Contacts of the strand formed by residues 340 - 349 (chain A) in PDB entry 5EMV


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 340 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  HIS*     5.3     3.3    +      -       -      -
    339A  MET*     1.3    78.1    +      -       -      +
    341A  LEU*     1.3    62.2    +      -       -      +
    360A  THR*     3.7    25.4    -      -       +      -
    361A  GLU      3.8     9.4    -      -       -      +
    362A  ARG*     4.2    12.8    -      -       +      +
    414A  ASN*     3.9     5.5    +      -       -      +
    415A  ARG*     3.0    69.7    +      -       +      +
    416A  ASP*     4.7    10.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  LEU*     4.1    12.3    -      -       +      -
    333A  TYR*     4.2    11.7    -      -       +      -
    339A  MET*     4.3    10.1    -      -       +      -
    340A  THR*     1.3    77.7    -      -       -      +
    342A  THR*     1.3    60.0    +      -       -      +
    343A  CYS*     3.9    14.4    -      -       -      -
    359A  GLU      3.8     0.2    -      -       -      +
    360A  THR*     3.3    10.6    -      -       -      +
    361A  GLU*     3.0    34.4    +      -       +      +
    372A  TYR*     3.5    47.3    -      -       +      -
    374A  LEU*     5.4     0.9    -      -       +      -
    412A  VAL*     4.1    17.7    -      -       +      -
    413A  THR      3.6     1.8    -      -       -      +
    421A  LEU*     3.6    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  THR      3.9     0.4    +      -       -      -
    341A  LEU*     1.3    70.8    +      -       -      +
    343A  CYS*     1.3    64.5    +      -       -      +
    344A  SER*     5.0     4.0    -      -       -      +
    358A  VAL*     3.9    23.8    -      -       +      -
    359A  GLU      3.6     3.8    -      -       -      +
    360A  THR*     4.6     5.7    +      -       -      +
    411A  VAL      3.5     2.6    -      -       -      +
    412A  VAL*     3.4     3.5    -      -       -      -
    413A  THR*     2.9    51.7    +      -       -      +
    415A  ARG*     3.2    30.5    -      -       -      +
    418A  GLN*     5.3     1.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333A  TYR*     4.4    15.7    -      -       -      +
    341A  LEU*     4.2    14.1    -      -       -      -
    342A  THR*     1.3    75.0    -      -       -      +
    344A  SER*     1.3    60.4    +      -       -      +
    345A  SER*     4.1     4.1    +      -       -      +
    357A  LYS      3.6     1.9    -      -       -      +
    358A  VAL*     3.3     4.7    -      -       -      -
    359A  GLU*     2.9    44.0    +      -       +      +
    361A  GLU*     5.7     0.4    -      -       -      -
    374A  LEU*     4.0    28.3    -      -       +      -
    410A  GLN*     6.2     1.8    -      -       -      +
    411A  VAL      3.6     3.8    -      -       -      -
    412A  VAL*     4.1    26.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  THR*     3.9     4.6    +      -       -      -
    343A  CYS*     1.3    73.4    -      -       -      +
    345A  SER*     1.3    63.0    +      -       -      +
    346A  LYS*     3.9    13.6    +      -       -      +
    356A  GLU*     2.8    29.6    +      -       -      +
    357A  LYS      3.4     4.3    -      -       -      -
    358A  VAL*     4.4     9.2    -      -       -      +
    409A  LEU      3.6     1.0    -      -       -      +
    410A  GLN*     3.2     4.9    -      -       -      +
    411A  VAL*     2.8    53.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  CYS*     4.1     3.5    +      -       -      +
    344A  SER*     1.3    73.6    +      -       -      +
    346A  LYS*     1.3    62.4    +      -       -      +
    347A  VAL*     3.9     2.5    +      -       -      +
    355A  VAL*     3.7     1.6    -      -       -      +
    356A  GLU*     3.4     1.7    -      -       -      -
    357A  LYS*     2.8    43.0    +      -       -      +
    380A  P1L      3.8    28.0    -      -       -      +
    408A  ILE*     4.9     2.2    -      -       -      -
    409A  LEU      3.5     4.5    -      -       -      -
    410A  GLN*     3.2    30.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  PRO*     5.5     5.6    -      -       +      -
    283A  GLY*     4.3    26.2    +      -       -      +
    288A  LEU*     5.7     1.0    -      -       -      +
    344A  SER*     3.9    15.1    +      -       -      +
    345A  SER*     1.3    73.3    -      -       -      +
    347A  VAL*     1.3    63.3    +      -       -      +
    348A  CYS*     3.7    14.3    +      -       -      -
    353A  GLN*     3.3    32.3    -      -       +      +
    355A  VAL      3.2     6.5    -      -       -      +
    356A  GLU*     3.9    23.3    +      -       +      -
    408A  ILE*     3.4     3.9    -      -       -      -
    409A  LEU*     2.8    51.4    +      -       +      +
    411A  VAL*     4.8    14.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  SER      5.1     1.3    -      -       -      +
    346A  LYS*     1.3    73.8    -      -       -      +
    348A  CYS*     1.3    61.6    +      -       -      +
    353A  GLN*     3.6     2.8    -      -       -      -
    354A  VAL*     2.9    40.5    +      -       +      +
    355A  VAL*     2.7    29.9    +      -       +      +
    380A  P1L      4.3    27.1    -      -       +      -
    382A  TYR*     4.2     7.4    -      -       +      -
    383A  LEU*     4.3    10.8    -      -       +      -
    406A  PHE*     3.6    31.4    -      -       +      -
    407A  THR      3.7     3.6    -      -       -      +
    408A  ILE*     4.1    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277A  LYS      4.1     5.8    -      -       -      +
    278A  PHE*     4.1    12.1    -      -       -      -
    279A  PRO*     3.7    29.6    -      -       -      -
    346A  LYS*     3.9    18.8    -      -       -      -
    347A  VAL*     1.3    79.4    -      -       -      +
    349A  SER*     1.3    61.4    +      -       -      +
    350A  PHE      4.2     0.2    -      -       -      -
    351A  GLY      4.4     0.7    -      -       -      -
    352A  LYS      3.2    11.9    -      -       -      +
    353A  GLN*     4.1     9.4    -      -       -      -
    354A  VAL*     4.7     2.0    -      -       -      -
    405A  ASN      4.2     0.4    -      -       -      -
    406A  PHE*     3.5     8.0    -      -       -      -
    407A  THR*     2.7    49.4    +      -       -      +
    409A  LEU*     5.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  CYS*     1.3    74.3    -      -       -      +
    350A  PHE*     1.3    90.2    +      -       -      +
    351A  GLY      3.1     0.2    -      -       -      -
    352A  LYS*     2.9    22.8    +      -       -      +
    354A  VAL*     3.9    20.7    -      -       -      +
    382A  TYR*     4.0    15.7    +      -       -      -
    405A  ASN      3.3     5.8    +      -       -      -
    406A  PHE*     4.8     4.0    -      -       -      +
----------------------------------------------------------
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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