Contacts of the strand formed by residues 330 - 346 (chain N) in PDB entry 5D4D


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 N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224N  ARG*     3.2    32.7    +      -       +      -
    225N  LEU      3.2    16.6    -      -       -      +
    226N  PRO*     4.0     9.2    -      -       +      -
    227N  LEU*     3.8     5.8    -      -       -      +
    249N  TYR*     5.3     5.8    -      -       +      +
    326N  GLU*     3.8     5.9    -      -       -      +
    327N  GLU*     2.8    40.8    +      -       -      +
    328N  GLY      3.2     0.6    -      -       -      +
    329N  GLU*     1.3    89.9    -      -       +      +
    331N  VAL*     1.3    62.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 331 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223N  LEU      4.0     0.2    -      -       -      +
    224N  ARG*     3.7     5.0    -      -       -      -
    225N  LEU*     2.9    43.5    +      -       +      +
    226N  PRO      4.2     1.6    -      -       -      +
    227N  LEU*     3.7    25.6    -      -       +      -
    230N  TRP*     3.9    31.6    -      -       +      -
    324N  ALA*     3.8    18.8    -      -       +      -
    325N  GLU      3.4    13.5    -      -       -      +
    326N  GLU*     4.6     4.3    -      -       +      +
    330N  THR*     1.3    75.6    -      -       -      +
    332N  TYR*     1.3    63.2    +      -       -      +
    333N  LEU*     3.7    23.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 332 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222N  GLY*     3.6    20.2    +      -       -      -
    223N  LEU*     3.5    23.8    -      -       -      -
    224N  ARG*     3.7    23.0    -      -       +      +
    251N  PHE*     5.4     0.4    -      +       -      -
    254N  GLU*     3.6    34.4    +      -       -      -
    281N  THR      4.7     1.7    +      -       -      -
    282N  TYR*     4.1    18.8    -      +       -      -
    324N  ALA*     3.6     2.3    -      -       -      -
    325N  GLU*     2.9    51.4    +      -       +      +
    331N  VAL*     1.3    72.1    -      -       -      +
    333N  LEU*     1.3    64.2    +      -       -      +
    334N  THR*     3.7    23.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 333 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222N  GLY*     3.2     4.7    -      -       -      -
    223N  LEU*     2.8    46.9    +      -       +      +
    225N  LEU*     3.6    24.9    -      -       +      -
    230N  TRP*     3.4    49.6    -      -       +      +
    242N  LEU*     4.0    16.8    -      -       +      -
    322N  VAL*     4.4     4.0    -      -       +      -
    323N  GLU      3.4     4.7    -      -       -      +
    324N  ALA*     4.0     5.2    -      -       +      -
    331N  VAL*     3.7    22.7    -      -       +      +
    332N  TYR*     1.3    72.5    -      -       -      +
    334N  THR*     1.3    61.4    +      -       -      +
    335N  LEU*     3.7    22.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 334 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220N  ARG*     3.4    48.9    +      -       +      +
    221N  ALA      4.1     4.5    -      -       -      +
    222N  GLY*     4.4     2.6    -      -       -      -
    321N  GLN      3.9     0.7    -      -       -      +
    322N  VAL*     3.7     1.9    -      -       -      -
    323N  GLU*     2.9    56.5    +      -       -      +
    332N  TYR*     3.7    21.2    +      -       -      -
    333N  LEU*     1.3    70.2    -      -       -      +
    335N  LEU*     1.3    63.1    +      -       -      +
    336N  PHE*     4.0     3.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 335 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220N  ARG*     3.6     4.3    -      -       -      +
    221N  ALA      2.9    42.9    +      -       -      +
    223N  LEU*     5.0    12.1    -      -       +      -
    236N  TYR*     5.0     4.7    -      -       +      -
    242N  LEU*     5.4     5.2    -      -       +      -
    283N  PHE*     3.7    35.0    -      -       +      -
    313N  MET*     5.3     5.4    -      -       -      -
    319N  ALA*     4.7     4.3    -      -       +      -
    321N  GLN      3.7     2.9    -      -       -      +
    322N  VAL*     3.7    36.1    -      -       +      -
    333N  LEU*     3.8    24.0    -      -       +      +
    334N  THR*     1.3    72.5    -      -       -      +
    336N  PHE*     1.3    62.5    +      -       -      +
    337N  LEU*     3.6    21.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 336 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219N  GLU      4.0     3.4    -      -       -      -
    220N  ARG*     3.7    39.3    -      -       +      -
    319N  ALA*     3.3     3.7    -      -       -      -
    320N  ALA*     3.0    31.7    +      -       +      +
    321N  GLN*     2.9    52.1    +      -       +      +
    323N  GLU*     3.8    33.7    -      -       +      -
    334N  THR*     4.6     4.9    -      -       +      -
    335N  LEU*     1.3    71.3    -      -       -      +
    337N  LEU*     1.3    61.9    +      -       -      +
    338N  GLU*     5.2     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 337 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218N  LYS*     3.1     4.3    -      -       -      +
    219N  GLU      2.9    38.7    +      -       -      +
    221N  ALA*     4.1    11.0    -      -       +      -
    269N  PHE*     3.6    13.2    -      -       +      -
    283N  PHE*     3.5    41.5    -      -       +      -
    313N  MET*     3.9     7.2    -      -       +      -
    317N  VAL*     3.7    22.9    -      -       +      -
    318N  ARG      3.5     1.1    -      -       -      +
    319N  ALA*     3.8    24.5    -      -       +      -
    335N  LEU*     3.9    18.6    -      -       +      +
    336N  PHE*     1.3    73.9    -      -       -      +
    338N  GLU*     1.3    62.7    +      -       -      +
    339N  TRP*     3.7    14.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 338 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217N  LYS      3.6     4.3    -      -       -      -
    218N  LYS*     3.6    42.3    +      -       +      +
    316N  GLN      4.2     0.3    -      -       -      +
    317N  VAL*     3.1     3.5    -      -       -      +
    318N  ARG*     2.8    61.6    +      -       +      +
    320N  ALA*     3.9    22.6    -      -       +      +
    336N  PHE      4.8     4.5    -      -       -      +
    337N  LEU*     1.3    79.0    -      -       -      +
    339N  TRP*     1.3    61.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 339 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216N  VAL*     3.7     2.9    -      -       -      +
    217N  LYS*     2.9    70.8    +      -       +      +
    218N  LYS*     5.0     0.2    -      -       -      +
    219N  GLU*     3.4    30.7    -      -       +      -
    262N  LYS*     6.1     1.8    -      -       +      -
    264N  LEU*     4.2    13.0    -      -       +      +
    269N  PHE*     3.4    46.7    -      +       -      -
    316N  GLN*     3.7    11.0    -      -       +      +
    317N  VAL*     3.5    23.8    -      -       +      -
    337N  LEU*     3.7    21.5    -      -       +      -
    338N  GLU*     1.3    81.9    -      -       -      +
    340N  THR*     1.3    72.3    +      -       -      +
    341N  GLU*     3.4    37.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 340 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214N  GLU*     3.5    27.4    +      -       +      +
    215N  TYR      3.0    18.4    -      -       -      +
    216N  VAL*     4.2    12.6    -      -       +      -
    316N  GLN*     3.0    51.2    +      -       -      +
    339N  TRP*     1.3    87.0    -      -       -      +
    341N  GLU*     1.3    59.8    +      -       -      +
    342N  PRO*     3.6     2.3    -      -       -      +
    384N  VAL*     5.7     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 341 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213N  VAL      3.4     1.9    -      -       -      +
    214N  GLU*     3.6     2.2    -      -       -      -
    215N  TYR*     2.9    38.9    +      -       +      +
    217N  LYS*     3.6    20.5    -      -       +      +
    262N  LYS*     3.1    42.9    +      -       -      +
    264N  LEU*     3.9    16.7    -      -       +      +
    339N  TRP*     3.4    31.3    +      -       +      +
    340N  THR*     1.3    71.9    -      -       -      +
    342N  PRO*     1.3    70.9    -      -       +      +
    343N  LYS*     5.0     1.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 342 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212N  ARG*     3.4    29.2    -      -       -      +
    213N  VAL      3.5     4.9    -      -       -      +
    214N  GLU*     3.2    26.2    -      -       -      +
    316N  GLN*     4.8     5.8    -      -       +      +
    340N  THR      3.6     5.2    -      -       -      +
    341N  GLU*     1.3    88.5    -      -       +      +
    343N  LYS*     1.3    66.4    +      -       -      +
    344N  ASP*     5.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 343 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212N  ARG*     3.5     0.6    -      -       -      +
    213N  VAL      2.9    30.9    +      -       -      +
    215N  TYR*     3.9    26.7    -      -       +      -
    341N  GLU*     5.0     1.1    -      -       +      +
    342N  PRO*     1.3    78.5    -      -       -      +
    344N  ASP*     1.3    80.6    +      -       -      +
    345N  TYR*     3.4    33.9    +      -       +      -
    380N  GLU*     4.0    19.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 344 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210N  ARG*     3.8    23.7    +      -       +      +
    211N  VAL      3.5     2.7    -      -       -      -
    212N  ARG*     3.4    51.8    +      -       -      +
    343N  LYS*     1.3    83.5    -      -       -      +
    345N  TYR*     1.3    68.7    +      -       -      +
    346N  ARG      4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 345 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210N  ARG*     3.6     3.5    -      -       -      -
    211N  VAL*     2.9    44.4    +      -       +      +
    213N  VAL*     3.5    22.4    -      -       +      -
    215N  TYR*     2.7    30.7    +      -       -      -
    343N  LYS*     3.4    46.7    +      -       +      -
    344N  ASP*     1.3    78.1    -      -       -      +
    346N  ARG*     1.3    63.5    +      -       -      +
    347N  VAL*     3.6     3.7    +      -       -      +
    368N  VAL*     5.6     1.1    -      -       +      -
    377N  VAL*     3.4    45.8    -      -       +      -
    378N  ILE      4.5     6.5    +      -       -      -
    380N  GLU*     4.4     6.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 346 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174N  GLY*     5.6     2.6    -      -       -      -
    209N  ARG*     3.2    17.9    +      -       -      +
    210N  ARG*     3.9    15.1    -      -       -      +
    344N  ASP      4.3     0.4    -      -       -      -
    345N  TYR*     1.3    73.3    -      -       -      +
    347N  VAL*     1.3    63.5    +      -       -      +
    348N  GLN*     3.8    25.8    +      -       -      +
    351N  MET*     4.4    10.9    -      -       -      +
    377N  VAL*     5.1     4.2    -      -       -      +
    389N  GLU*     2.8    36.5    +      -       -      -
----------------------------------------------------------
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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