Contacts of the strand formed by residues 298 - 306 (chain C) in PDB entry 4ZTZ


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 GLU 298 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92C  LEU*     3.6    27.4    -      -       +      +
    290C  TYR*     3.3     7.9    -      -       -      -
    291C  TYR*     2.9    33.6    +      -       -      +
    293C  PHE*     4.5    13.7    -      -       +      -
    295C  TRP*     4.9     4.3    +      -       -      -
    296C  GLY*     3.4    15.3    -      -       -      +
    297C  LYS*     1.3    84.1    -      -       -      +
    299C  LEU*     1.3    65.1    +      -       -      +
    300C  ILE*     3.5     6.1    +      -       +      +
    344C  ARG*     3.4    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 299 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288C  LYS*     4.1    20.6    -      -       +      -
    289C  LEU      4.0     4.0    -      -       -      +
    290C  TYR*     3.6    20.6    -      -       +      +
    298C  GLU*     1.3    74.9    -      -       -      +
    300C  ILE*     1.3    73.2    +      -       -      +
    301C  GLU      3.6    23.1    -      -       -      +
    302C  THR*     3.8    24.7    -      -       +      -
    341C  ASP*     5.4     0.5    -      -       -      +
    344C  ARG*     3.6    22.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 300 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263C  TRP*     3.6    39.7    -      -       +      +
    273C  PHE*     5.0     4.9    -      -       +      -
    289C  LEU*     2.9    20.7    +      -       +      +
    290C  TYR      5.2     0.9    -      -       -      -
    291C  TYR*     3.8    30.1    -      -       +      -
    293C  PHE*     5.5     2.9    -      -       +      -
    298C  GLU*     4.0     9.2    -      -       +      +
    299C  LEU*     1.3    84.4    -      -       -      +
    301C  GLU*     1.3    67.8    +      -       +      +
    341C  ASP*     2.9    32.7    +      -       -      +
    344C  ARG*     3.7    39.0    -      -       +      +
    345C  GLY*     4.4     3.8    -      -       -      +
    348C  ALA*     4.7     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 301 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259C  ARG*     2.6    40.0    +      -       -      +
    263C  TRP*     2.7    31.9    +      -       -      -
    288C  LYS*     3.5     2.8    -      -       -      -
    289C  LEU*     2.7    46.6    +      -       +      +
    299C  LEU*     3.6     5.2    -      -       -      +
    300C  ILE*     1.3    90.2    -      -       +      +
    302C  THR*     1.3    67.0    +      -       -      +
    303C  LEU*     3.6    10.6    -      -       +      +
    338C  VAL*     3.3    19.9    -      -       -      +
    339C  ASN      3.3    17.0    -      -       -      +
    340C  GLY*     3.6     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 302 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287C  ASN      3.8     3.1    -      -       -      -
    288C  LYS*     4.5     8.7    -      -       +      +
    299C  LEU*     3.8    31.4    -      -       +      -
    301C  GLU*     1.3    78.9    -      -       -      +
    303C  LEU*     1.3    64.5    +      -       -      +
    304C  TRP*     4.1    24.3    -      -       -      +
    337C  SER*     3.3     4.3    +      -       -      +
    339C  ASN*     2.9    52.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 303 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  LEU*     3.9    17.5    -      -       +      +
    255C  TRP*     4.1     5.8    -      -       +      +
    256C  LEU*     3.6    45.1    -      -       +      +
    259C  ARG*     4.4     9.2    -      -       +      -
    286C  GLY*     3.3     2.6    -      -       -      -
    287C  ASN*     2.7    48.0    +      -       +      +
    289C  LEU*     4.7     8.7    -      -       +      -
    301C  GLU*     3.6    25.8    -      -       +      +
    302C  THR*     1.3    85.4    -      -       -      +
    304C  TRP*     1.3    64.6    +      -       -      +
    337C  SER      3.4     2.9    -      -       -      -
    338C  VAL*     3.7    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 304 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  LEU*     3.8     7.8    -      -       -      +
    278C  CYS*     3.8    25.1    -      -       +      -
    279C  GLN*     4.8     3.4    -      -       -      -
    280C  ASP*     3.2    30.1    -      -       -      -
    283C  GLY*     4.3    11.9    -      -       -      -
    285C  LYS      4.2     2.0    -      -       -      -
    286C  GLY*     3.7    28.5    -      -       -      -
    287C  ASN      5.8     0.2    -      -       -      -
    288C  LYS*     5.0    11.0    -      -       +      +
    302C  THR*     4.1    29.4    -      -       -      +
    303C  LEU*     1.3    76.0    -      -       -      +
    305C  ASN*     1.3    63.5    +      -       -      +
    306C  LEU*     3.6    28.0    -      -       +      +
    336C  LEU*     3.5     4.3    -      -       -      -
    337C  SER*     2.9    35.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 305 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248C  SER*     3.4    31.1    +      -       -      -
    249C  ASN*     4.0     9.5    +      -       -      +
    252C  LEU*     3.8     9.0    -      -       +      +
    283C  GLY*     4.6     3.1    -      -       -      -
    284C  ARG*     4.4    16.9    +      -       -      +
    285C  LYS*     3.2    30.6    +      -       -      +
    304C  TRP*     1.3    76.4    -      -       -      +
    306C  LEU*     1.3    62.8    +      -       -      +
    307C  GLY      3.6     1.2    +      -       -      -
    334C  CYS*     3.1    24.4    -      -       -      -
    335C  VAL      3.8     2.2    -      -       -      -
    336C  LEU*     3.3    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 306 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186C  LEU*     5.7     5.2    -      -       +      -
    282C  GLU*     4.7    15.3    -      -       +      +
    283C  GLY*     4.9     6.7    -      -       -      -
    304C  TRP*     3.6    29.8    -      -       +      -
    305C  ASN*     1.3    75.7    -      -       -      +
    307C  GLY*     1.3    63.2    +      -       -      +
    310C  GLU*     4.0    35.2    -      -       +      +
    334C  CYS*     3.1     4.9    -      -       -      -
    335C  VAL*     2.8    46.2    +      -       +      +
    337C  SER*     3.6    21.3    -      -       -      +
----------------------------------------------------------
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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