Contacts of the strand formed by residues 615 - 620 (chain B) in PDB entry 3E0D


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 615 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294B  ARG      3.7     7.5    +      -       -      +
    295B  ILE*     5.1     3.6    -      -       +      -
    296B  PRO*     3.4    30.7    -      -       +      -
    402B  TYR*     3.0    44.2    -      -       +      -
    405B  ILE*     3.8    24.2    -      -       +      -
    461B  MET*     3.6    14.4    -      -       +      -
    579B  VAL      4.0     0.2    -      -       -      +
    580B  VAL*     3.3     6.7    -      -       -      +
    581B  ILE*     3.1    43.0    +      -       +      +
    614B  LEU*     1.3    69.8    -      -       -      +
    616B  LYS*     1.3    62.7    +      -       -      +
    617B  MET*     3.7    23.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 616 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402B  TYR*     4.5     0.9    +      -       -      -
    461B  MET*     3.8     5.8    -      -       -      +
    463B  ASP*     3.0    43.4    +      -       -      +
    465B  ASP*     5.2     0.2    -      -       -      -
    492B  ILE*     3.2    28.0    -      -       +      -
    579B  VAL      3.4     3.8    -      -       -      -
    606B  MET*     3.6    24.3    -      -       +      +
    609B  VAL*     4.9     0.4    -      -       +      -
    610B  GLU*     3.4    44.1    +      -       +      +
    614B  LEU      3.1     5.0    +      -       -      +
    615B  LEU*     1.3    77.4    -      -       -      +
    617B  MET*     1.3    76.3    +      -       -      +
    618B  ASP*     3.8     9.2    -      -       -      -
     21F  DOC      2.3    36.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 617 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402B  TYR*     3.3    39.5    -      -       +      +
    405B  ILE*     4.9     1.3    -      -       -      -
    406B  VAL*     3.8    13.9    -      -       +      -
    409B  TYR*     3.4    28.0    -      -       -      +
    464B  ILE      4.0    10.8    -      -       -      +
    465B  ASP*     4.7     1.6    -      -       -      -
    579B  VAL*     2.9    30.6    +      -       +      +
    581B  ILE*     4.2    22.7    -      -       +      -
    615B  LEU*     3.7    17.9    -      -       +      +
    616B  LYS*     1.3    80.4    -      -       -      +
    618B  ASP*     1.3    71.1    +      -       -      +
    619B  PHE*     3.5    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 618 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409B  TYR*     5.3     0.5    +      -       -      -
    464B  ILE      4.0     3.3    +      -       -      +
    465B  ASP*     3.3    23.2    +      -       +      +
    466B  THR*     3.0    29.2    +      -       -      -
    575B  HIS*     3.3    16.0    +      -       -      -
    577B  ALA*     3.3    17.0    -      -       -      +
    616B  LYS*     3.8    12.3    -      -       -      -
    617B  MET*     1.3    83.5    -      -       -      +
    619B  PHE*     1.3    65.9    +      -       -      +
    620B  LEU*     3.6    13.9    -      -       +      -
     21F  DOC      2.4    43.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 619 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409B  TYR*     3.5    31.9    -      +       -      -
    466B  THR      3.7     3.8    -      -       -      -
    468B  PHE*     3.5    20.9    -      +       +      -
    473B  ARG*     3.1    37.7    +      -       +      +
    476B  VAL*     3.5    31.6    -      -       +      -
    477B  ILE*     4.0    17.5    -      -       +      -
    480B  VAL*     4.0    19.3    -      -       +      -
    576B  ALA      3.5     0.3    -      -       -      +
    577B  ALA*     2.9    16.9    +      -       -      +
    579B  VAL*     4.0    20.0    -      -       +      -
    581B  ILE*     5.5     0.9    -      -       +      -
    617B  MET*     3.5    28.9    -      -       +      -
    618B  ASP*     1.3    77.4    -      -       -      +
    620B  LEU*     1.3    60.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 620 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    424B  ARG*     3.4    40.6    -      -       -      +
    465B  ASP*     4.4     0.2    -      -       +      -
    466B  THR      2.9    12.4    +      -       -      +
    467B  ASP*     3.4    19.2    -      -       -      +
    468B  PHE*     2.8    32.2    +      -       -      +
    473B  ARG*     3.8     2.0    -      -       -      -
    577B  ALA*     3.8    10.8    -      -       +      -
    618B  ASP*     3.6    34.3    -      -       +      +
    619B  PHE*     1.3    73.6    -      -       -      +
    621B  GLY*     1.3    60.8    +      -       -      +
    622B  LEU*     5.4     1.1    -      -       +      -
    821B  TYR*     4.6     0.4    -      -       -      +
      7E    G      4.3     4.7    -      -       -      +
      8E    T      4.4     6.3    -      -       -      +
      9E    G      4.2    10.3    -      -       -      +
     20F    A      5.6     0.7    -      -       +      -
     21F  DOC      3.3    25.8    -      -       +      +
----------------------------------------------------------
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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