Contacts of the strand formed by residues 203 - 208 (chain A) in PDB entry 1XTB


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 SER 203 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  ILE*     4.4     0.9    -      -       -      -
    150A  ASP*     3.4     8.2    +      -       -      +
    152A  ILE*     3.9    16.6    -      -       -      -
    198A  LEU*     3.6    22.7    -      -       -      +
    199A  ASN      2.7    26.5    +      -       -      -
    200A  PRO*     3.9     6.6    +      -       -      +
    201A  GLU      3.3     2.2    -      -       -      -
    202A  SER*     1.3    78.2    -      -       -      +
    204A  LEU*     1.3    57.3    +      -       -      +
    205A  PHE*     4.1    14.9    +      -       -      -
    241A  HIS*     2.7    33.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  PHE*     3.9    28.7    -      -       +      -
    135A  VAL*     4.2    20.2    -      -       +      -
    140A  TRP*     4.8     5.8    -      -       -      +
    148A  ILE*     3.8    21.8    -      -       +      -
    150A  ASP      2.7    11.3    +      -       -      +
    151A  VAL*     3.2    14.2    -      -       +      +
    152A  ILE*     2.7    32.4    +      -       -      +
    202A  SER      4.0     0.2    +      -       -      -
    203A  SER*     1.3    72.0    -      -       -      +
    205A  PHE*     1.3    69.4    +      -       -      +
    206A  ILE*     4.8     6.3    -      -       +      -
    240A  LYS      4.1     7.2    -      -       -      +
    241A  HIS*     3.7    23.3    -      -       -      +
    242A  PHE      4.2     1.3    -      -       -      +
    243A  VAL*     4.4    12.8    -      -       +      -
    285A  LEU*     4.6     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  ILE*     3.4    43.1    -      -       +      +
    154A  ILE*     3.9    18.2    -      -       +      -
    191A  ILE*     5.2     0.4    -      -       +      -
    195A  LEU*     3.7    18.4    -      -       +      -
    203A  SER*     4.1    13.2    -      -       -      -
    204A  LEU*     1.3    77.1    -      -       -      +
    206A  ILE*     1.3    61.8    +      -       -      +
    207A  ILE*     4.0     5.6    -      -       +      -
    224A  ALA*     3.9    12.1    -      -       +      -
    227A  TRP*     3.5    35.7    -      +       -      -
    228A  PHE*     5.1     5.8    -      +       +      -
    241A  HIS*     2.9    21.8    +      -       +      +
    242A  PHE*     3.5    35.6    -      +       +      -
    243A  VAL*     3.1    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  VAL*     3.4    31.2    -      -       +      -
    152A  ILE      2.8    11.1    +      -       -      +
    153A  ASN*     3.5    11.9    +      -       +      +
    154A  ILE      2.8    28.8    +      -       -      -
    204A  LEU*     4.8     4.5    -      -       +      -
    205A  PHE*     1.3    75.1    -      -       -      +
    207A  ILE*     1.3    61.3    +      -       -      +
    208A  ALA      3.3     2.9    +      -       -      -
    243A  VAL*     3.7    18.4    -      -       +      -
    245A  LEU*     3.5    43.5    -      -       +      -
    281A  LEU*     4.2    11.7    -      -       +      -
    282A  SER*     4.3    13.0    -      -       -      +
    285A  LEU*     3.8    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  ILE*     3.7    29.8    -      -       +      +
    205A  PHE*     4.4     2.9    -      -       +      -
    206A  ILE*     1.3    76.1    -      -       -      +
    208A  ALA*     1.3    59.2    +      -       -      +
    209A  SER      3.7     1.4    +      -       -      -
    212A  PHE*     3.5    31.2    -      -       +      -
    217A  THR*     4.1    17.0    -      -       +      -
    218A  ILE*     5.2     2.5    -      -       +      -
    221A  ALA*     3.8    27.1    -      -       +      -
    242A  PHE*     4.1    26.0    -      -       +      -
    243A  VAL      3.0    16.0    +      -       -      +
    244A  ALA*     3.4     2.1    -      -       -      -
    245A  LEU      3.0    23.4    +      -       -      +
    255A  PHE*     4.4     2.7    -      -       +      -
    257A  ILE*     4.3     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  ASN*     3.8    19.5    -      -       -      +
    154A  ILE      2.8    19.3    +      -       -      +
    155A  GLY*     3.4     5.9    -      -       -      -
    159A  SER*     3.4    38.5    -      -       -      +
    206A  ILE      3.3     0.8    +      -       -      -
    207A  ILE*     1.3    69.1    -      -       -      +
    209A  SER*     1.3    63.6    +      -       -      +
    217A  THR*     3.7     2.1    +      -       -      +
    245A  LEU*     3.8    21.1    -      -       +      -
    279A  ILE*     4.1     6.7    -      -       +      -
   2002A  S6P      4.4     0.2    +      -       -      -
----------------------------------------------------------
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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