Contacts of the strand formed by residues 25 - 32 (chain S) in PDB entry 5IYB


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 LYS 25 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22S  THR      5.7     2.0    -      -       -      +
     23S  THR      4.1     2.1    +      -       -      +
     24S  LYS*     1.3    76.6    -      -       -      +
     26S  TYR*     1.3    61.5    +      -       -      +
     94S  GLU*     5.2     7.5    +      -       -      -
    141S  HIS*     3.4    41.5    +      -       +      -
     97T  THR*     3.7     7.1    -      -       -      -
     98T  GLU*     3.3    52.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 26 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22S  THR*     3.9    27.5    -      -       +      +
     24S  LYS*     3.5    28.6    -      -       +      -
     25S  LYS*     1.3    74.9    -      -       -      +
     27S  ASN*     1.3    62.5    +      -       -      +
    126S  ILE*     5.8     6.1    -      -       +      -
    138S  PHE*     3.3    65.4    -      +       +      +
    139S  PRO*     3.1    25.4    -      -       +      +
    140S  VAL*     4.8     2.0    -      -       -      -
    141S  HIS*     2.8    37.4    +      -       -      +
     95T  VAL*     4.7     9.0    -      -       +      -
     96T  PHE      4.6     0.2    -      -       -      -
     97T  THR*     3.5    28.3    -      -       +      -
    107T  GLU*     5.0     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 27 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26S  TYR*     1.3    84.0    +      -       -      +
     28S  ILE*     1.3    64.3    +      -       -      +
    126S  ILE*     5.6     1.1    -      -       -      +
    140S  VAL*     5.1     2.2    -      -       -      -
    141S  HIS*     4.0     1.0    -      -       -      +
    142S  ASN*     3.3    39.8    -      -       -      +
    144S  TYR*     4.0     6.0    -      -       +      -
     95T  VAL*     3.1    31.1    -      -       -      +
     96T  PHE*     3.3    49.5    +      -       +      +
     98T  GLU*     3.3    35.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 28 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27S  ASN*     1.3    75.8    -      -       -      +
     29S  MET*     1.3    69.7    +      -       -      +
     30S  ALA*     4.1     6.1    -      -       +      +
    126S  ILE*     3.9    16.2    -      -       +      -
    140S  VAL*     4.0    23.6    -      -       +      -
    142S  ASN      3.0    12.7    +      -       -      +
    143S  TRP*     3.8    41.1    -      -       +      -
    144S  TYR*     3.5    20.3    +      -       -      +
     20T  LEU*     4.6     7.2    -      -       +      -
     93T  LEU*     4.2    17.7    -      -       +      -
     94T  THR      4.1     2.7    -      -       -      +
     95T  VAL*     3.5    23.1    -      -       +      -
     96T  PHE*     3.3    11.6    -      -       -      -
    110T  VAL*     4.6     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 29 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28S  ILE*     1.3    74.2    -      -       -      +
     30S  ALA*     1.3    59.9    +      -       -      +
     31S  PHE*     3.5    31.2    -      -       +      -
     42S  TRP*     4.6     9.6    -      -       +      -
     47S  LEU*     5.0     5.4    -      -       +      -
    100S  LEU*     4.6     7.4    -      -       +      -
    144S  TYR      4.5     1.1    -      -       -      -
    146S  PHE*     3.5    28.7    -      -       +      -
      7T  LEU*     4.4    14.1    -      -       +      -
     92T  THR      3.9     0.7    -      -       -      +
     93T  LEU*     3.3     1.4    -      -       -      -
     94T  THR*     2.8    60.3    +      -       -      +
     95T  VAL*     4.8     0.2    -      -       -      -
     96T  PHE*     3.4    33.6    -      -       +      -
    106T  LEU*     3.9    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 30 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28S  ILE*     4.2     1.3    -      -       +      -
     29S  MET*     1.3    74.2    -      -       -      +
     31S  PHE*     1.3    72.6    +      -       -      +
    143S  TRP*     3.9    21.8    -      -       +      +
    144S  TYR      3.5    17.4    +      -       -      +
    145S  ASN*     4.7     4.0    -      -       -      +
    146S  PHE*     3.3    21.9    +      -       -      +
     91T  GLN*     5.1     3.8    -      -       -      +
     92T  THR      3.3     4.0    -      -       -      -
     93T  LEU*     3.8    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 31 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29S  MET*     3.5    28.3    -      -       +      -
     30S  ALA*     1.3    78.1    -      -       -      +
     32S  ASN*     1.3    59.9    +      -       -      +
     35S  ASP*     5.1     3.6    -      -       +      -
     37S  VAL*     3.6    31.0    -      -       +      -
     39S  PHE*     3.7    19.1    -      +       -      -
     42S  TRP*     3.4    36.6    -      +       -      -
    100S  LEU*     4.5     2.7    -      -       +      -
    110S  PHE*     4.4    13.2    -      +       -      -
    146S  PHE*     3.4    39.5    -      +       +      -
     91T  GLN*     3.3    10.2    -      -       -      +
     92T  THR*     2.4    61.4    +      -       +      +
     94T  THR*     4.4     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 32 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283B  ASP*     4.9     5.7    +      -       -      -
    286B  GLU*     4.0    18.2    +      -       -      +
    557B  SER*     3.7    21.6    +      -       -      -
     31S  PHE*     1.3    77.5    -      -       -      +
     33S  ALA*     1.3    70.7    +      -       -      +
     34S  ALA*     2.7    39.5    +      -       -      +
     35S  ASP*     3.1    29.8    +      -       +      +
     36S  LYS      4.1     1.6    +      -       -      -
     37S  VAL*     4.8     1.9    +      -       -      +
    146S  PHE      4.7     6.3    +      -       -      +
    147S  THR*     6.4     1.8    -      -       +      -
     90T  GLY      3.9     1.4    -      -       -      +
     91T  GLN*     4.6     7.4    -      -       -      +
     92T  THR*     4.4     3.1    +      -       -      -
----------------------------------------------------------
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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