Contacts of the strand formed by residues 149 - 159 (chain D) in PDB entry 4A12


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 THR 149 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94D  ILE*     3.2    33.9    -      -       +      -
     95D  LEU      3.4     3.1    -      -       -      +
     96D  ASP*     3.3    28.9    +      -       -      +
    147D  ASN      3.9     5.9    +      -       -      -
    148D  ASP*     1.3    74.5    +      -       -      +
    150D  VAL*     1.3    62.0    +      -       -      +
    151D  ARG*     3.7     4.4    +      -       +      +
    171D  TYR      3.7     6.4    -      -       -      +
    172D  VAL*     3.9    13.4    -      -       -      +
    173D  LYS      4.7     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 150 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94D  ILE*     3.4     2.0    -      -       -      -
     95D  LEU*     2.8    39.1    +      -       +      +
     97D  ILE*     3.8    17.9    -      -       +      -
    114D  LEU*     3.7    15.9    -      -       +      -
    117D  GLN*     3.1    29.6    +      -       -      +
    144D  VAL*     3.7    29.6    -      -       +      -
    148D  ASP      4.9     0.2    -      -       -      +
    149D  THR*     1.3    71.7    -      -       -      +
    151D  ARG*     1.3    61.6    +      -       -      +
    170D  SER*     3.6    26.2    -      -       -      -
    171D  TYR      3.5     7.4    -      -       -      +
    172D  VAL*     3.9     6.7    -      -       +      -
    177D  VAL*     4.5     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 151 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92D  GLN*     3.4    21.5    +      -       +      +
     93D  SER      3.7     4.0    -      -       -      +
     94D  ILE*     4.2    23.8    -      -       +      -
    149D  THR*     3.7     3.9    +      -       +      +
    150D  VAL*     1.3    69.4    -      -       -      +
    152D  ALA*     1.3    61.4    +      -       -      +
    153D  GLU*     2.8    40.0    +      -       -      +
    169D  LYS      3.8     2.6    -      -       -      +
    170D  SER*     3.5     1.8    -      -       -      -
    171D  TYR*     2.8    68.2    +      -       -      +
    173D  LYS      4.7    11.2    +      -       -      +
    174D  HIS*     5.8     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 152 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92D  GLN*     3.2     6.8    -      -       -      +
     93D  SER      2.9    32.4    +      -       -      +
    117D  GLN*     3.5    28.5    -      -       +      +
    118D  ALA*     5.3     1.3    -      -       -      -
    121D  LEU*     3.4    15.9    -      -       +      +
    150D  VAL      3.6     1.6    +      -       -      -
    151D  ARG*     1.3    73.4    -      -       -      +
    153D  GLU*     1.3    59.9    +      -       -      +
    168D  VAL*     4.5     5.8    -      -       +      -
    169D  LYS      3.7     0.7    -      -       -      -
    170D  SER*     3.3    24.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 153 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90D  LYS*     4.0    19.0    +      -       -      -
     91D  ALA      3.4     7.0    -      -       -      +
     92D  GLN*     3.8    15.3    -      -       +      +
    121D  LEU*     4.1     0.9    -      -       -      -
    151D  ARG*     2.8    37.9    +      -       -      +
    152D  ALA*     1.3    73.2    -      -       -      +
    154D  ALA*     1.3    59.7    +      -       -      +
    155D  ARG*     3.3    25.9    +      -       -      +
    167D  GLU      3.7     2.1    -      -       -      +
    168D  VAL*     3.4     2.1    -      -       -      -
    169D  LYS*     2.9    47.3    +      -       -      +
    171D  TYR*     3.3    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90D  LYS*     3.3     6.6    -      -       -      +
     91D  ALA      2.8    36.0    +      -       -      +
    121D  LEU*     3.6    26.4    -      -       +      +
    122D  CYS*     4.6     3.1    -      -       -      -
    125D  LEU*     3.7    11.7    -      -       +      +
    153D  GLU*     1.3    73.5    -      -       -      +
    155D  ARG*     1.3    60.3    +      -       -      +
    166D  VAL*     3.8    18.8    -      -       +      -
    167D  GLU      3.4     4.3    -      -       -      -
    168D  VAL*     3.8    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 155 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89D  VAL      3.5     5.8    -      -       -      +
     90D  LYS*     3.7    25.6    -      -       +      +
    153D  GLU*     3.3    38.2    +      -       -      +
    154D  ALA*     1.3    77.2    -      -       -      +
    156D  VAL*     1.3    65.7    +      -       -      +
    157D  VAL*     3.4     9.6    +      -       +      +
    166D  VAL*     3.4     5.5    -      -       -      +
    167D  GLU*     2.9    49.4    +      -       +      +
    169D  LYS*     3.3    42.8    -      -       -      +
    171D  TYR*     5.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 156 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  ASN*     3.4    37.2    -      -       -      +
     89D  VAL*     2.9    12.3    +      -       -      +
    125D  LEU*     3.8    21.1    -      -       +      -
    126D  ILE*     4.8     1.3    -      -       +      -
    155D  ARG*     1.3    70.8    -      -       -      +
    157D  VAL*     1.3    60.1    +      -       -      +
    158D  ASN      3.5    25.8    -      -       -      +
    159D  GLN*     4.8     2.7    -      -       +      +
    164D  TYR*     3.7    25.8    -      -       +      -
    165D  TYR      3.5     5.6    -      -       -      +
    166D  VAL*     4.4     6.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 157 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155D  ARG*     3.4    10.1    +      -       +      +
    156D  VAL*     1.3    75.8    -      -       -      +
    158D  ASN*     1.3    60.5    +      -       +      +
    165D  TYR*     2.7    34.5    +      -       +      +
    166D  VAL      4.4     0.9    -      -       -      +
    167D  GLU*     3.7    50.7    -      -       +      +
    181D  ASN*     5.2     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 158 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156D  VAL*     3.5     8.8    -      -       -      +
    157D  VAL*     1.3    80.8    -      -       +      +
    159D  GLN*     1.3    69.8    +      -       -      +
    160D  THR*     4.0    12.1    -      -       -      +
    164D  TYR      3.7     0.2    -      -       -      -
    165D  TYR*     2.7    64.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 159 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88D  ASN*     5.3     0.9    -      -       -      +
    156D  VAL*     4.8     3.4    -      -       +      +
    158D  ASN*     1.3    82.0    +      -       -      +
    160D  THR*     1.3    69.5    +      -       -      +
    163D  HIS      3.4    10.3    -      -       -      +
    164D  TYR*     3.1    45.5    +      -       +      -
    186D  TYR*     3.2    24.4    +      -       -      -
    188D  LYS*     5.6     3.0    -      -       -      +
----------------------------------------------------------
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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