Contacts of the strand formed by residues 561 - 573 (chain E) in PDB entry 4OMC


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 561 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    460E  ASP*     3.2     9.6    +      -       -      +
    461E  ILE*     3.0    27.7    +      -       -      +
    462E  GLY      4.8     0.4    -      -       -      +
    494E  SER*     3.1    19.5    -      -       -      -
    495E  TYR*     3.7     6.4    -      -       -      -
    560E  TYR*     1.3    80.8    -      -       -      +
    562E  THR*     1.3    66.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 562 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458E  PRO*     3.9    21.3    -      -       +      -
    459E  LYS      3.3    16.6    -      -       -      +
    460E  ASP*     4.1     7.7    +      -       -      +
    461E  ILE*     3.8     6.0    -      -       -      +
    493E  LEU*     3.1     3.5    -      -       -      -
    494E  SER*     2.9    43.8    +      -       -      -
    561E  GLY*     1.3    77.5    +      -       -      -
    563E  LEU*     1.3    71.1    +      -       -      +
    564E  THR*     3.6    12.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 563 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455E  LEU*     3.6    21.7    -      -       +      +
    458E  PRO*     3.5     1.9    -      -       -      +
    459E  LYS*     2.7    38.5    +      -       +      +
    461E  ILE*     3.9     6.3    -      -       +      +
    465E  LEU*     3.9    19.1    -      -       +      -
    467E  VAL*     4.3     8.7    -      -       +      -
    491E  LEU*     4.4    10.5    -      -       +      -
    492E  THR      3.5     9.2    -      -       -      +
    493E  LEU*     3.8    20.9    -      -       +      -
    549E  LEU*     4.0    16.4    -      -       +      -
    551E  ILE*     3.9    20.6    -      -       +      -
    562E  THR*     1.3    71.3    -      -       -      +
    564E  THR*     1.3    59.3    +      -       -      +
    565E  LYS      3.5    20.6    -      -       -      +
    566E  PHE*     4.5     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 564 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455E  LEU*     3.7    10.8    -      -       -      +
    457E  GLU      5.6     0.5    -      -       -      -
    458E  PRO*     4.5    18.5    -      -       +      +
    492E  THR*     2.9    33.3    +      -       -      +
    493E  LEU*     4.5     1.0    +      -       -      -
    494E  SER*     5.7     1.6    -      -       -      +
    562E  THR*     3.6    22.4    +      -       +      +
    563E  LEU*     1.3    76.0    -      -       -      +
    565E  LYS*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 565 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453E  ASP*     4.1    11.9    -      -       -      +
    455E  LEU*     3.6     6.9    -      -       -      +
    490E  ARG*     3.4    17.6    +      -       -      +
    491E  LEU*     3.4     4.9    -      -       -      -
    492E  THR*     3.0    56.5    +      -       -      +
    530E  ASP*     2.9    34.7    +      -       -      +
    563E  LEU*     3.5    10.0    -      -       -      +
    564E  THR*     1.3    81.5    -      -       -      +
    566E  PHE*     1.3    62.6    +      -       -      +
    567E  THR*     3.4    24.0    -      -       -      +
    232F  THR*     6.3     2.7    -      -       -      -
    233F  ASP*     6.0     8.7    -      -       +      -
    269F  LEU*     6.2     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 566 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453E  ASP*     3.4     2.4    +      -       -      +
    454E  ILE*     2.9    58.4    +      -       +      +
    455E  LEU*     3.9    19.9    +      -       +      +
    467E  VAL*     4.2    13.9    -      -       +      -
    469E  LYS*     5.9     1.6    -      -       +      -
    489E  ALA*     3.8    24.2    -      -       +      -
    490E  ARG      3.4     2.7    -      -       -      -
    491E  LEU*     3.4    18.2    -      -       +      -
    505E  LEU*     4.1    14.8    -      -       +      -
    547E  TRP*     5.7     5.4    -      -       +      -
    548E  VAL      5.6     0.2    -      -       -      -
    549E  LEU*     3.6    42.2    -      -       +      -
    563E  LEU*     4.5     2.5    -      -       +      -
    565E  LYS*     1.3    76.5    -      -       -      +
    567E  THR*     1.3    69.9    +      -       -      +
    568E  LEU*     4.4    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 567 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    451E  ILE*     3.8    27.4    -      -       +      -
    452E  ILE      3.5    12.3    -      -       -      +
    453E  ASP*     2.9    19.3    +      -       -      +
    488E  GLN      3.6     0.9    -      -       -      +
    489E  ALA*     3.6     1.7    -      -       -      -
    490E  ARG*     2.8    49.7    +      -       -      +
    565E  LYS*     3.4    20.7    -      -       -      +
    566E  PHE*     1.3    74.9    -      -       -      +
    568E  LEU*     1.3    62.1    +      -       -      +
    569E  VAL*     3.7     6.8    +      -       +      -
    234F  ALA*     4.5     3.7    -      -       +      +
    269F  LEU*     4.0    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 568 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    450E  CYS      3.7     2.4    -      -       -      +
    451E  ILE*     3.8     0.2    -      -       -      -
    452E  ILE*     2.8    56.5    +      -       +      +
    454E  ILE*     4.3    14.3    -      -       +      +
    471E  VAL*     4.5     5.6    -      -       +      -
    487E  ALA*     5.2     2.0    -      -       +      -
    488E  GLN      3.5    14.1    -      -       -      +
    505E  LEU*     4.3    23.3    -      -       +      -
    547E  TRP*     3.8    45.5    -      -       +      +
    566E  PHE*     4.0    14.4    +      -       +      -
    567E  THR*     1.3    70.7    -      -       -      +
    569E  VAL*     1.3    61.2    +      -       -      +
    570E  LEU*     3.8    21.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 569 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449E  LYS*     3.7    28.7    -      -       +      -
    450E  CYS      3.6     4.5    -      -       -      +
    451E  ILE*     4.5     5.4    -      -       +      -
    486E  HIS      4.2     0.2    -      -       -      +
    487E  ALA*     3.3     5.5    -      -       -      +
    488E  GLN*     2.8    51.1    +      -       -      +
    490E  ARG*     3.9    31.4    -      -       +      -
    567E  THR*     4.2     9.4    -      -       +      -
    568E  LEU*     1.3    76.6    -      -       -      +
    570E  LEU*     1.3    63.1    +      -       -      +
    571E  TYR*     3.7    24.3    +      -       +      -
    269F  LEU*     4.2    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 570 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449E  LYS*     3.3     5.7    -      -       -      +
    450E  CYS*     2.8    46.9    +      -       +      +
    452E  ILE*     3.7    26.9    -      -       +      -
    471E  VAL*     4.9     0.4    -      -       +      -
    473E  ALA*     4.1    17.9    -      -       +      -
    481E  ILE*     3.3    10.2    -      -       +      +
    484E  LEU*     3.8    17.7    -      -       +      -
    486E  HIS      4.1     2.5    -      -       -      -
    487E  ALA*     4.3     4.3    -      -       +      -
    543E  PRO*     4.0    21.8    -      -       +      +
    547E  TRP*     3.9    21.8    -      -       +      -
    568E  LEU*     3.8    25.1    -      -       +      -
    569E  VAL*     1.3    75.8    -      -       -      +
    571E  TYR*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 571 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312E  ILE*     3.6    24.6    -      -       +      +
    447E  GLN*     3.5    28.0    -      -       +      +
    448E  ARG      3.3     6.3    -      -       -      +
    449E  LYS*     3.3    41.7    +      -       +      -
    481E  ILE*     3.7     3.4    -      -       -      -
    484E  LEU*     3.2     9.0    -      -       -      +
    485E  GLU*     2.8    25.4    +      -       +      +
    486E  HIS*     3.1    40.8    +      -       +      +
    488E  GLN*     3.4    37.5    +      -       +      -
    569E  VAL*     3.7     9.9    -      -       +      -
    570E  LEU*     1.3    76.8    -      -       -      +
    572E  GLY*     1.3    58.7    +      -       -      +
    604E  FMT      3.6    19.8    -      -       -      -
    272F  GLU*     4.1     3.8    +      -       -      -
    276F  ARG*     4.4     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 572 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391E  ARG*     4.8     0.4    -      -       -      -
    447E  GLN*     3.8     1.3    -      -       -      +
    448E  ARG*     2.7    41.2    +      -       -      +
    481E  ILE*     3.6    10.4    -      -       -      +
    483E  ARG      3.4    11.2    -      -       -      -
    485E  GLU*     3.8    17.7    +      -       -      +
    571E  TYR*     1.3    76.2    -      -       -      +
    573E  THR*     1.3    66.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 573 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391E  ARG*     3.2    31.4    -      -       -      +
    395E  HIS*     6.2     0.4    -      -       +      -
    444E  VAL*     5.2     2.2    -      -       +      -
    445E  ALA*     3.6    23.7    -      -       +      +
    446E  PRO      3.6    10.8    -      -       -      +
    448E  ARG*     4.5     7.0    -      -       -      +
    480E  HIS      4.3     1.1    -      -       -      -
    481E  ILE*     3.6     4.6    -      -       -      -
    482E  THR      3.0     6.9    +      -       -      -
    483E  ARG*     3.0    47.2    +      -       -      +
    485E  GLU*     3.9     5.9    +      -       -      +
    572E  GLY*     1.3    75.9    -      -       -      +
    574E  ALA*     1.3    67.9    +      -       -      +
----------------------------------------------------------
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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