Contacts of the strand formed by residues 251 - 254 (chain E) in PDB entry 4O9U


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 VAL 251 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147E  ALA*     3.9    11.2    -      -       +      +
    151E  SER*     4.4     4.0    -      -       -      +
    155E  PHE*     3.7    27.4    -      -       +      -
    168E  ALA*     5.4     1.1    -      -       +      -
    169E  LYS      3.3     3.1    +      -       -      +
    170E  VAL*     3.3    18.2    -      -       +      +
    171E  MET*     2.7    31.9    +      -       -      -
    249E  MET*     4.5     0.5    -      -       -      +
    250E  ASP*     1.3    88.5    -      -       +      +
    252E  LEU*     1.3    62.2    +      -       -      +
    253E  ILE*     3.7    24.9    -      -       +      -
    280E  VAL*     3.0    25.4    -      -       +      +
    282E  VAL*     3.9    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 252 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171E  MET*     3.3    45.5    -      -       +      -
    173E  MET*     3.7    16.2    -      -       -      -
    246E  VAL*     3.8    13.7    -      -       +      -
    249E  MET*     3.7    20.9    -      -       +      -
    251E  VAL*     1.3    73.6    -      -       -      +
    253E  ILE*     1.3    58.7    +      -       -      +
    254E  THR*     3.9     1.3    +      -       -      +
    267E  LEU*     4.2    14.6    -      -       +      -
    275E  LEU*     3.7    14.6    -      -       +      -
    279E  THR*     3.5    29.2    -      -       +      -
    280E  VAL      2.6    10.3    +      -       -      +
    281E  VAL*     3.5     5.9    -      -       +      +
    282E  VAL      2.7    33.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 253 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143E  ALA*     4.1    21.8    -      -       +      +
    144E  ALA*     4.5     7.6    -      -       +      -
    147E  ALA*     4.3     5.6    -      -       +      -
    155E  PHE*     5.9     0.9    -      -       +      -
    170E  VAL*     3.7    21.8    -      -       +      -
    171E  MET      2.8     8.5    +      -       -      +
    172E  VAL*     3.1    15.3    -      -       +      +
    173E  MET      2.7    31.7    +      -       -      -
    182E  ALA*     4.1    31.9    -      -       +      +
    186E  ALA*     5.5     1.6    -      -       +      -
    251E  VAL*     3.7    20.6    -      -       +      -
    252E  LEU*     1.3    72.7    -      -       -      +
    254E  THR*     1.3    56.0    +      -       -      +
    255E  THR*     4.7    10.8    -      -       +      -
    282E  VAL*     3.5    26.0    -      -       +      -
    284E  LEU*     6.1     1.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 254 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173E  MET*     3.5    36.3    -      -       +      -
    252E  LEU      4.3     2.7    -      -       -      +
    253E  ILE*     1.3    79.4    -      -       -      +
    255E  THR*     1.3    62.7    +      -       -      +
    266E  LEU*     5.1     1.3    -      -       +      -
    267E  LEU*     4.3    17.3    -      -       +      -
    281E  VAL*     5.3     1.6    -      -       +      +
    282E  VAL      2.8    25.2    +      -       -      +
    283E  ASP*     3.5     9.5    -      -       -      +
    284E  LEU      3.2    22.2    +      -       -      -
    285E  ALA      3.9     0.5    +      -       -      -
    291E  ASN*     3.3    37.5    +      -       +      +
    292E  CYS      4.9     0.5    +      -       -      -
----------------------------------------------------------
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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