Contacts of the strand formed by residues 227 - 233 (chain N) in PDB entry 7K60


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 227 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170N  PRO*     4.0     9.4    -      -       +      -
    171N  CYS      3.1    21.1    -      -       -      +
    172N  LYS*     3.4    14.9    -      -       +      +
    178N  PHE*     4.0     4.5    -      -       -      -
    221N  SER*     3.7     0.5    -      -       -      -
    222N  ASP*     2.8    34.2    +      -       -      +
    225N  SER*     2.9    31.2    +      -       -      -
    226N  SER*     1.3    75.4    -      -       -      +
    228N  VAL*     1.3    59.0    +      -       -      +
    229N  TYR*     3.4    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 228 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169N  MET      3.7     0.9    -      -       -      +
    170N  PRO*     3.4     1.7    -      -       -      +
    171N  CYS*     2.7    59.0    +      -       +      +
    178N  PHE*     4.7     6.7    -      -       +      -
    183N  ILE*     3.7    29.8    -      -       +      -
    185N  TRP*     4.2    13.2    -      -       -      +
    200N  ILE*     3.4    30.7    -      -       +      -
    219N  LEU*     5.4     0.9    -      -       +      -
    220N  THR      3.2    18.8    -      -       -      +
    221N  SER*     4.3     5.6    -      -       -      +
    227N  THR*     1.3    74.0    -      -       -      +
    229N  TYR*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 229 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168N  LYS*     3.3    43.1    -      -       +      +
    169N  MET      3.3     4.5    -      -       -      +
    170N  PRO*     3.7    24.5    -      -       +      -
    185N  TRP*     4.8     0.4    -      -       -      -
    218N  THR      3.7     0.5    -      -       -      +
    219N  LEU*     3.4     4.9    -      -       -      +
    220N  THR*     2.7    54.2    +      -       -      +
    221N  SER      5.1     0.7    -      -       -      -
    222N  ASP*     4.3    20.8    +      -       +      +
    225N  SER*     4.1     7.8    +      -       -      -
    227N  THR*     3.4    32.1    -      -       +      +
    228N  VAL*     1.3    76.6    -      -       -      +
    230N  MET*     1.3    59.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 230 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167N  VAL      3.7     1.0    -      -       -      +
    168N  LYS*     3.5     2.2    -      -       -      -
    169N  MET*     2.9    64.6    +      -       +      +
    185N  TRP*     3.6    48.3    -      -       +      -
    197N  ILE*     3.9    22.2    -      -       +      -
    217N  ALA*     4.3    11.9    -      -       +      -
    218N  THR      3.2     5.4    -      -       -      +
    219N  LEU*     3.5    19.5    -      -       +      -
    229N  TYR*     1.3    72.3    -      -       -      +
    231N  GLU*     1.3    63.4    +      -       -      +
    232N  LEU*     4.0     7.5    +      -       +      -
    243N  TYR*     3.6    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 231 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166N  SER*     3.5    20.1    +      -       -      +
    167N  VAL      3.1    17.3    -      -       -      +
    168N  LYS*     4.1    28.1    -      -       +      +
    216N  LYS      3.4     1.0    -      -       -      +
    217N  ALA*     3.2     5.2    -      -       -      -
    218N  THR*     2.6    59.9    +      -       +      +
    229N  TYR      4.1     0.6    -      -       -      -
    230N  MET*     1.3    71.9    -      -       -      +
    232N  LEU*     1.3    67.1    +      -       -      +
    233N  SER*     4.1     3.9    +      -       -      +
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Residues in contact with LEU 232 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166N  SER*     3.1     5.7    -      -       -      -
    167N  VAL*     2.6    43.7    +      -       +      +
    169N  MET*     3.9    17.5    -      -       +      -
    197N  ILE*     5.3     2.0    -      -       +      -
    213N  PHE*     5.6     2.2    -      -       +      -
    216N  LYS*     3.1    29.6    -      -       +      +
    217N  ALA*     4.0    18.8    -      -       +      -
    230N  MET*     4.3    14.6    -      -       +      +
    231N  GLU*     1.3    74.6    -      -       -      +
    233N  SER*     1.3    60.2    +      -       -      +
    235N  LEU*     3.3    25.6    -      -       +      +
    239N  ASP*     5.5     1.3    -      -       -      +
    243N  TYR*     3.6    40.6    -      -       +      +
    265N  VAL*     5.0     4.5    -      -       +      -
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Residues in contact with SER 233 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165N  THR      4.1     1.6    -      -       -      -
    166N  SER*     4.3     9.0    -      -       -      -
    215N  GLY      3.0    25.4    +      -       -      -
    216N  LYS*     2.8    24.7    +      -       -      +
    231N  GLU*     4.1     4.7    +      -       -      -
    232N  LEU*     1.3    75.2    -      -       -      +
    234N  SER*     1.3    78.7    +      -       -      +
    235N  LEU*     3.5     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