Contacts of the strand formed by residues 250 - 255 (chain A) in PDB entry 3SMZ


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 PHE 250 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  PRO*     3.3    10.6    -      -       -      +
    249A  THR*     1.3    82.4    -      -       +      +
    251A  CYS*     1.3    65.2    +      -       -      +
    252A  GLN*     3.4    38.4    -      -       +      -
    266A  VAL*     3.2    31.6    -      -       +      -
    267A  LEU*     3.3     3.3    -      -       -      -
    268A  GLU*     3.0    38.9    +      -       +      +
    303A  GLY*     3.5    33.9    -      -       -      -
    304A  ARG*     3.6    28.0    -      -       +      -
    307A  LEU*     4.6     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  VAL*     3.4     9.1    -      -       -      +
    238A  LEU*     4.4     7.2    -      -       -      -
    239A  CYS*     2.0    64.5    -      -       +      -
    248A  PRO*     4.2     8.1    -      -       +      +
    250A  PHE*     1.3    78.2    -      -       -      +
    252A  GLN*     1.3    60.7    +      -       -      +
    266A  VAL      4.0     0.4    -      -       -      -
    267A  LEU*     3.6    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235A  VAL*     4.3     3.1    -      -       +      -
    250A  PHE*     3.4    37.0    -      -       +      -
    251A  CYS*     1.3    75.8    -      -       -      +
    253A  LEU*     1.3    74.4    +      -       -      +
    255A  CYS*     6.1     1.2    -      -       -      -
    265A  ALA*     3.3     6.6    -      -       -      +
    266A  VAL      3.2    30.1    +      -       -      +
    304A  ARG*     5.6     2.4    -      -       -      +
    307A  LEU*     3.5    26.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  LEU*     5.0     5.4    -      -       +      -
    232A  PHE*     3.6    37.5    -      -       +      +
    233A  ASN*     3.6    28.3    -      -       -      +
    235A  VAL*     3.8    32.1    -      -       +      +
    238A  LEU*     3.7    30.3    -      -       +      -
    252A  GLN*     1.3    88.8    +      -       -      +
    254A  ALA*     1.3    64.0    +      -       -      +
    255A  CYS*     3.9     8.5    +      -       -      -
    261A  LEU*     4.3     9.2    -      -       +      -
    264A  PHE      3.8     6.3    -      -       -      +
    265A  ALA*     4.1     3.8    -      -       +      -
    307A  LEU*     4.5     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  GLN      4.1     0.8    +      -       -      -
    253A  LEU*     1.3    70.6    -      -       -      +
    255A  CYS*     1.4    61.5    +      -       -      +
    261A  LEU*     3.6    10.2    -      -       -      +
    262A  LYS*     3.0    20.1    +      -       +      -
    263A  GLY      4.2     1.0    +      -       -      -
    264A  PHE*     2.8    64.9    +      -       +      +
    307A  LEU*     3.9    10.7    -      -       +      +
    311A  ILE*     3.8    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  GLN*     6.1     0.9    -      -       -      -
    253A  LEU      3.9     7.8    +      -       -      -
    254A  ALA*     1.4    76.4    -      -       -      +
    256A  GLY*     1.3    62.9    +      -       -      +
    259A  GLY*     4.0    15.9    -      -       -      +
    260A  GLN      3.4    23.6    -      -       -      +
    261A  LEU*     4.0     8.3    -      -       +      +
    262A  LYS*     3.9     5.8    -      -       -      +
    311A  ILE*     3.8    14.7    -      -       -      +
----------------------------------------------------------
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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