Contacts of the strand formed by residues 11 - 14 (chain A) in PDB entry 6YBO


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 11 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  PRO*     3.8    17.5    -      -       +      -
      6A  THR      4.9     1.9    +      -       -      -
      9A  ASP*     3.3    33.8    -      -       +      -
     10A  ARG*     1.3    77.1    -      -       -      +
     12A  THR*     1.3    58.7    +      -       -      +
     13A  PHE*     4.7     1.6    -      -       +      -
     47A  GLY      5.0     1.1    -      -       -      +
     48A  ALA*     3.7     7.3    -      -       -      +
     49A  HIS*     2.8    34.5    +      -       -      +
     50A  GLY      3.4     0.9    +      -       -      -
    284A  ARG*     3.4    17.9    -      -       +      -
    286A  PHE*     3.5    22.2    -      +       +      -
    307A  MET*     3.6    43.3    -      -       +      -
    310A  TYR*     3.7    46.7    -      +       +      -
    311A  LEU*     4.0    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 12 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  ARG      3.9     8.7    -      -       -      +
     11A  PHE*     1.3    79.7    -      -       -      +
     13A  PHE*     1.3    65.1    +      -       -      +
     49A  HIS*     3.9    13.9    -      -       +      -
     50A  GLY*     3.2    27.4    -      -       -      +
     51A  VAL      4.5     1.1    -      -       -      -
     52A  THR*     4.5     5.8    -      -       -      +
     87A  PRO*     4.0    14.4    -      -       +      -
    243A  HIS*     4.9     0.2    +      -       -      -
    283A  PRO*     3.8    10.6    -      -       +      +
    284A  ARG      3.0     4.6    +      -       -      -
    285A  HIS*     3.2    30.5    -      -       -      +
    286A  PHE*     2.9    31.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 13 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     4.7     2.0    -      -       +      -
     12A  THR*     1.3    78.8    -      -       -      +
     14A  GLY*     1.3    62.6    +      -       -      +
     17A  THR*     3.9     8.1    -      -       -      +
     18A  VAL*     4.7     0.9    -      -       +      -
     43A  LEU*     3.7    35.7    -      -       +      -
     48A  ALA*     4.1    13.2    -      -       +      -
     50A  GLY      3.3     4.4    +      -       -      -
     51A  VAL*     3.1    10.2    -      -       -      +
     52A  THR*     3.0    17.6    +      -       -      -
    285A  HIS*     3.8     5.2    -      -       -      -
    286A  PHE*     3.6    36.1    -      +       +      -
    288A  PHE*     3.8    31.6    -      +       -      -
    303A  ALA*     3.6    32.8    -      -       +      -
    306A  CYS*     4.3     1.3    -      -       -      -
    307A  MET*     3.9    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  PHE*     1.3    74.6    -      -       -      +
     15A  LEU*     1.3    65.5    +      -       -      +
     16A  TRP*     3.1    18.6    -      -       -      -
     17A  THR*     2.7    28.7    +      -       -      -
     18A  VAL*     4.0     3.6    +      -       -      +
     43A  LEU*     5.4     0.6    -      -       -      +
     51A  VAL*     5.4     0.7    -      -       -      -
     52A  THR*     3.1    19.3    -      -       -      -
    285A  HIS*     3.4     8.7    +      -       -      -
    286A  PHE      3.7     6.5    +      -       -      -
----------------------------------------------------------
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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