Contacts of the strand formed by residues 208 - 215 (chain M) in PDB entry 5DST


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 LEU 208 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178M  LYS*     3.7    12.0    -      -       -      -
    179M  VAL*     3.6    17.0    -      -       -      +
    180M  ASP      3.6    19.3    -      -       -      +
    181M  ILE      4.3     0.2    -      -       -      +
    182M  ILE*     4.0    18.3    -      -       +      +
    203M  ALA      3.7     1.0    +      -       -      -
    204M  ARG*     2.8    52.4    +      -       +      +
    205M  ASP      5.0     1.2    -      -       -      +
    207M  TRP*     1.3    74.3    -      -       -      +
    209M  LYS*     1.3    71.2    +      -       -      +
    210M  PRO*     3.9     0.5    -      -       -      +
    212M  GLY*     3.9    16.8    -      -       -      +
    213M  LEU      4.1     9.2    -      -       -      +
    214M  MET*     3.9    20.2    -      -       +      -
    281M  TYR*     4.8     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 209 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113M  LYS*     3.8    18.0    -      -       -      +
    178M  LYS*     3.6    18.4    -      -       +      -
    179M  VAL      3.0    18.8    +      -       -      +
    180M  ASP*     2.7    37.6    +      -       -      +
    207M  TRP      3.4     1.2    +      -       -      -
    208M  LEU*     1.3    81.7    -      -       -      +
    210M  PRO*     1.3    86.8    -      -       +      +
    211M  GLY      3.2     3.7    +      -       -      -
    212M  GLY*     3.0    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 210 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210F  PRO*     4.0    29.8    -      -       +      -
    178M  LYS*     4.8    10.3    -      -       +      -
    208M  LEU      4.4     1.6    -      -       -      +
    209M  LYS*     1.3    98.8    -      -       +      +
    211M  GLY*     1.3    60.8    +      -       -      +
    212M  GLY      3.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 211 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209M  LYS*     3.2     6.0    +      -       -      -
    210M  PRO*     1.3    71.9    -      -       -      +
    212M  GLY*     1.3    66.1    +      -       -      +
    213M  LEU*     3.9    11.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 212 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180M  ASP      3.3    15.0    -      -       -      -
    208M  LEU*     3.9    13.9    -      -       -      +
    209M  LYS*     3.0    27.6    +      -       -      -
    210M  PRO      3.2     1.8    +      -       -      -
    211M  GLY*     1.3    83.6    -      -       -      +
    213M  LEU*     1.3    62.1    +      -       -      +
    281M  TYR*     3.6    16.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 213 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109M  VAL*     3.3    35.9    -      -       +      -
    113M  LYS*     6.5     0.9    -      -       +      -
    180M  ASP      3.2     7.5    +      -       -      +
    181M  ILE*     3.3    12.2    -      -       +      +
    182M  ILE      3.0    25.6    +      -       -      +
    208M  LEU*     4.1     1.2    -      -       -      +
    211M  GLY      3.9     9.0    -      -       -      +
    212M  GLY*     1.3    79.8    -      -       -      +
    214M  MET*     1.3    67.2    +      -       -      +
    215M  PHE*     4.2    11.2    -      -       +      -
    281M  TYR*     3.8     4.3    -      -       -      +
    317M  LYS*     3.9    42.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 214 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182M  ILE*     3.3    26.0    -      -       +      +
    200M  VAL*     3.6    31.0    -      -       +      -
    204M  ARG*     3.9    31.9    -      -       +      -
    208M  LEU*     3.9     8.7    -      -       +      -
    213M  LEU*     1.3    81.1    -      -       -      +
    215M  PHE*     1.3    68.8    +      -       -      +
    216M  PRO      3.4    16.0    -      -       -      +
    217M  ASP*     3.2    25.2    -      -       +      +
    280M  ILE*     3.6    29.6    -      -       +      +
    281M  TYR*     3.3    25.2    +      -       +      -
    315M  PHE*     5.2     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 215 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99M  TYR*     4.0     3.6    -      -       +      -
    102M  SER*     3.3    43.1    -      -       -      -
    103M  MET*     4.6     2.5    -      -       +      -
    106M  ASN*     5.6     0.7    -      -       +      -
    109M  VAL*     4.2    17.3    -      -       +      -
    110M  PHE*     3.7    27.6    -      +       -      -
    181M  ILE*     4.0    16.6    -      -       +      -
    182M  ILE*     3.0     5.5    +      -       -      +
    183M  ILE*     3.4    19.4    -      -       +      -
    184M  SER*     3.0    25.3    +      -       -      +
    213M  LEU*     4.2    19.3    -      -       +      -
    214M  MET*     1.3    84.0    -      -       -      +
    216M  PRO*     1.3    60.6    -      -       -      +
    315M  PHE*     3.7    16.6    -      +       +      -
    317M  LYS*     4.9    11.9    -      -       +      -
    318M  CYS*     4.3    11.7    -      -       -      -
----------------------------------------------------------
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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