Contacts of the strand formed by residues 147 - 151 (chain Q) in PDB entry 3SDI


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 147 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41Q  LYS*     4.4     5.2    -      -       -      +
     46Q  VAL*     3.5     9.4    -      -       -      +
    109Q  VAL*     3.9    27.4    -      -       +      -
    110Q  GLU*     5.9     1.6    -      -       +      +
    138Q  ILE      4.6     0.7    -      -       -      -
    139Q  ALA*     3.5     4.5    -      -       -      -
    140Q  GLY      3.2    37.2    +      -       -      +
    142Q  ASP*     3.5    29.8    +      -       -      +
    144Q  ASP*     4.5     5.0    +      -       -      -
    145Q  GLU*     3.4    43.3    +      -       -      +
    146Q  PRO*     1.3    79.5    -      -       -      +
    148Q  LEU*     1.3    62.1    +      -       -      +
    149Q  TYR*     4.5    17.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 148 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39Q  GLY*     3.4    28.9    -      -       -      +
     40Q  VAL*     4.4     3.6    -      -       -      +
     41Q  LYS*     4.2    11.0    -      -       +      +
     46Q  VAL*     4.1     6.5    -      -       +      -
     48Q  LEU*     3.9    17.0    -      -       +      -
    137Q  LEU*     4.3    20.2    -      -       +      -
    138Q  ILE      3.6     6.3    -      -       -      +
    139Q  ALA*     3.8    22.4    -      -       +      -
    147Q  LYS*     1.3    75.4    -      -       -      +
    149Q  TYR*     1.3    65.5    +      -       -      +
    159Q  SER*     3.1    10.9    -      -       -      -
    160Q  TRP*     3.0    51.9    +      -       +      +
    161Q  SER      4.3     2.9    -      -       -      +
    162Q  ALA*     4.0     9.2    -      -       -      -
    163Q  GLN      4.2     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 149 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109Q  VAL*     4.3    11.0    -      -       +      -
    110Q  GLU*     3.3    44.6    -      -       +      +
    113Q  THR*     3.4    39.7    -      -       +      +
    136Q  THR      3.7     0.3    -      -       -      +
    137Q  LEU*     3.3     9.6    -      -       -      +
    138Q  ILE*     2.9    36.0    +      -       +      +
    147Q  LYS*     4.5    21.8    -      -       +      +
    148Q  LEU*     1.3    80.8    -      -       -      +
    150Q  GLN*     1.3    59.9    +      -       -      +
    157Q  TYR*     4.2     9.0    -      +       -      -
    158Q  SER*     3.2    25.8    -      -       -      -
    159Q  SER*     3.5    25.1    +      -       -      +
    160Q  TRP*     4.7     1.6    -      -       -      -
     63R  SER*     4.9     7.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 150 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135Q  SER*     4.6     1.6    +      -       -      -
    136Q  THR      3.2     9.2    -      -       -      +
    137Q  LEU*     4.4     6.3    -      -       +      -
    149Q  TYR*     1.3    75.5    -      -       -      +
    151Q  THR*     1.3    71.6    +      -       -      +
    152Q  GLU*     3.3    25.5    +      -       -      +
    156Q  ILE      3.9     0.2    -      -       -      +
    157Q  TYR*     3.1    25.6    -      -       -      +
    158Q  SER*     2.9    13.0    +      -       -      -
    160Q  TRP*     2.9    37.4    -      -       +      +
    163Q  GLN*     3.1    23.2    +      -       +      +
    165Q  ILE*     3.8    26.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 151 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113Q  THR*     3.8    28.7    -      -       +      +
    116Q  VAL*     4.1     1.4    -      -       +      +
    117Q  ALA*     4.1    15.0    -      -       +      +
    120Q  GLN*     2.8    24.2    +      -       -      -
    135Q  SER*     3.2     8.7    +      -       -      -
    136Q  THR*     2.5    55.0    +      -       -      +
    138Q  ILE*     4.2     7.0    -      -       +      -
    150Q  GLN*     1.3    82.9    -      -       -      +
    152Q  GLU*     1.3    62.5    +      -       -      +
    156Q  ILE      3.4     8.5    -      -       -      -
    157Q  TYR*     3.9     5.6    -      -       +      -
----------------------------------------------------------
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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