Contacts of the strand formed by residues 327 - 333 (chain F) in PDB entry 5YL4


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 327 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93F  TRP*     3.9    18.7    -      -       -      +
    283F  ILE*     3.5    45.3    -      -       +      +
    286F  GLN*     3.2    30.5    +      -       +      +
    287F  ILE*     3.8    10.8    -      -       +      -
    290F  ILE*     4.1     6.6    -      -       +      +
    319F  PHE*     3.5    38.8    -      -       +      -
    320F  MET      3.5     5.6    -      -       -      +
    321F  VAL*     4.3     4.5    -      -       +      +
    326F  LYS*     1.3    79.7    -      -       -      +
    328F  TRP*     1.3    66.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 328 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92F  THR      3.8    10.3    -      -       -      -
     93F  TRP      3.3     9.9    -      -       -      +
     94F  PHE      3.8    16.4    -      -       -      -
     95F  PRO*     3.7    33.0    -      -       +      -
     96F  GLU      5.4     0.7    -      -       -      -
    186F  LEU*     3.7    38.7    -      -       +      +
    290F  ILE*     4.9     0.2    -      -       -      -
    319F  PHE*     3.2    11.6    -      -       -      -
    320F  MET*     2.8    38.6    +      -       +      +
    322F  ASP*     3.3    26.7    +      -       +      -
    326F  LYS*     3.3    50.0    +      -       +      +
    327F  VAL*     1.3    76.0    -      -       -      +
    329F  LEU*     1.3    61.3    +      -       -      +
    330F  ILE*     3.7     1.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 329 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77F  LEU*     4.7     9.0    -      -       +      -
     81F  ILE*     4.8     0.4    -      -       +      -
     93F  TRP*     2.9    42.5    +      -       +      +
     94F  PHE*     3.4    19.6    -      -       +      -
     95F  PRO*     3.2    24.3    -      -       -      +
    290F  ILE*     4.1     8.3    -      -       +      +
    294F  CYS*     3.9    17.9    -      -       -      -
    317F  PHE*     3.9    21.1    -      -       +      -
    318F  ASP      3.8    14.8    -      -       -      +
    319F  PHE*     3.8    18.1    -      -       +      -
    328F  TRP*     1.3    70.1    -      -       -      +
    330F  ILE*     1.3    61.1    -      -       -      +
    331F  GLU*     4.0    13.2    -      -       -      +
    332F  VAL*     4.3    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 330 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74F  LYS*     5.5     2.6    -      -       -      +
     77F  LEU*     4.4     3.6    -      -       -      +
     94F  PHE*     4.3    11.6    -      -       -      -
     95F  PRO*     4.5     7.0    -      -       +      -
    150F  LYS*     3.6    17.6    +      -       -      +
    183F  GLN*     4.4     7.6    +      -       -      +
    186F  LEU*     4.6     1.8    -      -       +      -
    200F  ASP*     5.8     1.3    -      -       +      -
    318F  ASP*     3.0    19.8    +      -       +      +
    319F  PHE      4.3     1.8    -      -       -      -
    320F  MET*     3.7    41.3    -      -       +      +
    328F  TRP      4.5     1.6    -      -       -      +
    329F  LEU*     1.3    81.7    -      -       -      +
    331F  GLU*     1.3    62.7    +      -       -      +
    401F  ACP      3.2    72.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 331 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72F  CYS      4.0    11.8    -      -       -      +
     74F  LYS*     2.8    43.2    +      -       +      +
     77F  LEU*     4.4     7.9    -      -       +      -
    316F  GLY      3.9     1.1    -      -       -      +
    317F  PHE*     3.8     1.4    -      -       -      -
    318F  ASP*     2.9    37.4    +      -       -      +
    329F  LEU*     4.0     2.8    -      -       -      +
    330F  ILE*     1.3    86.7    -      -       +      +
    332F  VAL*     1.3    79.7    +      -       -      +
    333F  ASN*     3.5    13.4    +      -       -      -
    401F  ACP      2.9    39.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 332 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71F  LEU*     3.7    41.1    -      -       +      +
     72F  CYS*     3.2    30.3    -      -       -      +
     77F  LEU*     4.3     7.0    -      -       +      +
    294F  CYS*     5.3     0.4    -      -       -      -
    315F  PHE*     4.2    15.3    -      -       +      -
    316F  GLY      3.5     4.5    -      -       -      +
    317F  PHE*     3.6    46.7    -      -       +      -
    329F  LEU*     4.3    15.7    -      -       +      -
    331F  GLU*     1.3    82.8    -      -       -      +
    333F  ASN*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 333 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44F  ARG*     5.6     2.6    +      -       -      -
     72F  CYS*     3.9     2.7    -      -       -      -
    202F  ARG*     4.2    11.4    -      -       -      +
    315F  PHE*     3.4     8.4    -      -       -      -
    316F  GLY*     2.8    44.1    +      -       -      +
    318F  ASP*     5.4     0.4    -      -       -      +
    331F  GLU*     3.5     9.0    +      -       -      -
    332F  VAL*     1.3    72.0    -      -       -      +
    334F  GLY*     1.3    59.7    +      -       -      +
    335F  ALA*     3.3    29.1    +      -       -      +
    336F  PRO*     3.6     8.9    -      -       +      +
    401F  ACP      2.8    32.4    +      -       -      +
----------------------------------------------------------
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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