Contacts of the strand formed by residues 135 - 140 (chain A) in PDB entry 4DTP


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 135 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  ILE*     3.1     5.8    -      -       -      +
    116A  GLU*     2.8    50.5    +      -       +      +
    133A  ILE*     3.6     2.3    -      -       -      +
    134A  ASP*     1.3    84.1    +      -       -      +
    136A  ILE*     1.3    68.0    +      -       -      +
    148A  VAL*     6.2     0.9    -      -       +      -
    149A  PHE      3.3     8.1    -      -       -      +
    197A  LEU*     5.0     0.9    -      -       -      +
    320A  TYR*     4.6     1.3    -      -       +      -
    321A  ILE*     3.8    24.5    -      -       +      -
    324A  ASN*     3.9     8.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PHE*     4.2     9.9    -      -       +      -
    114A  ASP      3.5    12.1    -      -       -      +
    115A  ILE*     4.0     8.1    -      -       +      -
    133A  ILE*     3.8    16.8    -      -       +      -
    135A  ALA*     1.3    80.5    -      -       -      +
    137A  THR*     1.3    72.7    +      -       -      +
    138A  HIS*     4.1     0.9    -      -       +      -
    147A  TYR      3.5     1.4    -      -       -      +
    148A  VAL*     3.4     3.3    -      -       -      +
    149A  PHE*     2.7    42.9    +      -       +      +
    197A  LEU*     3.9    23.3    -      -       +      -
    198A  LEU*     4.6     5.4    -      -       +      -
    201A  TYR*     3.8    55.9    -      -       +      +
    226A  VAL*     5.2     3.6    -      -       +      -
    324A  ASN*     3.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PHE*     3.2     4.7    -      -       -      +
    114A  ASP      3.1    30.6    +      -       -      -
    136A  ILE*     1.3    73.4    +      -       -      +
    138A  HIS*     1.3    63.4    +      -       -      +
    146A  PHE*     4.2    20.0    -      -       +      -
    147A  TYR      3.4     3.1    -      -       -      +
    148A  VAL*     3.8    20.0    -      -       +      +
    324A  ASN*     2.7    25.1    +      -       -      -
    325A  ILE*     3.6    25.5    -      -       -      +
    328A  VAL*     3.5    29.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  ALA*     3.5    25.4    -      -       +      +
    112A  ASN      3.5     3.1    -      -       -      -
    113A  PHE*     3.9    10.7    -      -       +      +
    136A  ILE*     4.5     1.1    -      -       +      -
    137A  THR*     1.3    75.6    -      -       -      +
    139A  TYR*     1.3    71.2    +      -       -      +
    140A  ASP*     4.3     7.1    +      -       +      +
    146A  PHE*     4.5     1.3    -      -       -      -
    147A  TYR*     2.9    41.6    +      -       -      +
    149A  PHE*     4.6     0.9    -      -       +      -
    201A  TYR*     2.8    39.6    +      -       +      -
    204A  PHE*     3.5    32.4    -      +       +      -
    205A  TRP*     4.0    18.8    -      +       -      -
    208A  LYS      4.7     5.4    +      -       -      -
    210A  PRO*     4.3     5.2    -      -       +      +
    213A  LEU*     5.1     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  VAL      4.6     2.7    -      -       -      -
    111A  ALA*     3.3     6.6    -      -       -      -
    112A  ASN*     2.7    43.5    +      -       +      +
    137A  THR      4.1     0.8    -      -       -      -
    138A  HIS*     1.3    75.0    -      -       -      +
    140A  ASP*     1.3    63.9    +      -       -      +
    141A  SER*     3.6    27.5    +      -       -      -
    144A  ASP*     2.6    35.5    +      -       -      +
    145A  ARG      3.3    26.0    -      -       -      -
    146A  PHE*     3.7    42.6    -      +       +      +
    328A  VAL*     4.0     9.3    -      -       +      +
    332A  LEU*     3.6    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  ARG*     2.8    46.1    +      -       -      +
    110A  VAL      3.9     2.2    -      -       -      -
    111A  ALA*     4.8     1.9    -      -       -      +
    138A  HIS*     3.8     9.3    +      -       +      -
    139A  TYR*     1.3    77.1    -      -       -      +
    141A  SER*     1.3    53.7    +      -       -      +
    142A  ILE      2.8    10.6    +      -       -      -
    143A  ASP*     2.7    35.0    +      -       +      +
    144A  ASP*     2.8    34.5    +      -       -      -
    145A  ARG      3.1     7.5    +      -       -      -
    147A  TYR*     4.1    22.0    -      -       +      -
    208A  LYS*     3.7    10.6    -      -       +      +
----------------------------------------------------------
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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