      -       -      +
    143E  PHE*     1.3    65.1    +      -       -      +
    153E  LEU*     4.2    15.7    -      -       +      -
    154E  PHE      3.9     2.0    -      -       -      -
    155E  HIS*     3.8    30.1    -      -       +      -
    168E  ARG*     4.6     6.7    -      -       +      +
    170E  ILE*     3.8    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 143 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48E  LEU*     4.5     0.2    -      -       -      -
     70E  ILE*     4.6     2.2    -      -       +      -
     74E  ILE*     4.0    11.2    -      -       +      -
     75E  GLY      3.3     7.4    -      -       -      +
     76E  CYS*     4.1    20.4    -      -       +      +
     88E  LEU      6.5     0.2    -      -       -      -
     89E  ILE*     6.5     0.4    -      -       -      -
     92E  ALA*     4.5     9.9    -      -       +      -
    109E  VAL*     3.9    13.9    -      -       +      -
    112E  VAL*     3.8    32.3    -      -       +      -
    113E  THR*     3.5    39.5    -      -       +      +
    116E  VAL*     4.0    20.0    -      -       +      -
    141E  LEU*     3.6    38.4    -      -       +      -
    142E  LEU*     1.3    73.1    -      -       -      +
    144E  GLY*     1.3    58.1    +      -       -      +
    145E  GLY      4.1     0.2    -      -       -      -
    153E  LEU*     3.7     6.8    -      -       -      +
    154E  PHE      3.2    29.0    +      -       -      +
    156E  MET*     4.3     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 144 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46E  VAL*     4.0    24.8    -      -       -      +
     48E  LEU*     3.8     7.5    -      -       -      +
     73E  HIS      3.8     0.7    -      -       -      +
     74E  ILE*     3.3     2.9    -      -       -      -
     75E  GLY*     2.6    39.3    +      -       -      -
    142E  LEU      3.5     2.6    +      -       -      -
    143E  PHE*     1.3    74.7    -      -       -      +
    145E  GLY*     1.3    56.2    +      -       -      -
    152E  GLN      3.8     9.0    -      -       -      -
    153E  LEU*     4.5     2.0    -      -       -      -
    220E  VAL*     5.0     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46E  VAL*     4.3     0.4    -      -       -      +
     73E  HIS*     3.0    15.0    -      -       -      -
     74E  ILE*     3.8     2.9    -      -       -      -
    109E  VAL*     3.3    31.9    -      -       -      +
    144E  GLY*     1.3    76.3    -      -       -      -
    146E  VAL*     1.3    64.8    +      -       -      -
    147E  ASP*     3.5     2.6    +      -       -      +
    152E  GLN*     3.3    26.3    +      -       -      +
    220E  VAL*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44E  GLU      5.1     0.4    -      -       -      +
     45E  GLY*     4.8     2.5    -      -       -      -
     46E  VAL*     3.8    21.5    -      -       +      +
     73E  HIS*     3.3    24.4    +      -       -      +
    145E  GLY*     1.3    68.7    -      -       -      -
    147E  ASP*     1.3    59.1    -      -       -      +
    150E  GLY*     3.7    26.0    -      -       -      -
    151E  PRO*     3.8     7.6    -      -       +      -
    220E  VAL*     3.7    38.1    -      -       +      +
    221E  GLN      4.7     1.1    -      -       -      +
    222E  PRO*     4.0    29.6    -      -       +      +
    224E  GLN      6.0     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