Contacts of the strand formed by residues 113 - 119 (chain M) in PDB entry 5D4D


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 VAL 113 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95M  TYR*     3.4     6.1    -      -       -      -
     96M  ALA*     2.7    57.8    +      -       +      +
    111M  ASP*     4.5     8.5    -      -       -      +
    112M  GLU*     1.3    76.5    -      -       -      +
    114M  PHE*     1.3    64.4    +      -       -      +
    115M  LEU*     3.6    12.5    +      -       +      +
    369M  PRO*     4.2    14.8    -      -       +      +
    370M  ALA*     3.7    37.0    -      -       +      +
    373M  VAL*     4.8    14.8    -      -       +      -
    280P  GLN*     4.3    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 114 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93M  PRO*     3.5    26.5    -      -       +      -
     94M  LEU      3.9     2.9    -      -       -      -
     95M  TYR*     3.3    29.1    -      +       +      -
    112M  GLU      4.2     0.6    +      -       -      -
    113M  VAL*     1.3    73.5    -      -       -      +
    115M  LEU*     1.3    63.8    +      -       -      +
    116M  GLY*     3.7    20.0    +      -       -      -
    117M  HIS*     3.2    21.1    -      +       -      -
    373M  VAL*     5.9     0.7    -      -       -      +
    375M  SER*     3.8    10.2    +      -       -      -
    279P  GLN*     3.4    42.4    +      -       +      +
    280P  GLN*     3.5    33.1    +      -       -      +
    283P  GLY*     3.1    34.8    -      -       -      -
    284P  ARG*     3.6     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 115 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48M  PHE*     3.4    36.6    -      -       +      -
     94M  LEU*     2.8    36.2    +      -       +      +
     96M  ALA*     3.6    16.8    -      -       +      -
    113M  VAL*     4.0    14.1    -      -       +      +
    114M  PHE*     1.3    76.0    -      -       -      +
    116M  GLY*     1.3    57.8    +      -       -      +
    348M  LEU*     5.3     0.9    -      -       +      -
    351M  LEU*     5.0     8.3    -      -       +      -
    373M  VAL*     4.1    25.6    -      -       +      -
    375M  SER*     3.4    21.2    -      -       -      +
    378M  LEU*     4.3    16.2    -      -       +      +
    379M  GLU*     3.3    17.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 116 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94M  LEU*     2.9    26.4    +      -       -      +
    114M  PHE*     3.4    26.1    +      -       -      -
    115M  LEU*     1.3    80.7    -      -       -      +
    117M  HIS*     1.3    66.2    +      -       -      -
    379M  GLU*     3.6    21.8    -      -       -      -
    279P  GLN*     4.0     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 117 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77M  PRO*     4.7    13.2    -      -       +      +
     91M  GLN*     3.2    43.4    +      -       +      +
     92M  ALA      3.3     7.2    -      -       -      +
     93M  PRO*     3.4    28.1    -      -       +      +
     94M  LEU*     5.2     0.4    -      -       -      -
    114M  PHE*     3.2    25.9    -      +       -      -
    116M  GLY*     1.3    78.1    -      -       -      -
    118M  ILE*     1.3    61.3    +      -       -      +
    119M  PRO*     3.3    11.1    -      -       -      +
    379M  GLU*     4.5    10.6    +      -       -      +
    382M  ILE*     4.6     5.7    -      -       -      +
    283P  GLY      3.7    11.9    +      -       -      -
    284P  ARG*     4.2    10.6    -      -       +      +
    285P  GLU*     4.7    12.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 118 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26M  TYR*     3.3    24.7    -      -       -      +
     30M  LEU*     3.6    26.7    -      -       +      -
     44M  ILE*     3.6    20.4    -      -       +      -
     73M  LEU*     4.3    11.2    -      -       +      -
     91M  GLN*     3.9     2.0    -      -       -      -
     92M  ALA*     2.9    38.6    +      -       -      +
     94M  LEU*     4.0    14.5    -      -       +      +
    116M  GLY      4.3     0.6    +      -       -      -
    117M  HIS*     1.3    72.5    -      -       -      +
    119M  PRO*     1.3    69.0    -      -       +      +
    120M  LEU*     3.5     0.7    +      -       -      +
    340M  MET*     4.9     7.9    -      -       -      -
    344M  PHE*     3.6    34.8    -      -       +      -
    382M  ILE*     5.3     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 119 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26M  TYR*     2.4    32.4    +      -       -      -
     89M  THR*     4.3    14.4    -      -       +      -
     90M  TYR      3.7     6.7    -      -       -      +
     91M  GLN*     3.9     6.3    -      -       +      +
    117M  HIS      3.3    10.5    -      -       -      +
    118M  ILE*     1.3    87.5    -      -       +      +
    120M  LEU*     1.3    59.7    +      -       -      +
    127M  PHE*     4.4     1.8    -      -       +      -
    129M  ILE*     4.2    12.1    -      -       +      -
    382M  ILE*     3.5    19.3    -      -       +      +
    383M  ARG*     5.9     1.8    -      -       -      -
    386M  PHE*     3.9    41.1    -      -       +      -
----------------------------------------------------------
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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