Contacts of the strand formed by residues 259 - 265 (chain A) in PDB entry 1TAD


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 259 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215A  THR*     3.3    16.3    +      -       -      +
    216A  CYS*     3.2    16.3    -      -       -      -
    217A  ILE      2.8    24.8    +      -       -      -
    257A  THR      3.8     2.7    +      -       -      -
    258A  THR*     1.3    74.8    -      -       -      +
    260A  ILE*     1.3    59.6    -      -       -      +
    261A  VAL*     5.6     1.3    -      -       -      -
    313A  LYS*     4.7     2.9    -      -       -      +
    338A  ILE*     4.9    13.4    -      -       -      +
    339A  ILE*     5.1     5.9    -      -       -      -
    342A  GLU      3.5    26.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  ILE*     3.4    31.2    -      -       +      +
    219A  PHE*     5.1     1.6    -      -       +      -
    246A  PHE*     4.4    15.5    -      -       +      -
    249A  ILE*     4.6     2.9    -      -       +      +
    250A  CYS*     4.2    30.3    -      -       -      +
    255A  PHE*     4.4    17.7    -      -       +      +
    258A  THR      3.4    12.4    +      -       -      +
    259A  SER*     1.3    77.9    -      -       -      +
    261A  VAL*     1.3    75.9    +      -       -      +
    313A  LYS*     3.6    22.1    +      -       -      +
    314A  GLU      4.6     1.4    +      -       -      +
    315A  ILE*     3.4    39.0    -      -       +      +
    316A  TYR      3.7     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  CYS*     4.5     7.6    -      -       -      -
    217A  ILE      2.8     9.9    +      -       -      +
    218A  ILE*     3.4    36.3    -      -       +      -
    219A  PHE*     2.8    29.7    +      -       -      +
    259A  SER*     5.3     1.1    -      -       -      -
    260A  ILE*     1.3    82.4    -      -       -      +
    262A  LEU*     1.3    59.6    +      -       -      +
    263A  PHE*     4.2    11.2    -      -       +      -
    315A  ILE*     4.2     2.5    -      -       -      -
    316A  TYR*     3.2    35.4    -      -       +      +
    335A  VAL*     4.4    17.7    -      -       +      -
    338A  ILE*     4.7    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  PHE*     3.3    35.9    -      -       +      +
    221A  ALA*     4.1    17.9    -      -       +      -
    246A  PHE*     4.4     8.3    -      -       +      -
    261A  VAL*     1.3    72.7    -      -       -      +
    263A  PHE*     1.3    64.5    +      -       -      +
    264A  LEU*     4.0    23.3    -      -       +      -
    300A  LYS      4.9     1.1    -      -       -      +
    303A  PHE*     3.6    36.8    -      -       +      -
    304A  LEU*     4.3    13.7    -      -       +      -
    315A  ILE*     4.1     9.8    -      -       +      +
    316A  TYR*     2.8    10.0    +      -       -      +
    317A  SER*     3.1    32.6    -      -       -      -
    318A  HIS      3.1     6.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ILE*     4.2    32.3    -      -       +      -
    218A  ILE*     3.6    36.3    -      -       +      -
    219A  PHE      2.7    12.5    +      -       -      +
    220A  ILE*     3.5    16.3    -      -       +      +
    221A  ALA*     2.9    27.0    +      -       -      -
    261A  VAL*     4.2     6.5    -      -       +      -
    262A  LEU*     1.3    80.6    -      -       -      +
    264A  LEU*     1.3    60.6    +      -       -      +
    265A  ASN*     3.2     2.3    +      -       -      -
    316A  TYR*     5.2     3.1    -      +       -      -
    318A  HIS      3.6     5.6    -      -       -      -
    320A  THR*     3.8    24.0    -      -       +      +
    328A  VAL*     5.7     4.3    -      -       +      -
    331A  VAL*     3.6    31.9    -      -       +      -
    332A  PHE*     5.1     6.5    -      +       +      -
    335A  VAL*     3.9    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  ALA*     3.4    11.4    -      -       +      +
    223A  LEU*     3.4    31.0    -      -       +      +
    239A  MET*     5.8     0.2    -      -       +      -
    262A  LEU*     3.9    26.9    +      -       +      +
    263A  PHE*     1.3    69.2    -      -       -      +
    265A  ASN*     1.3    58.0    +      -       -      +
    296A  GLY      4.3     3.6    -      -       -      +
    299A  ILE*     4.2    19.3    -      -       +      -
    300A  LYS*     3.7    39.5    -      -       +      +
    303A  PHE*     4.2    12.6    -      -       +      -
    317A  SER*     5.0     3.8    -      -       -      -
    318A  HIS      2.8    14.6    +      -       -      +
    319A  MET*     3.2    16.3    -      -       +      -
    320A  THR      2.8    26.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  SER      2.9    23.3    +      -       -      +
     41A  GLY*     3.8     3.6    -      -       -      -
     45A  ILE*     5.9     0.7    -      -       -      -
    220A  ILE*     3.5    24.3    -      -       +      +
    221A  ALA      2.8    10.9    +      -       -      +
    223A  LEU*     2.9    27.6    +      -       -      +
    263A  PHE*     3.2     0.4    +      -       -      -
    264A  LEU*     1.3    75.3    -      -       -      +
    266A  LYS*     1.3    76.2    +      -       +      +
    267A  LYS      3.3     1.3    -      -       -      -
    320A  THR*     3.0    16.4    +      -       -      +
    322A  ALA*     2.8    35.4    +      -       -      +
    351A  GDP      3.0    26.6    +      -       -      -
----------------------------------------------------------
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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