Contacts of the strand formed by residues 125 - 131 (chain A) in PDB entry 1YH7


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 125 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  LEU*     6.0     1.1    -      -       +      -
     66A  SER      3.3     9.2    -      -       -      +
     68A  ARG*     3.8     7.2    -      -       -      -
     72A  LEU      3.8     5.7    +      -       -      +
     73A  VAL*     3.3    21.8    -      -       +      +
     74A  SER      3.1    21.0    +      -       -      -
     75A  LEU*     3.9     5.6    -      -       +      -
    110A  VAL*     3.2    34.3    -      -       +      -
    114A  ILE*     3.6    23.6    -      -       +      -
    123A  PRO*     4.0    14.1    -      -       +      -
    124A  GLY*     1.4    77.4    -      -       -      +
    126A  SER*     1.4    60.5    +      -       -      +
    127A  ALA*     3.7    28.7    -      -       +      -
    149A  THR*     5.8     2.7    -      -       +      -
    152A  PHE*     3.6    24.9    -      +       +      -
    153A  LEU*     4.1    26.0    -      -       +      -
    156A  LEU*     3.9     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  PHE*     3.4    24.3    -      -       -      -
     24A  PHE*     4.5    16.8    -      -       -      -
     65A  GLY*     3.0     4.5    -      -       -      -
     66A  SER*     2.6    45.9    +      -       -      +
     67A  PRO      5.2     0.6    +      -       -      -
     68A  ARG*     3.8    15.7    -      -       -      +
     74A  SER      3.5     6.5    -      -       -      +
    125A  PHE*     1.4    76.4    -      -       -      +
    127A  ALA*     1.4    61.0    +      -       -      +
    152A  PHE*     3.9     3.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  PHE*     4.1     0.9    -      -       -      -
     63A  LEU*     3.5    20.4    -      -       +      -
     64A  VAL      3.6     4.3    -      -       -      -
     74A  SER      2.7    11.1    +      -       -      +
     75A  LEU*     3.1    24.7    -      -       +      +
     76A  LEU      2.8    24.3    +      -       -      +
    110A  VAL*     6.3     0.7    -      -       +      -
    125A  PHE*     3.7    14.8    -      -       +      -
    126A  SER*     1.4    78.2    -      -       -      +
    128A  VAL*     1.3    64.9    +      -       -      +
    129A  VAL*     5.0     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ALA*     5.2     4.3    -      -       +      +
     19A  ALA*     5.9     2.2    -      -       +      -
     20A  PHE*     3.0    40.8    -      -       +      +
     23A  GLU*     5.1     2.5    -      -       +      -
     24A  PHE*     3.5    20.0    -      -       +      -
     63A  LEU*     2.7    14.6    -      -       -      +
     64A  VAL*     2.7    64.6    +      -       +      +
     76A  LEU*     3.2    17.3    -      -       +      +
    127A  ALA*     1.3    72.7    -      -       -      +
    129A  VAL*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  THR*     5.8     3.1    -      -       -      -
     62A  VAL      3.2     7.6    -      -       -      +
     63A  LEU*     2.9    40.2    -      -       +      -
     76A  LEU      3.0     9.4    +      -       -      +
     77A  THR*     3.8    19.9    +      -       -      +
     78A  THR*     3.0    25.5    +      -       -      -
    106A  TRP*     6.3     2.7    -      -       +      -
    127A  ALA*     5.0     3.1    -      -       +      -
    128A  VAL*     1.3    72.6    -      -       -      +
    130A  VAL*     1.4    69.7    +      -       -      +
    131A  SER*     6.3     1.1    -      -       -      -
    145A  LEU*     4.6    23.1    -      -       +      -
    148A  ALA*     5.8     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLU*     4.4    27.8    -      -       +      +
     16A  ALA*     5.2    13.2    -      -       +      -
     60A  MET      4.3     0.3    -      -       -      +
     61A  THR*     3.3     1.0    -      -       -      -
     62A  VAL*     2.6    53.1    +      -       +      +
     77A  THR*     5.4     0.2    -      -       -      -
     78A  THR*     2.9    37.7    -      -       +      +
     79A  SER*     4.6     1.6    -      -       -      +
    129A  VAL*     1.4    77.2    -      -       -      +
    131A  SER*     1.4    67.6    +      -       -      +
    132A  SER*     5.0     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  MET      3.4     3.4    -      -       -      -
     61A  THR*     2.9    31.4    -      -       -      -
     79A  SER*     3.7    20.8    +      -       -      -
    129A  VAL*     6.3     1.6    -      -       -      -
    130A  VAL*     1.4    82.3    -      -       -      +
    132A  SER*     1.3    62.0    +      -       -      +
    133A  VAL*     3.4    18.9    +      -       -      +
----------------------------------------------------------
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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