Contacts of the strand formed by residues 330 - 346 (chain D) in PDB entry 4OIO


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 THR 330 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224D  ARG*     3.0    36.6    +      -       +      -
    225D  LEU      3.3    15.7    -      -       -      +
    226D  PRO*     4.2     8.7    -      -       +      -
    227D  LEU*     4.2     2.9    -      -       -      +
    249D  TYR*     5.0     9.4    -      -       +      +
    326D  GLU*     3.8     3.3    -      -       -      +
    327D  GLU*     2.8    36.8    +      -       -      +
    328D  GLY      4.5     0.7    -      -       -      +
    329D  GLU*     1.3    89.1    +      -       +      +
    331D  VAL*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 331 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223D  LEU      3.8     1.2    -      -       -      +
    224D  ARG*     3.2     6.7    -      -       -      +
    225D  LEU*     2.9    34.6    +      -       +      +
    227D  LEU*     3.6    41.5    -      -       +      -
    230D  TRP*     3.7    45.5    -      -       +      -
    324D  ALA*     4.3    13.9    -      -       +      -
    325D  GLU      3.8     9.4    -      -       -      +
    326D  GLU*     3.9     9.2    -      -       +      -
    330D  THR*     1.3    73.9    -      -       -      +
    332D  TYR*     1.3    65.4    +      -       -      +
    333D  LEU*     4.1     5.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 332 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222D  GLY*     3.5    21.0    +      -       -      -
    223D  LEU*     3.4    29.6    -      -       -      -
    224D  ARG*     3.5    40.1    -      -       +      +
    251D  PHE*     5.4     0.9    -      +       -      -
    254D  GLU*     4.6    17.8    -      -       +      +
    281D  THR      4.9     1.0    +      -       -      -
    282D  TYR*     4.3    13.5    -      +       -      -
    323D  GLU      4.1     1.0    -      -       -      +
    324D  ALA      3.9     0.2    -      -       -      -
    325D  GLU*     2.9    52.9    +      -       +      +
    327D  GLU*     6.1     0.2    -      -       +      -
    330D  THR      4.3     0.2    -      -       -      -
    331D  VAL*     1.3    74.5    -      -       -      +
    333D  LEU*     1.3    59.7    +      -       -      +
    334D  THR*     4.0    18.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 333 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221D  ALA      4.0     0.2    -      -       -      +
    222D  GLY*     3.2     2.7    -      -       -      -
    223D  LEU*     2.9    59.3    +      -       +      +
    225D  LEU*     4.0    15.7    -      -       +      -
    230D  TRP*     3.3    42.8    -      -       +      +
    242D  LEU*     4.6     9.9    -      -       +      -
    322D  VAL*     4.0    22.0    -      -       +      -
    323D  GLU      3.5     4.9    -      -       -      +
    324D  ALA*     4.2     6.5    -      -       +      +
    331D  VAL*     5.0     4.9    -      -       +      +
    332D  TYR*     1.3    75.2    -      -       -      +
    334D  THR*     1.3    61.1    -      -       -      +
    335D  LEU*     3.7    21.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 334 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220D  ARG*     3.4    38.8    +      -       +      +
    221D  ALA      4.0     7.4    -      -       -      +
    222D  GLY*     4.2     3.1    -      -       -      +
    321D  GLN      4.1     0.3    -      -       -      +
    322D  VAL*     3.8     1.4    -      -       -      -
    323D  GLU*     2.9    52.8    +      -       -      +
    332D  TYR*     4.0    18.4    +      -       -      -
    333D  LEU*     1.3    71.8    -      -       -      +
    335D  LEU*     1.3    66.9    +      -       -      +
    336D  PHE*     4.1     6.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 335 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220D  ARG*     3.2     7.3    -      -       -      +
    221D  ALA      2.9    42.3    +      -       -      +
    223D  LEU*     5.1     2.9    -      -       +      -
    236D  TYR*     4.6    10.1    -      -       +      -
    242D  LEU*     5.3     6.1    -      -       +      -
    283D  PHE*     3.8    35.2    -      -       +      -
    313D  MET*     5.3     4.3    -      -       -      -
    319D  ALA*     4.8     4.3    -      -       +      -
    321D  GLN      3.8     1.8    -      -       -      +
    322D  VAL*     3.6    39.0    -      -       +      -
    333D  LEU*     4.0    25.4    -      -       +      -
    334D  THR*     1.3    73.0    -      -       -      +
    336D  PHE*     1.3    62.9    +      -       -      +
    337D  LEU*     3.8    19.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 336 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219D  GLU      4.1     2.5    -      -       -      -
    220D  ARG*     3.9    45.1    -      -       +      -
    319D  ALA*     3.7     1.9    -      -       -      -
    320D  ALA*     2.9    36.6    +      -       +      +
    321D  GLN*     3.1    49.6    +      -       +      +
    323D  GLU*     3.8    39.9    -      -       +      -
    334D  THR*     4.4     6.3    -      -       +      -
    335D  LEU*     1.3    71.2    -      -       -      +
    337D  LEU*     1.3    60.5    +      -       -      +
    338D  GLU*     5.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 337 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217D  LYS      3.8     0.3    -      -       -      +
    218D  LYS*     3.3     5.4    -      -       -      +
    219D  GLU      2.9    40.8    +      -       -      +
    221D  ALA*     4.7     2.9    -      -       +      -
    269D  PHE*     3.6    22.9    -      -       +      -
    283D  PHE*     3.6    39.3    -      -       +      -
    313D  MET*     4.0     9.4    -      -       +      -
    317D  VAL*     3.7    14.4    -      -       +      -
    318D  ARG      3.6    12.8    -      -       -      +
    319D  ALA*     3.7    22.0    -      -       +      -
    335D  LEU*     4.1    20.4    -      -       +      +
    336D  PHE*     1.3    75.8    -      -       -      +
    338D  GLU*     1.3    62.8    +      -       -      +
    339D  TRP*     4.2     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 338 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216D  VAL*     5.4     5.6    -      -       +      -
    217D  LYS      3.4     6.1    -      -       -      +
    218D  LYS*     3.4    36.7    -      -       +      +
    316D  GLN      4.5     0.5    -      -       -      +
    317D  VAL*     3.3    12.6    -      -       -      +
    318D  ARG*     3.1    60.6    +      -       -      +
    320D  ALA*     4.0    26.2    -      -       +      +
    336D  PHE      5.0     0.7    -      -       -      +
    337D  LEU*     1.3    78.0    -      -       -      +
    339D  TRP*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 339 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215D  TYR      3.7     1.0    -      -       -      +
    216D  VAL*     3.7     1.7    -      -       -      +
    217D  LYS*     2.9    69.8    +      -       +      +
    219D  GLU*     4.2    17.3    -      -       +      +
    262D  LYS*     5.0    21.1    -      -       +      -
    264D  LEU*     3.5    40.2    -      -       +      -
    269D  PHE*     4.8    20.7    -      +       +      -
    316D  GLN*     4.6     4.9    -      -       +      +
    317D  VAL*     3.5    28.7    -      -       +      +
    318D  ARG*     5.8     0.4    -      -       -      +
    337D  LEU*     4.7     9.0    -      -       +      -
    338D  GLU*     1.3    77.2    -      -       -      +
    340D  THR*     1.3    76.4    +      -       -      +
    341D  GLU*     3.1    40.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 340 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214D  GLU*     3.9    26.3    +      -       +      +
    215D  TYR      3.3     6.3    -      -       -      -
    216D  VAL*     3.9    26.2    -      -       +      -
    316D  GLN*     2.8    49.8    +      -       -      +
    318D  ARG*     5.6     9.9    -      -       -      +
    339D  TRP*     1.3    83.4    -      -       -      +
    341D  GLU*     1.3    60.6    +      -       -      +
    342D  PRO*     3.7     0.9    -      -       -      +
    384D  VAL*     5.7     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 341 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213D  VAL      3.7     0.3    -      -       -      +
    214D  GLU*     3.3     1.7    -      -       -      -
    215D  TYR*     2.9    35.1    +      -       +      +
    217D  LYS*     3.3    23.8    -      -       -      -
    264D  LEU*     5.8     2.7    -      -       +      -
    339D  TRP*     3.1    37.9    +      -       +      -
    340D  THR*     1.3    72.9    -      -       -      +
    342D  PRO*     1.3    76.6    -      -       +      +
    343D  LYS*     3.2    34.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 342 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212D  ARG*     4.2    20.0    -      -       +      +
    213D  VAL      3.9     0.4    -      -       -      +
    214D  GLU*     3.7    29.3    -      -       +      +
    316D  GLN*     4.1     9.2    -      -       -      +
    340D  THR      3.7     8.3    -      -       -      +
    341D  GLU*     1.3    93.5    -      -       +      +
    343D  LYS*     1.3    69.1    +      -       -      +
    344D  ASP*     4.3     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 343 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212D  ARG*     3.7     0.6    -      -       -      +
    213D  VAL      2.9    40.6    +      -       -      +
    215D  TYR*     3.6    33.0    -      -       +      -
    217D  LYS*     6.1     2.0    -      -       -      +
    341D  GLU*     3.2    33.6    +      -       -      +
    342D  PRO*     1.3    79.8    -      -       -      +
    344D  ASP*     1.3    65.8    +      -       -      +
    345D  TYR*     3.5    18.9    -      -       +      +
    380D  GLU*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 344 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210D  ARG*     3.8    23.5    +      -       +      -
    211D  VAL      3.9     0.9    -      -       -      -
    212D  ARG*     3.1    51.8    +      -       -      +
    342D  PRO*     5.9     1.3    -      -       -      -
    343D  LYS*     1.3    73.9    -      -       -      +
    345D  TYR*     1.3    67.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 345 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210D  ARG*     3.6     5.7    -      -       -      +
    211D  VAL*     2.9    53.9    +      -       +      +
    213D  VAL*     4.3    13.9    -      -       +      -
    215D  TYR*     3.2    28.2    +      -       -      -
    343D  LYS*     3.5    32.3    -      -       +      +
    344D  ASP*     1.3    77.6    -      -       -      +
    346D  ARG*     1.3    60.0    +      -       -      +
    367D  ILE*     4.8     1.8    -      -       +      -
    377D  VAL*     4.0    39.0    -      -       +      -
    378D  ILE      4.4     8.6    +      -       -      -
    380D  GLU*     3.6    15.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 346 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209D  ARG*     3.3    34.2    +      -       -      +
    210D  ARG*     3.8    23.3    -      -       -      +
    345D  TYR*     1.3    74.8    -      -       -      +
    347D  VAL*     1.3    78.2    +      -       -      +
    348D  GLN*     3.9     9.4    +      -       +      +
    351D  MET*     4.0    10.2    -      -       -      +
    377D  VAL*     4.9     6.4    -      -       -      +
    389D  GLU*     3.7    14.1    +      -       -      -
----------------------------------------------------------
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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