Contacts of the strand formed by residues 47 - 56 (chain A) in PDB entry 5UHE


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 PRO 47 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  SER      3.8     6.7    -      -       -      +
     46A  ILE*     1.3    94.4    -      -       +      +
     48A  GLY*     1.3    58.8    +      -       -      +
    142A  ARG*     4.1    16.8    +      -       -      +
    143A  GLY      3.5    11.2    -      -       -      +
    144A  ARG*     4.0    10.3    -      -       +      -
    170A  PRO*     3.6    12.5    -      -       -      +
    202A  ILE*     4.9     5.5    -      -       -      +
    210A  SER*     3.5    25.6    -      -       -      +
    228B  GLU*     5.1     8.4    -      -       -      +
    229B  ALA*     4.2    22.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  ILE      3.9     0.4    +      -       -      -
     47A  PRO*     1.3    76.1    -      -       -      +
     49A  ALA*     1.3    60.7    +      -       -      -
    142A  ARG*     3.3    17.7    -      -       -      +
    143A  GLY      2.8    33.5    +      -       -      +
    168A  TYR*     3.9    14.1    +      -       -      -
    170A  PRO*     4.7     5.6    -      -       -      -
    201A  SER*     6.0     1.3    -      -       -      -
    202A  ILE*     6.2     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  GLY*     1.3    75.1    -      -       -      +
     50A  ALA*     1.3    63.3    +      -       -      +
     85A  VAL*     3.0    26.8    +      -       -      +
     86A  SER*     4.4     1.6    -      -       -      +
     87A  SER*     3.6    37.9    -      -       -      +
    140A  VAL*     4.1     4.9    -      -       +      -
    141A  GLU      3.1    20.0    -      -       -      +
    142A  ARG*     4.3     4.3    -      -       +      +
    167A  ILE      5.1     0.3    -      -       -      +
    168A  TYR*     4.0    10.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  ALA*     1.3    78.0    -      -       -      +
     51A  VAL*     1.3    68.4    +      -       -      +
     52A  THR*     3.7     3.2    +      -       -      +
     83A  LEU      5.5     6.1    -      -       -      +
     85A  VAL*     4.6     8.5    -      -       -      +
    140A  VAL*     3.3     9.5    -      -       -      +
    141A  GLU      3.3    25.4    +      -       -      +
    166A  SER*     4.7     0.9    -      -       -      -
    167A  ILE      4.2    31.0    -      -       -      +
    168A  TYR*     4.0    10.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ALA*     1.3    77.3    -      -       -      +
     52A  THR*     1.3    64.1    +      -       -      +
     53A  SER      3.6    16.6    -      -       -      +
     54A  ILE*     3.6    19.3    -      -       +      -
     80A  LEU*     4.7    12.3    -      -       +      +
     83A  LEU*     3.8    30.7    +      -       +      +
     85A  VAL*     4.8     3.4    -      -       +      -
    138A  LEU*     4.0    14.1    -      -       +      -
    139A  VAL      3.3    15.0    -      -       -      +
    140A  VAL*     4.4    10.1    -      -       +      -
    164A  VAL*     4.1     9.4    -      -       +      +
    165A  ASP      4.0     9.2    -      -       -      +
    166A  SER*     3.3    16.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ALA      4.0     2.5    -      -       -      +
     51A  VAL*     1.3    77.2    -      -       -      +
     53A  SER*     1.3    69.0    +      -       -      +
    139A  VAL*     3.1    18.3    +      -       -      +
    141A  GLU*     3.6    52.4    +      -       +      +
    152A  ASN*     4.6    11.5    +      -       -      +
    163A  PRO*     3.6     1.0    -      -       -      +
    164A  VAL*     2.6    40.4    +      -       -      +
    166A  SER*     3.8     8.3    -      -       -      +
    168A  TYR*     3.9    15.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  VAL*     3.6     1.9    -      -       -      +
     52A  THR*     1.3    86.4    +      -       -      +
     54A  ILE*     1.3    72.7    +      -       -      +
    139A  VAL*     3.0    38.5    +      -       -      +
    152A  ASN*     4.2    17.1    +      -       -      -
    161A  ARG*     4.5    15.4    -      -       -      +
    162A  ILE      3.7    15.3    -      -       -      -
    163A  PRO*     4.0     9.9    -      -       -      -
    164A  VAL*     4.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  VAL*     3.6    19.7    -      -       +      -
     53A  SER*     1.3    81.3    +      -       -      +
     55A  ARG*     1.3    68.5    +      -       -      +
     56A  ILE*     4.2    24.0    -      -       +      -
     76A  ILE*     5.5     0.4    -      -       +      -
     77A  ILE*     4.1    22.9    -      -       +      -
     80A  LEU*     4.0    21.3    -      -       +      -
    136A  VAL*     4.5     4.5    -      -       +      -
    137A  GLU*     3.2    11.9    -      -       -      +
    138A  LEU*     3.6    20.4    -      -       +      -
    139A  VAL*     5.8     0.4    -      -       -      -
    161A  ARG*     3.6     4.0    -      -       -      +
    162A  ILE*     3.0    41.7    +      -       +      +
    164A  VAL*     4.3     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  ILE*     1.3    82.1    -      -       -      +
     56A  ILE*     1.3    65.5    +      -       -      +
     59A  VAL      5.6     0.4    -      -       -      +
    135A  GLU      3.9     0.3    -      -       -      +
    136A  VAL*     3.3     7.1    -      -       -      +
    137A  GLU*     3.0    59.5    +      -       +      +
    158A  GLU*     5.4     7.1    -      -       -      +
    160A  GLY*     3.2    34.0    -      -       -      +
    161A  ARG*     3.6    33.0    -      -       -      +
    162A  ILE*     5.1     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  ILE*     4.2    16.6    -      -       +      -
     55A  ARG*     1.3    84.0    -      -       -      +
     57A  ASP*     1.3    71.0    +      -       +      +
     58A  GLY      3.2     0.7    +      -       -      -
     59A  VAL*     2.9    46.8    +      -       +      +
     66A  VAL*     4.1     4.5    -      -       +      -
     73A  VAL*     4.1    31.0    -      -       +      -
     76A  ILE*     4.6    16.2    -      -       +      -
    134A  LEU*     3.7    28.3    -      -       +      -
    135A  GLU      3.5     7.2    -      -       -      +
    136A  VAL*     3.7    16.8    -      -       +      -
    162A  ILE*     5.2     4.6    -      -       +      +
----------------------------------------------------------
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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