Contacts of the strand formed by residues 316 - 320 (chain B) 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 TYR 316 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259B  SER*     5.1     7.6    -      -       -      -
    260B  ILE      3.4    13.5    +      -       -      -
    261B  VAL*     3.5    13.4    -      -       +      -
    262B  LEU*     2.7    31.6    +      -       -      +
    314B  GLU*     3.4    30.1    +      -       +      +
    315B  ILE*     1.3    81.8    -      -       -      +
    317B  SER*     1.3    55.7    +      -       -      +
    318B  HIS*     4.8     5.2    -      -       -      +
    338B  ILE*     3.5    56.0    -      -       +      +
    341B  LYS*     5.9     3.1    -      -       -      +
    342B  GLU      5.6     4.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  LEU*     3.3    14.0    +      -       -      +
    264B  LEU*     3.5    15.4    -      -       -      +
    300B  LYS*     3.2    36.6    +      -       -      +
    304B  LEU*     4.4    16.6    -      -       -      -
    315B  ILE      4.1     0.6    +      -       -      -
    316B  TYR*     1.3    76.0    -      -       -      +
    318B  HIS*     1.3    78.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261B  VAL*     3.9    24.7    -      -       +      +
    262B  LEU      3.0     8.4    +      -       -      +
    263B  PHE*     3.6     2.8    -      -       +      -
    264B  LEU*     2.8    32.4    +      -       -      +
    300B  LYS*     4.4     4.7    -      -       -      +
    316B  TYR*     4.8     7.5    -      -       -      +
    317B  SER*     1.3    92.8    +      -       -      +
    319B  MET*     1.3    59.8    +      -       -      +
    320B  THR*     3.6     7.0    +      -       +      -
    330B  PHE*     5.2     7.9    -      +       -      -
    331B  VAL*     3.7    35.2    -      -       +      +
    334B  ALA*     3.9    27.2    -      -       +      +
    335B  VAL*     4.7     4.0    -      -       +      +
    338B  ILE*     4.9     5.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 319 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223B  LEU*     3.5    26.9    -      -       +      -
    264B  LEU*     3.3    24.0    -      -       -      +
    267B  LYS*     3.8    13.0    -      -       +      +
    270B  PHE*     4.6     0.7    -      -       +      -
    292B  TYR*     3.8    40.2    -      -       +      +
    296B  GLY*     4.0    20.4    -      -       -      +
    300B  LYS*     3.6    27.6    -      -       -      +
    318B  HIS*     1.3    72.5    -      -       -      +
    320B  THR*     1.3    63.5    +      -       -      +
    327B  ASN*     4.0     8.1    +      -       -      +
    331B  VAL*     4.6     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  ILE*     5.4     0.4    -      -       -      +
    263B  PHE*     3.9    25.2    -      -       +      +
    264B  LEU      2.7    11.1    +      -       -      -
    265B  ASN*     3.0    28.1    +      -       -      +
    266B  LYS      3.0     8.0    +      -       -      -
    267B  LYS*     2.9    31.4    +      -       -      +
    318B  HIS*     3.9     9.2    -      -       +      +
    319B  MET*     1.3    79.7    -      -       -      +
    321B  CYS*     1.3    63.2    +      -       -      +
    322B  ALA*     4.5     1.7    -      -       -      -
    327B  ASN*     3.3    11.2    -      -       -      +
    328B  VAL*     5.7     3.8    -      -       +      -
    331B  VAL*     4.0    28.7    -      -       +      -
----------------------------------------------------------
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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