Contacts of the strand formed by residues 137 - 148 (chain A) in PDB entry 5D4E


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 ARG 137 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  GLU*     4.2    21.8    +      -       -      -
     60A  ASP*     4.8    10.3    +      -       -      -
     68A  ILE*     3.9    19.8    -      -       -      +
     69A  PRO      4.3     5.3    +      -       -      +
     70A  GLY      4.8     0.2    +      -       -      -
     71A  VAL*     4.5     1.4    -      -       -      +
    103A  ALA      3.6     5.4    -      -       -      +
    104A  GLU*     3.6    26.3    +      -       +      +
    132A  LEU*     3.8     2.8    -      -       -      +
    135A  GLY      3.7    11.2    +      -       -      +
    136A  GLY*     1.3    79.3    -      -       -      +
    138A  LEU*     1.3    61.1    +      -       -      +
    139A  ASN      4.2     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ILE*     3.8     8.7    -      -       +      -
     68A  ILE*     3.7    29.6    -      -       +      -
     71A  VAL*     4.8     3.1    -      -       +      -
     78A  ILE*     4.9     3.1    -      -       +      -
    101A  LEU*     3.7    10.5    -      -       +      +
    102A  LYS*     3.5     3.6    -      -       -      +
    103A  ALA*     2.9    38.9    +      -       +      +
    109A  VAL*     5.0     3.8    -      -       +      -
    129A  ILE*     5.0     2.7    -      -       +      -
    130A  ALA*     4.1    17.3    -      -       +      -
    132A  LEU*     3.5    31.1    -      -       +      +
    137A  ARG*     1.3    74.1    -      -       -      +
    139A  ASN*     1.3    59.1    +      -       -      +
    140A  MET*     3.6    45.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  TYR*     5.3     3.0    -      -       -      -
     58A  ILE*     3.4     6.2    -      -       -      +
     59A  GLU*     3.0    60.4    +      -       +      +
    100A  LEU*     6.0     0.7    -      -       -      +
    101A  LEU      3.2    12.3    +      -       -      +
    102A  LYS*     3.3    37.6    -      -       +      +
    137A  ARG      4.2     0.6    +      -       -      -
    138A  LEU*     1.3    75.1    -      -       -      +
    140A  MET*     1.3    65.6    +      -       -      +
    141A  GLU*     5.1     9.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  VAL*     5.1     1.6    -      -       +      -
     57A  TYR      3.2     6.7    -      -       -      +
     58A  ILE*     3.7    17.3    -      -       +      -
     78A  ILE*     4.2    20.9    -      -       -      -
     82A  LEU*     4.4    12.8    -      -       +      -
     99A  LEU      3.8     0.6    -      -       -      +
    100A  LEU*     3.6     2.8    -      -       -      -
    101A  LEU*     2.9    67.3    +      -       +      +
    114A  PHE*     4.4     9.6    -      -       +      -
    129A  ILE*     4.2    13.2    -      -       +      -
    138A  LEU*     3.6    38.8    -      -       +      -
    139A  ASN*     1.3    79.4    +      -       -      +
    141A  GLU*     1.3    66.8    +      -       -      +
    142A  VAL*     4.1     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  SER      4.9     0.2    -      -       -      -
     56A  VAL*     3.8     0.3    -      -       -      -
     57A  TYR*     2.9    51.9    +      -       +      +
     98A  THR*     4.2    11.0    -      -       +      +
     99A  LEU      3.4     4.5    -      -       -      -
    100A  LEU*     3.6    25.0    -      -       +      +
    139A  ASN*     5.1     9.9    +      -       -      +
    140A  MET*     1.3    77.7    -      -       -      +
    142A  VAL*     1.3    61.8    +      -       -      +
    143A  ARG      4.2     0.3    +      -       -      -
    161A  ARG*     3.4    35.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  VAL*     3.6    26.2    -      -       +      -
     55A  SER      3.4     9.0    -      -       -      +
     56A  VAL*     4.3     8.5    -      -       +      +
     82A  LEU*     4.7    11.4    -      -       +      -
     85A  LEU*     5.0     5.6    -      -       +      -
     97A  VAL      3.6     1.4    -      -       -      +
     98A  THR*     3.3     6.5    -      -       -      -
     99A  LEU*     2.9    35.8    +      -       +      +
    114A  PHE*     3.6    32.5    -      -       +      -
    140A  MET*     4.6    10.8    -      -       +      -
    141A  GLU*     1.3    77.5    -      -       -      +
    143A  ARG*     1.3    60.5    +      -       -      +
    144A  VAL*     3.8    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  VAL*     3.5     1.6    -      -       -      -
     54A  THR*     2.6    33.2    +      -       -      +
     55A  SER*     2.9    30.7    +      -       -      +
     96A  THR*     3.5    24.9    +      -       -      +
     97A  VAL      3.7     3.6    -      -       -      +
     98A  THR*     4.6     5.4    -      -       -      +
    141A  GLU      4.2     0.8    +      -       -      -
    142A  VAL*     1.3    71.4    -      -       -      +
    144A  VAL*     1.3    54.6    +      -       -      +
    145A  ASP*     3.0    33.7    +      -       -      +
    158A  ILE*     3.4    35.9    -      -       -      +
    159A  LYS      5.2     1.4    +      -       -      -
    160A  ASP*     2.9    42.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  THR*     4.2     1.6    -      -       -      -
     52A  ALA      3.3    26.0    -      -       -      +
     53A  VAL*     3.7    24.7    -      -       +      -
     85A  LEU*     4.7     1.3    -      -       +      -
     87A  VAL*     4.0    35.2    -      -       +      -
     89A  PHE*     3.9    16.4    -      -       +      -
     96A  THR*     3.4     3.6    +      -       -      -
     97A  VAL      2.9    36.0    +      -       -      +
     99A  LEU*     4.2    12.8    -      -       +      -
    142A  VAL*     3.8    11.7    -      -       +      -
    143A  ARG*     1.3    76.8    -      -       -      +
    145A  ASP*     1.3    60.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  THR*     3.3     5.2    -      -       -      -
     52A  ALA      3.0    29.8    +      -       -      -
     54A  THR*     2.4    41.5    +      -       +      -
     89A  PHE*     4.4     2.5    -      -       -      -
     95A  GLN*     3.7     5.2    -      -       -      +
     96A  THR*     3.3    20.0    +      -       -      -
    143A  ARG*     3.0    34.2    +      -       -      +
    144A  VAL*     1.3    75.5    -      -       -      +
    146A  ARG*     1.3    70.4    +      -       -      +
    158A  ILE*     4.9     5.6    -      -       +      +
    171A  PHE*     3.5     4.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  PRO*     5.8     4.9    -      -       -      +
     50A  GLY*     3.4    11.3    +      -       -      +
     51A  THR*     4.0     8.9    -      -       +      +
     89A  PHE*     3.4    41.6    +      -       +      +
     91A  ASN      3.4    20.0    +      -       -      -
     92A  PRO*     3.9    15.5    +      -       -      +
     94A  LEU      2.8    23.4    +      -       -      -
     95A  GLN*     3.2    38.0    +      -       -      +
    145A  ASP*     1.3    82.4    -      -       -      +
    147A  GLY*     1.3    59.6    +      -       -      +
    171A  PHE*     3.9     4.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  PRO*     3.4     6.9    -      -       -      +
     50A  GLY      2.9    31.9    +      -       -      +
    146A  ARG*     1.3    75.9    -      -       -      +
    148A  VAL*     1.3    62.2    +      -       -      -
    171A  PHE*     3.4    22.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  SER      4.0     0.7    -      -       -      +
     47A  SER*     3.4    40.4    -      -       -      +
     48A  ILE      4.3     2.5    -      -       -      -
     49A  PRO*     4.3    11.9    -      -       +      -
    147A  GLY*     1.3    75.1    -      -       -      +
    149A  GLY*     1.3    69.9    +      -       -      +
    150A  TYR      4.1     0.2    +      -       -      -
    151A  VAL*     4.4     8.7    -      -       -      +
    171A  PHE*     3.4     9.4    -      -       -      -
----------------------------------------------------------
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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