Contacts of the strand formed by residues 225 - 230 (chain B) in PDB entry 6A5T


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 ILE 225 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219B  LYS*     3.9    13.7    -      -       +      +
    223B  SER*     3.0    17.2    -      -       -      +
    224B  PRO*     1.3    81.1    -      -       -      +
    226B  SER*     1.3    57.6    +      -       -      +
    227B  HIS      3.6    23.8    -      -       -      +
    228B  VAL*     3.8    18.8    -      -       +      -
    248B  LYS*     3.5    37.9    -      -       +      -
    249B  LEU      3.2    12.6    -      -       -      +
    250B  TYR*     3.6    25.4    -      -       +      +
    252B  ARG*     2.5    31.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 226 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  LYS*     3.3    26.7    -      -       -      +
    219B  LYS      3.6     4.4    +      -       -      +
    224B  PRO      4.2     0.6    +      -       -      -
    225B  ILE*     1.3    76.0    -      -       -      +
    227B  HIS*     1.3   102.1    +      -       -      +
    249B  LEU*     3.4    20.0    +      -       -      +
    251B  GLY      5.1     9.5    +      -       -      -
    252B  ARG*     3.4    15.9    -      -       -      +
    382B  ALA*     4.3     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 227 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216B  VAL*     5.0     0.2    -      -       +      -
    217B  PHE      3.4     5.6    -      -       -      +
    218B  LYS*     3.5    28.5    -      -       +      +
    225B  ILE*     3.6     2.6    -      -       -      +
    226B  SER*     1.3   117.3    +      -       -      +
    228B  VAL*     1.3    63.4    +      -       -      +
    249B  LEU*     3.3    26.1    +      -       +      +
    378B  LEU*     3.4    27.4    -      -       +      +
    381B  CYS*     2.7    42.8    +      -       -      -
    382B  ALA*     3.3    31.5    -      -       +      -
    384B  GLU*     5.0     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 228 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215B  GLN      3.5     1.6    -      -       -      +
    216B  VAL*     3.4     3.8    -      -       -      -
    217B  PHE*     2.9    42.8    +      -       +      +
    218B  LYS      5.2     0.7    -      -       -      -
    219B  LYS*     4.6    20.2    -      -       +      +
    225B  ILE*     3.8    21.1    -      -       +      -
    227B  HIS*     1.3    77.1    -      -       -      +
    229B  ALA*     1.3    64.3    +      -       -      +
    230B  GLU*     3.7    14.6    +      -       +      +
    246B  GLN*     4.7    16.4    -      -       -      +
    247B  ILE      3.2    19.5    -      -       -      +
    248B  LYS*     4.9     4.7    -      -       +      -
    378B  LEU*     4.3     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 229 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214B  VAL*     5.1     6.3    -      -       +      -
    215B  GLN      3.4     7.9    -      -       -      +
    216B  VAL*     4.6     7.4    -      -       +      +
    228B  VAL*     1.3    69.7    -      -       -      +
    230B  GLU*     1.3    59.1    +      -       -      +
    245B  MET      4.1     2.8    -      -       -      +
    246B  GLN      4.1     0.9    -      -       -      -
    247B  ILE*     3.2    43.2    +      -       +      +
    374B  MET*     4.3    20.2    -      -       +      +
    378B  LEU*     4.0    29.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 230 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  ILE      3.7     0.5    -      -       -      +
    214B  VAL*     3.8     1.6    -      -       -      -
    215B  GLN*     2.9    45.3    +      -       +      +
    217B  PHE*     4.5    15.3    -      -       +      -
    228B  VAL*     3.7    15.1    +      -       +      +
    229B  ALA*     1.3    74.6    -      -       -      +
    231B  ILE*     1.3    73.2    +      -       -      +
    232B  ARG*     3.8    30.1    +      -       +      +
    244B  THR*     4.0    13.8    -      -       +      +
    245B  MET      4.2     4.3    -      -       -      +
    246B  GLN*     4.6    24.5    +      -       +      +
    374B  MET*     5.2     1.8    -      -       -      -
----------------------------------------------------------
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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