Contacts of the strand formed by residues 145 - 150 (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 GLY 145 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143M  SER      3.7     0.8    +      -       -      -
    144M  PRO*     1.3    74.6    -      -       -      +
    146M  VAL*     1.3    65.7    +      -       -      +
    147M  TYR*     4.2     4.0    -      -       -      -
    161M  SER      3.7     0.7    -      -       -      +
    162M  ILE*     3.5     5.0    -      -       -      +
    163M  ILE*     2.9    35.5    +      -       -      +
    269M  LEU*     4.8     3.9    -      -       -      +
    273M  GLY*     4.0    15.0    -      -       -      -
    276M  LYS*     4.4     9.6    -      -       -      -
    277M  ALA*     4.5     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145M  GLY*     1.3    78.3    -      -       -      +
    147M  TYR*     1.3    72.1    +      -       -      +
    148M  PHE*     3.5    28.5    -      -       +      -
    160M  ALA*     5.1     0.7    -      -       +      -
    161M  SER      3.3     7.2    -      -       -      +
    162M  ILE*     3.8    19.1    -      -       +      -
    276M  LYS*     4.6     4.8    +      -       -      +
    277M  ALA*     4.7    11.6    -      -       +      +
    280M  LYS*     3.3    26.4    -      -       +      +
    281M  LEU*     3.8    28.5    -      -       +      -
    290M  LEU*     6.3     0.2    -      -       +      -
    302M  VAL*     4.7     4.3    -      -       +      -
    306M  THR*     3.9    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 147 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142M  ARG*     3.8    23.3    -      -       +      +
    143M  SER*     2.2    41.8    +      -       -      -
    145M  GLY      4.4     6.3    -      -       -      -
    146M  VAL*     1.3    75.0    -      -       -      +
    148M  PHE*     1.3    69.6    +      -       -      +
    149M  THR*     4.1     3.6    -      -       +      +
    159M  ILE      3.7     0.2    -      -       -      +
    160M  ALA*     3.3     5.5    -      -       -      +
    161M  SER*     2.9    36.4    +      -       -      +
    163M  ILE*     3.4    31.4    -      -       +      -
    276M  LYS*     3.1    33.6    +      -       -      -
    323M  ASP*     3.7    28.5    -      -       +      -
    324M  ASP      5.5     0.2    -      -       -      -
    325M  ILE*     5.2     7.6    -      -       +      -
    330M  ASN*     3.5    30.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 148 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146M  VAL*     3.5    25.8    -      -       +      -
    147M  TYR*     1.3    74.3    -      -       -      +
    149M  THR*     1.3    62.3    +      -       -      +
    150M  PRO*     4.3     0.4    -      -       -      -
    158M  TYR*     5.2     0.9    -      -       +      -
    159M  ILE      3.6     2.9    -      -       -      +
    160M  ALA*     3.5    31.4    -      -       +      -
    280M  LYS*     3.8    17.0    -      -       +      -
    281M  LEU*     4.3     2.5    -      -       +      -
    306M  THR      4.0     4.3    -      -       -      -
    309M  TYR*     3.4    53.4    -      +       +      -
    310M  LEU*     3.9    23.1    -      -       +      -
    313M  LEU*     3.7    22.7    -      -       +      -
    321M  GLU      4.6     3.6    -      -       -      +
    322M  VAL*     3.4    11.2    -      -       -      +
    323M  ASP*     3.2    37.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 149 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147M  TYR*     4.9     3.0    +      -       +      +
    148M  PHE*     1.3    77.2    +      -       -      +
    150M  PRO*     1.3    73.4    -      -       +      +
    151M  ASP      3.4     0.3    +      -       -      -
    158M  TYR*     4.3     1.3    -      -       -      -
    159M  ILE*     2.9    45.7    +      -       -      +
    161M  SER*     4.1    11.6    +      -       -      -
    323M  ASP      4.1     8.5    -      -       -      +
    325M  ILE*     4.0    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 150 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148M  PHE      3.8     0.4    -      -       -      +
    149M  THR*     1.3    92.1    -      -       +      +
    151M  ASP*     1.3    65.7    +      -       -      +
    152M  PRO*     3.1    13.3    -      -       -      +
    156M  GLY      6.4     0.2    -      -       -      +
    157M  ARG      3.7     2.9    -      -       -      +
    158M  TYR*     3.5    32.9    -      -       +      -
    159M  ILE*     5.0     0.2    -      -       -      +
    322M  VAL*     3.7    25.1    -      -       +      -
----------------------------------------------------------
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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