Contacts of the strand formed by residues 43 - 49 (chain H) in PDB entry 5T0G


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 43 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ILE      4.1     0.7    -      -       -      +
     39H  LYS*     4.4     0.2    -      -       -      +
     40H  ALA      3.0    26.3    +      -       -      +
     41H  ALA      3.5     0.6    -      -       -      -
     42H  ASN*     1.3    88.8    -      -       -      +
     44H  VAL*     1.3    65.5    +      -       -      -
     45H  VAL*     4.2     4.7    +      -       -      +
    144H  PRO*     3.6    12.1    -      -       -      -
    184H  LEU*     5.9     2.2    -      -       -      +
    187H  ALA*     5.6     1.2    -      -       -      +
    213H  CYS      3.2    15.7    -      -       -      -
    214H  ASN*     5.1     1.1    -      -       -      -
    215H  GLU      5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 44 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ILE      3.3    11.7    -      -       -      +
     39H  LYS*     3.6    26.0    -      -       +      -
     43H  GLY*     1.3    73.2    -      -       -      -
     45H  VAL*     1.3    65.2    +      -       -      +
     46H  LEU*     3.8    19.5    -      -       +      -
    137H  CYS*     3.6    26.2    -      -       +      -
    138H  GLY      4.4     1.8    -      -       -      +
    144H  PRO*     4.1     3.8    -      -       +      +
    145H  TYR      3.2    29.8    -      -       -      +
    146H  LEU*     3.9     9.6    -      -       +      -
    212H  ILE*     3.6     1.4    -      -       -      +
    213H  CYS*     2.7    41.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 45 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37H  GLY*     3.3     1.6    -      -       -      -
     38H  ILE*     2.8    38.2    +      -       +      +
     43H  GLY      5.0     2.2    -      -       -      +
     44H  VAL*     1.3    78.6    -      -       -      +
     46H  LEU*     1.3    65.3    +      -       -      +
     47H  ALA      4.4     0.2    +      -       -      -
    184H  LEU*     4.0    19.1    -      -       +      +
    187H  ALA*     3.6    30.7    -      -       +      +
    188H  ILE*     3.8    27.8    -      -       +      +
    191H  ALA*     5.0     5.8    -      -       +      +
    210H  VAL*     3.9    10.8    -      -       +      -
    211H  GLY      3.4    10.1    -      -       -      +
    212H  ILE*     3.7    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 46 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  VAL      3.5     4.7    -      -       -      +
     37H  GLY*     3.6    21.3    -      -       -      -
     44H  VAL*     3.8    17.9    -      -       +      +
     45H  VAL*     1.3    75.8    -      -       -      +
     47H  ALA*     1.3    60.4    +      -       -      +
     48H  THR      4.2     0.2    -      -       -      -
     74H  LEU      4.2     3.1    -      -       -      +
     75H  VAL*     3.7    47.3    -      -       +      +
    135H  LEU*     4.2     9.2    -      -       +      +
    137H  CYS*     3.4    29.4    -      -       -      -
    146H  LEU*     3.9    12.8    -      -       +      -
    210H  VAL*     3.4     4.7    -      -       -      +
    211H  GLY*     2.7    47.2    +      -       -      +
    218H  PHE*     6.3     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 47 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  SER*     3.4     4.3    -      -       -      -
     36H  VAL*     2.8    44.5    +      -       +      +
     45H  VAL      4.4     0.2    +      -       -      -
     46H  LEU*     1.3    74.0    -      -       -      +
     48H  THR*     1.3    61.9    +      -       -      +
    191H  ALA*     4.0    33.0    -      -       +      +
    192H  ILE*     5.2     2.7    -      -       +      +
    195H  LEU*     5.2     8.5    -      -       +      +
    208H  ILE*     6.1     1.3    -      -       +      -
    209H  GLU      3.5     7.6    -      -       -      +
    210H  VAL*     4.5    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 48 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  ALA*     6.0     0.2    -      -       -      +
     34H  PRO      4.1     3.9    +      -       -      -
     35H  SER*     4.0    16.8    +      -       -      -
     46H  LEU      4.2     0.4    -      -       -      -
     47H  ALA*     1.3    76.8    -      -       -      +
     49H  GLU*     1.3    75.0    +      -       -      +
     50H  LYS*     5.3     1.1    -      -       +      +
     64H  LYS*     4.1    22.8    +      -       +      +
     65H  VAL*     4.1    16.6    -      -       +      +
     75H  VAL*     4.7    12.0    -      -       -      +
     76H  TYR*     4.9     5.0    +      -       -      -
    195H  LEU*     5.5     2.5    -      -       -      +
    208H  ILE*     3.2    23.0    -      -       -      +
    209H  GLU*     3.0    33.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33H  ALA*     3.3    28.6    -      -       -      +
     34H  PRO*     3.3    32.2    +      -       +      +
     48H  THR*     1.3    87.2    +      -       -      +
     50H  LYS*     1.3    63.8    +      -       -      +
     51H  LYS*     3.2    36.6    +      -       +      +
     64H  LYS*     3.7    10.4    +      -       -      -
    195H  LEU*     6.0     3.6    -      -       +      -
    199H  PHE*     5.7     7.6    -      -       +      -
    207H  ASN      3.7     8.3    -      -       -      +
    208H  ILE*     3.6    14.8    -      -       +      +
----------------------------------------------------------
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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