Contacts of the strand formed by residues 244 - 248 (chain A) in PDB entry 1Z16


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 LEU 244 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  MET*     4.5     9.6    -      -       +      -
    210A  LEU*     4.2    13.7    -      -       +      -
    221A  GLN*     4.1     0.2    -      -       -      +
    222A  PHE*     3.5    34.1    -      -       +      +
    223A  MET*     4.0     3.6    -      -       -      +
    224A  GLY      4.2     4.3    -      -       -      +
    228A  VAL*     4.3    11.0    -      -       +      +
    233A  LEU*     4.0    27.6    -      -       +      -
    241A  ALA      3.1    18.2    +      -       -      +
    242A  GLU      3.3     1.0    +      -       -      -
    243A  GLY*     1.3    79.1    -      -       -      +
    245A  LEU*     1.3    74.9    +      -       -      +
    246A  VAL*     3.7    17.7    -      -       +      -
    333A  ASP*     3.6     2.9    -      -       -      -
    334A  TRP*     2.8    37.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  TYR*     4.1    32.3    -      -       +      +
    136A  VAL*     4.2    14.8    -      -       +      -
    196A  PHE*     4.4     6.7    -      -       +      -
    221A  GLN*     3.8    28.3    -      -       +      +
    222A  PHE      3.1    11.8    +      -       -      +
    223A  MET*     3.1    18.7    -      -       +      -
    224A  GLY      3.0    23.2    +      -       -      -
    243A  GLY      4.3     1.3    -      -       -      +
    244A  LEU*     1.3    74.5    -      -       -      +
    246A  VAL*     1.3    64.3    +      -       -      +
    331A  VAL*     4.4     2.0    -      -       +      -
    332A  PHE      3.5     7.6    -      -       -      +
    333A  ASP*     3.4    25.1    -      -       -      +
    343A  ALA*     4.3     8.7    -      -       +      -
    344A  LYS*     5.8     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  MET*     4.8     1.3    -      -       -      -
    224A  GLY      3.2     8.5    -      -       -      +
    225A  PRO      4.5     0.9    -      -       -      +
    228A  VAL*     3.8    17.9    -      -       +      -
    229A  ALA*     3.9    25.8    -      -       +      -
    244A  LEU*     3.7    25.4    -      -       +      -
    245A  LEU*     1.3    81.5    -      -       -      +
    247A  THR*     1.3    67.7    +      -       -      +
    248A  LYS*     4.4     6.3    -      -       +      -
    331A  VAL*     3.4     5.6    -      -       -      +
    332A  PHE*     2.9    53.6    +      -       +      +
    334A  TRP*     4.3    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  GLN*     2.7    38.1    +      -       -      +
    127A  THR*     4.3     9.0    -      -       +      -
    128A  ALA*     4.1    27.9    -      -       +      +
    198A  TYR*     5.0     1.9    +      -       -      -
    223A  MET*     4.2     5.8    -      -       +      -
    224A  GLY      3.2     4.9    +      -       -      +
    225A  PRO*     3.3    10.0    -      -       -      +
    226A  GLU*     2.9    25.6    +      -       -      -
    246A  VAL*     1.3    77.4    -      -       -      +
    248A  LYS*     1.3    63.5    +      -       -      +
    329A  PHE*     4.5     4.7    -      -       -      -
    330A  GLY      3.1    10.5    -      -       -      +
    331A  VAL*     4.2    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  GLU*     3.8    12.6    -      -       +      +
    229A  ALA*     3.9    23.8    -      -       +      +
    246A  VAL*     4.4     3.6    -      -       +      -
    247A  THR*     1.3    77.1    -      -       -      +
    249A  PRO*     1.3   100.1    +      -       +      +
    250A  LYS      3.9     5.1    +      -       -      -
    251A  ASN*     2.7    30.5    +      -       -      +
    275A  ALA*     5.3     9.3    -      -       +      +
    329A  PHE*     4.0     8.2    -      -       -      +
    330A  GLY      2.8    30.9    +      -       -      +
    332A  PHE*     3.6    19.6    -      -       +      -
    334A  TRP*     4.8     4.5    -      -       +      -
    340A  ALA*     3.8    24.2    -      -       +      -
----------------------------------------------------------
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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