Contacts of the strand formed by residues 190 - 196 (chain L) in PDB entry 2FD6


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 SER 190 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148L  LYS      3.6     0.7    -      -       -      +
    149L  ILE*     3.3     6.8    -      -       -      +
    150L  ASP*     2.6    54.2    +      -       -      -
    151L  GLY      4.8     2.6    +      -       -      -
    189L  ASN*     1.3    74.8    -      -       -      +
    191L  TYR*     1.3    62.9    +      -       -      +
    192L  THR*     4.0    11.8    +      -       -      -
    207L  SER*     4.8     3.6    +      -       -      -
    208L  PHE      4.5     0.3    +      -       -      -
    209L  ASN*     3.5    19.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 191 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116L  ILE*     3.4     6.0    -      -       -      +
    131L  VAL*     4.4    16.8    -      -       +      -
    147L  TRP*     5.3     1.8    -      +       +      -
    148L  LYS      3.7     1.1    -      -       -      -
    149L  ILE*     3.8    31.4    -      -       +      -
    178L  LEU*     4.9     4.7    -      -       +      -
    180L  LEU*     4.0    15.4    -      -       +      +
    184L  GLU      3.7     0.5    +      -       -      -
    185L  TYR*     2.8    50.6    +      +       -      -
    188L  HIS*     3.1    36.2    -      -       +      +
    189L  ASN      3.4    13.0    -      -       -      -
    190L  SER*     1.3    70.7    +      -       -      +
    192L  THR*     1.3    62.4    +      -       -      +
    207L  SER*     2.9    24.1    -      -       -      -
    208L  PHE*     2.9    51.0    +      +       +      -
    210L  ARG*     4.3     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 192 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116L  ILE*     4.1     0.2    -      -       -      -
    147L  TRP*     3.3    16.4    -      -       -      -
    148L  LYS*     2.9    51.5    +      -       +      +
    151L  GLY      5.8     1.0    +      -       -      -
    190L  SER*     4.0     9.9    +      -       -      -
    191L  TYR*     1.3    73.9    -      -       -      +
    193L  CYS*     1.3    68.9    +      -       -      +
    194L  GLU*     4.1    11.9    -      -       +      +
    205L  VAL*     3.3    33.4    -      -       +      +
    206L  LYS      3.5     4.7    -      -       -      +
    207L  SER*     2.9    16.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 193 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114L  VAL*     4.2     8.4    -      -       +      +
    116L  ILE*     3.9     9.8    -      -       +      +
    133L  CYS*     2.0    54.3    -      -       +      -
    135L  LEU*     4.6     3.6    -      -       -      -
    145L  VAL*     3.9    20.6    -      -       -      -
    146L  LYS      3.8     2.2    -      -       -      -
    147L  TRP*     4.4     6.7    -      -       +      -
    192L  THR*     1.3    73.9    -      -       -      +
    194L  GLU*     1.3    61.3    +      -       -      +
    195L  ALA      4.2     0.2    -      -       -      -
    204L  ILE      3.7     1.7    -      -       -      +
    205L  VAL*     3.6     2.4    -      -       -      -
    206L  LYS*     2.9    35.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 194 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144L  ASN*     3.5     2.1    +      -       -      +
    145L  VAL*     3.4     3.7    -      -       -      -
    146L  LYS*     2.7    61.5    +      -       +      +
    148L  LYS*     2.7    45.0    +      -       +      +
    192L  THR*     4.4     7.7    -      -       +      +
    193L  CYS*     1.3    75.8    -      -       -      +
    195L  ALA*     1.3    58.7    +      -       -      +
    196L  THR*     4.1     1.6    +      -       -      +
    203L  PRO*     3.5    31.6    -      -       +      +
    204L  ILE      3.6     2.5    -      -       -      -
    205L  VAL*     3.5    20.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 195 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112L  PRO*     4.7     4.3    -      -       +      -
    114L  VAL*     4.2    13.7    -      -       +      -
    135L  LEU*     3.2    35.0    -      -       +      -
    143L  ILE*     4.5     6.7    -      -       +      -
    144L  ASN      3.1     5.4    -      -       -      +
    145L  VAL*     4.5     0.2    -      -       -      +
    193L  CYS*     4.2     1.0    -      -       -      -
    194L  GLU*     1.3    72.9    -      -       -      +
    196L  THR*     1.3    62.3    +      -       -      +
    197L  HIS*     4.1     1.6    +      -       -      +
    202L  SER      4.8     0.2    -      -       -      +
    203L  PRO*     3.3     3.6    -      -       -      +
    204L  ILE*     2.8    46.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 196 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143L  ILE*     3.5     7.6    -      -       -      +
    144L  ASN*     2.7    57.0    +      -       +      +
    194L  GLU*     5.0     1.7    +      -       -      +
    195L  ALA*     1.3    73.3    -      -       -      +
    197L  HIS*     1.3    69.0    +      -       -      +
    200L  SER      5.1     5.4    -      -       -      +
    201L  THR      5.7     3.4    -      -       -      +
    202L  SER      5.8     0.4    -      -       -      -
    203L  PRO*     4.1    21.1    -      -       +      +
----------------------------------------------------------
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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