Contacts of the strand formed by residues 241 - 245 (chain B) in PDB entry 4IYM


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 ARG 241 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  TYR*     3.7     7.0    -      -       -      -
    457A  GLY      3.6    30.9    +      -       -      +
    458A  ASP*     3.6    28.5    +      -       +      +
    138B  VAL*     3.6    11.9    -      -       -      +
    217B  ALA*     3.2     8.4    +      -       +      +
    218B  ALA*     3.4    26.2    -      -       +      -
    219B  VAL*     3.1    22.0    +      -       -      +
    239B  GLY      4.0     1.0    +      -       -      -
    240B  LYS*     1.3    77.4    -      -       -      +
    242B  ALA*     1.3    61.6    +      -       -      +
    468B  LYS      3.4     7.5    +      -       -      -
    469B  PHE*     2.9    33.6    +      -       +      -
    471B  THR      2.8    29.0    +      -       -      -
    472B  ARG*     4.0    16.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 242 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  TYR*     4.4     4.1    +      -       -      +
    458A  ASP*     4.3     5.4    +      -       -      +
    219B  VAL*     3.2    10.8    -      -       +      +
    232B  TYR*     3.9    35.9    -      -       +      +
    235B  ALA*     3.9    22.9    -      -       +      -
    236B  ALA*     5.2     1.8    -      -       +      +
    240B  LYS      3.8     2.8    +      -       -      +
    241B  ARG*     1.3    78.8    -      -       -      +
    243B  GLN*     1.3    63.1    +      -       -      +
    244B  CYS*     4.3     6.7    -      -       -      -
    457B  GLY*     4.2     6.4    -      -       -      -
    458B  ASP*     5.1     0.3    +      -       -      +
    469B  PHE*     3.6     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 243 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157B  MSE      5.4     0.3    -      -       -      +
    219B  VAL      3.1     3.4    +      -       -      -
    220B  SER*     2.8    31.7    +      -       -      +
    221B  PHE      2.9    21.1    +      -       -      +
    242B  ALA*     1.3    76.0    -      -       -      +
    244B  CYS*     1.3    62.0    +      -       -      +
    245B  PHE*     3.6    14.5    -      -       +      -
    456B  PHE      3.6     7.2    -      -       -      +
    457B  GLY*     5.5     0.2    -      -       -      -
    459B  LEU*     3.0    30.4    +      -       -      +
    460B  ASN      3.0    20.4    +      -       -      +
    461B  GLN*     3.7     8.8    +      -       -      +
    466B  SER*     5.7     2.3    -      -       -      +
    469B  PHE*     3.7    34.7    -      -       +      +
    470B  TRP*     4.6     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 244 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219B  VAL      5.2     0.7    -      -       -      -
    221B  PHE*     3.4    20.9    -      -       +      -
    228B  ALA*     3.8    23.1    -      -       +      +
    231B  VAL*     3.9     5.6    -      -       -      -
    232B  TYR*     3.6    42.4    -      -       +      -
    242B  ALA*     4.5     2.7    -      -       -      -
    243B  GLN*     1.3    82.4    -      -       -      +
    245B  PHE*     1.3    65.7    +      -       -      +
    455B  SER*     3.2     4.0    -      -       -      -
    456B  PHE*     2.7    42.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 245 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221B  PHE*     2.9    21.8    +      -       -      +
    222B  VAL*     3.5    13.0    -      -       +      +
    223B  GLY      3.0    27.0    +      -       -      +
    228B  ALA*     4.4     2.7    -      -       -      -
    243B  GLN*     3.6    27.6    -      -       +      -
    244B  CYS*     1.3    75.9    -      -       -      +
    246B  GLY*     1.3    60.9    +      -       -      +
    409B  ASN*     6.1     0.7    -      -       -      +
    448B  PHE*     3.8    31.2    -      +       +      -
    449B  GLY*     3.9    17.5    -      -       -      -
    450B  GLY      4.6     0.2    -      -       -      -
    454B  SER      3.6     4.9    -      -       -      +
    455B  SER*     3.8    21.5    -      -       -      -
    456B  PHE      5.2     2.0    -      -       -      -
    459B  LEU      3.4    23.6    -      -       -      -
    460B  ASN*     3.9     7.2    -      -       -      -
    461B  GLN*     3.4    35.0    -      -       +      -
----------------------------------------------------------
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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