Contacts of the strand formed by residues 49 - 54 (chain N) in PDB entry 5A0Q


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 49 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44N  ARG      3.9     0.7    -      -       -      -
     45N  VAL*     3.0    35.4    +      -       -      +
     46N  ASN*     3.1    20.7    +      -       +      +
     48N  SER*     1.3    87.1    -      -       -      +
     50N  MET*     1.3    65.1    +      -       -      +
     84N  SER*     5.0     3.8    -      -       -      +
     85N  PRO*     4.2    28.3    -      -       +      +
     88N  ILE*     5.2     4.2    -      -       -      +
    112N  ILE*     5.3     4.0    -      -       -      +
    113N  GLY      3.4     8.3    -      -       -      -
    114N  GLY*     3.7    20.4    -      -       -      -
    115N  TYR      4.6     1.8    -      -       -      +
    197N  VAL*     4.0     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 50 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20N  VAL*     3.2    13.0    -      -       +      +
     22N  ILE*     3.8    25.5    -      -       +      +
     42N  ILE*     4.3     4.5    -      -       +      -
     43N  MET      3.1    17.0    -      -       -      +
     44N  ARG*     4.1     7.4    -      -       +      -
     45N  VAL*     3.8     6.9    -      -       -      +
     48N  SER      3.9     2.7    -      -       -      +
     49N  THR*     1.3    80.4    +      -       -      +
     51N  LEU*     1.4    65.6    +      -       -      +
    112N  ILE*     3.4     5.8    -      -       -      +
    113N  GLY      3.0    33.4    +      -       -      +
    190N  ALA*     3.7    24.2    -      -       -      -
    191N  THR      4.1     3.4    -      -       -      +
    192N  VAL*     2.7    52.3    -      -       +      +
    197N  VAL*     5.5     3.8    -      -       +      -
    198N  GLU      5.0     2.2    -      -       -      +
    199N  ILE*     6.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 51 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22N  ILE*     5.5     0.7    -      -       -      -
     41N  ARG      3.7     0.3    -      -       -      +
     42N  ILE*     3.5     5.0    -      -       -      -
     43N  MET*     2.8    48.3    +      -       +      +
     45N  VAL*     3.4    25.1    -      -       +      -
     50N  MET*     1.4    71.8    -      -       -      +
     52N  GLY*     1.3    62.1    +      -       -      +
     67N  LEU*     3.5    24.7    -      -       +      -
     88N  ILE*     4.0     3.6    -      -       +      -
     92N  LEU*     3.3    33.9    -      -       +      -
    110N  MET*     3.8    18.8    -      -       +      -
    111N  VAL      3.3     6.5    -      -       -      +
    112N  ILE*     3.5    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 52 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11N  VAL*     4.2    19.4    -      -       -      +
     22N  ILE*     5.1     4.9    -      -       -      +
     41N  ARG      3.2     9.9    -      -       -      -
     42N  ILE*     4.1    11.1    -      -       -      +
     51N  LEU*     1.3    74.6    -      -       -      +
     53N  ALA*     1.4    59.6    +      -       -      -
     60N  PHE*     4.7     0.2    -      -       -      -
    110N  MET*     3.2    25.7    -      -       -      +
    111N  VAL      3.1    11.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 53 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11N  VAL*     3.4     3.5    -      -       -      +
     41N  ARG*     3.1    36.9    +      -       +      +
     52N  GLY*     1.4    73.1    -      -       -      -
     54N  SER*     1.3    63.8    +      -       -      +
     55N  GLY      4.1     2.7    -      -       -      +
     57N  TYR*     5.9     0.4    -      -       +      -
     60N  PHE*     3.2    42.4    -      -       +      -
    108N  ASN*     4.9     5.4    -      -       +      +
    109N  THR      4.0     0.9    -      -       -      -
    110N  MET*     3.6    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 54 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7N  THR*     5.1     0.2    -      -       -      -
      8N  GLY      3.6     7.9    -      -       -      -
      9N  THR*     3.9    18.4    -      -       -      +
     10N  SER      3.8     2.7    +      -       -      -
     11N  VAL*     2.7    44.1    +      -       -      +
     53N  ALA*     1.3    70.7    +      -       -      +
     55N  GLY*     1.3    57.7    +      -       -      +
    107N  TRP      4.2     0.9    -      -       -      +
    109N  THR*     3.2    34.7    +      -       -      +
    139N  THR*     3.6    16.8    -      -       -      -
    140N  GLY      4.8     1.1    -      -       -      -
----------------------------------------------------------
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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