Contacts of the strand formed by residues 352 - 362 (chain B) in PDB entry 5DQE


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 LYS 352 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279B  PRO*     5.2     0.2    -      -       -      -
    280B  GLU      5.9     0.4    -      -       -      +
    348B  CYS*     4.0     1.6    -      -       -      -
    349B  SER      2.8    34.3    +      -       -      +
    350B  PHE*     4.0    13.5    +      -       +      +
    351B  GLY*     1.3    82.7    -      -       -      +
    353B  GLN*     1.3    70.2    +      -       -      +
    354B  VAL*     3.4     6.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 353 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  VAL      5.4     0.4    +      -       -      -
    381A  GLU      5.2     0.2    -      -       -      -
    382A  TYR*     3.7    42.7    +      -       +      +
    385A  ASN*     5.4     2.4    +      -       -      -
    279B  PRO*     4.0    22.1    -      -       +      +
    280B  GLU      6.0     0.4    -      -       -      +
    282B  LYS      5.1     4.5    -      -       -      +
    346B  LYS*     3.7    25.4    -      -       +      +
    347B  VAL      3.5     8.1    -      -       -      +
    348B  CYS*     3.9     5.5    -      -       -      -
    351B  GLY      4.0     2.2    +      -       -      -
    352B  LYS*     1.3    77.7    -      -       -      +
    354B  VAL*     1.3    63.3    +      -       -      +
    355B  VAL      4.0    11.1    +      -       -      +
    356B  GLU*     2.9    43.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 354 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  VAL*     3.6    24.4    -      -       -      +
    382A  TYR*     5.7     2.9    -      -       -      -
    347B  VAL*     2.9    32.6    +      -       +      +
    349B  SER*     3.7    22.9    -      -       -      +
    352B  LYS*     3.4    19.7    -      -       +      +
    353B  GLN*     1.3    76.8    -      -       -      +
    355B  VAL*     1.3    77.4    +      -       +      +
    382B  TYR*     4.8    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 355 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  GLN*     4.1    20.0    -      -       -      +
    354A  VAL      3.3     9.0    -      -       -      +
    355A  VAL      6.2     0.2    -      -       -      -
    346B  LYS*     3.4     3.8    -      -       -      -
    347B  VAL*     3.0    36.5    +      -       +      +
    353B  GLN*     3.8     6.4    -      -       -      +
    354B  VAL*     1.3    96.5    -      -       +      +
    356B  GLU*     1.3    74.4    +      -       -      +
    357B  LYS*     5.4     0.9    -      -       +      -
    380B  CYS*     4.6    13.0    -      -       -      -
    382B  TYR*     4.9    22.2    -      -       +      -
    501B  5E4      4.2    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 356 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  VAL      2.8    12.5    +      -       -      +
    355A  VAL*     3.3    11.4    -      -       +      +
    356A  GLU      2.9    25.1    +      -       -      +
    380A  CYS*     3.9     7.9    -      -       -      +
    381A  GLU*     3.1    19.8    +      -       -      +
    382A  TYR*     3.7    18.9    +      -       -      +
    344B  SER*     3.0    23.7    +      -       -      +
    345B  SER      3.3    10.3    -      -       -      +
    346B  LYS*     3.7    11.2    -      -       +      -
    353B  GLN*     2.9    27.5    +      -       -      +
    355B  VAL*     1.3    78.0    -      -       -      +
    357B  LYS*     1.3    62.1    +      -       -      +
    358B  VAL*     3.6    18.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 357 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  GLU*     3.3    30.9    +      -       +      +
    358A  VAL*     6.0     2.9    -      -       +      -
    343B  CYS      3.5     1.9    -      -       -      +
    344B  SER*     3.3     2.3    -      -       -      -
    345B  SER*     2.8    42.1    +      -       -      +
    355B  VAL*     5.4     1.1    -      -       +      -
    356B  GLU*     1.3    74.0    -      -       -      +
    358B  VAL*     1.3    63.5    +      -       -      +
    359B  GLU*     3.5    45.8    -      -       +      +
    377B  SER*     4.4     9.8    -      -       -      -
    378B  PRO*     3.5    18.9    +      -       -      +
    380B  CYS*     4.9     0.6    -      -       -      +
    501B  5E4      2.8    47.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 358 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  VAL*     5.2     2.0    -      -       +      -
    356A  GLU      2.7    15.0    +      -       -      +
    357A  LYS*     3.3    25.5    -      -       +      -
    358A  VAL*     2.7    33.6    +      -       -      +
    359A  GLU*     6.4     0.2    -      -       +      -
    380A  CYS*     4.7    11.4    -      -       +      -
    342B  THR*     3.7    27.1    -      -       +      -
    343B  CYS      3.4     4.7    -      -       -      +
    344B  SER*     4.2     6.3    -      -       -      -
    356B  GLU*     3.6    31.2    -      -       +      +
    357B  LYS*     1.3    80.5    -      -       -      +
    359B  GLU*     1.3    62.3    +      -       -      +
    360B  THR*     5.7     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 359 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  VAL*     3.8    14.4    -      -       +      +
    342B  THR*     3.4     3.9    -      -       -      +
    343B  CYS*     2.8    43.4    +      -       -      +
    345B  SER*     5.2     5.2    +      -       -      -
    357B  LYS*     3.5    34.9    -      -       +      +
    358B  VAL*     1.3    76.6    -      -       -      +
    360B  THR*     1.3    66.8    +      -       -      +
    374B  LEU*     4.2    28.8    -      -       +      +
    377B  SER*     3.0    25.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 360 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  VAL      3.5    17.1    +      -       -      +
    359A  GLU*     3.8    33.2    -      -       +      +
    360A  THR*     4.2    10.9    +      -       -      -
    340B  THR*     4.5     9.6    -      -       -      -
    341B  LEU      3.0     6.7    -      -       -      -
    342B  THR*     3.8    22.0    -      -       +      +
    358B  VAL*     5.7     2.0    -      -       +      -
    359B  GLU*     1.3    82.8    -      -       -      +
    361B  GLU*     1.3    68.9    +      -       -      +
    374B  LEU*     5.2     0.7    -      -       -      +
    415B  ARG*     4.2    10.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 361 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340B  THR*     3.7     3.3    -      -       -      -
    341B  LEU*     2.9    35.5    +      -       +      +
    343B  CYS*     5.5     0.6    -      -       -      -
    360B  THR*     1.3    80.3    -      -       -      +
    362B  ARG*     1.3    77.4    +      -       -      +
    364B  GLN*     3.9    12.1    -      -       -      +
    372B  TYR*     3.6    15.5    -      -       +      -
    373B  ARG      3.1    42.6    +      -       -      +
    374B  LEU*     4.0    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 362 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338B  HIS*     3.6    33.1    +      -       +      -
    339B  MET      4.1     2.7    -      -       -      -
    340B  THR*     3.9    23.8    +      -       +      +
    361B  GLU*     1.3    95.4    -      -       -      +
    363B  ALA*     1.3    73.1    +      -       -      +
    364B  GLN*     3.8     4.7    +      -       -      +
    371B  VAL      4.5     1.2    -      -       -      +
    372B  TYR*     4.0     1.9    -      -       -      -
----------------------------------------------------------
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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