Contacts of the strand formed by residues 56 - 62 (chain N) in PDB entry 1YHQ


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 ASP 56 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1179    G      5.1     1.2    +      -       -      -
    1189    C      3.2    31.1    +      -       -      +
     48N  VAL*     3.2     1.9    -      -       -      -
     49N  THR*     2.6    55.3    +      -       +      +
     50N  LEU      4.2     2.6    -      -       -      +
     51N  GLY*     4.0    17.3    -      -       -      -
     52N  PRO*     4.9     3.3    -      -       -      +
     54N  GLY      4.5     1.3    -      -       -      -
     55N  ASP*     1.3    74.9    -      -       -      +
     57N  THR*     1.3    61.6    +      -       -      +
     58N  LEU*     3.0     9.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 57 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      59    G      3.1    23.2    +      -       -      -
      69    C      5.1     0.3    +      -       -      -
    1189    C      3.0     8.5    +      -       -      +
    1199    C      3.4    54.0    -      -       -      +
     46N  GLN*     4.1    11.3    +      -       +      -
     47N  LEU      3.5     6.5    -      -       -      +
     48N  VAL*     3.8    14.5    -      -       -      +
     55N  ASP      4.2     0.6    -      -       -      -
     56N  ASP*     1.3    71.8    -      -       -      +
     58N  LEU*     1.3    59.6    +      -       -      +
     59N  ALA      3.3    26.0    -      -       -      +
     60N  SER*     4.0     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 58 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1199    C      6.1     0.2    -      -       -      -
     32N  PRO*     5.9     4.9    -      -       +      -
     47N  LEU*     2.9    16.2    +      -       +      +
     48N  VAL      4.4     0.2    -      -       -      -
     49N  THR*     3.3    28.7    -      -       +      +
     56N  ASP*     3.0    24.0    -      -       +      +
     57N  THR*     1.3    74.3    -      -       -      +
     59N  ALA*     1.3    63.3    +      -       -      +
     95N  ALA*     3.9    19.5    -      -       +      +
     97N  VAL*     4.1    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 59 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1199    C      5.3     0.2    -      -       -      -
     47N  LEU*     2.8    33.2    +      -       +      -
     57N  THR*     3.3     6.5    -      -       -      +
     58N  LEU*     1.3    82.1    -      -       +      +
     60N  SER*     1.3    64.4    +      -       -      +
     88N  ALA      4.3     2.5    -      -       -      +
     91N  ARG*     3.9    12.8    -      -       +      +
     92N  ALA*     3.8    37.7    -      -       +      +
     95N  ALA*     4.9     0.9    -      -       +      -
     97N  VAL*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 60 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1199    C      3.2    21.6    +      -       -      -
    1209    A      3.9    17.7    +      -       -      -
     44N  ARG*     5.5     3.1    -      -       -      -
     45N  ALA      3.1    13.0    -      -       -      -
     46N  GLN*     3.7    18.2    -      -       -      -
     57N  THR*     4.0     1.1    -      -       -      -
     59N  ALA*     1.3    79.3    -      -       -      +
     61N  ALA*     1.3    63.9    +      -       -      +
     88N  ALA*     4.0     5.3    -      -       -      +
     91N  ARG*     2.9    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 61 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44N  ARG*     3.5     3.7    -      -       -      +
     45N  ALA      2.9    30.5    +      -       -      +
     60N  SER*     1.3    78.7    -      -       -      +
     62N  HIS*     1.3    60.4    +      -       -      +
     84N  THR*     3.3    30.8    -      -       +      +
     87N  LEU*     3.9     9.6    -      -       +      -
     88N  ALA*     3.3    19.5    -      -       +      +
     91N  ARG*     3.5    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 62 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     269    C      5.0     4.4    +      -       -      -
     279    C      4.7     3.6    +      -       -      -
    1209    A      4.8    11.0    -      -       -      +
     42N  HIS*     3.3    44.7    -      +       +      +
     43N  VAL      3.7     2.2    -      -       -      -
     44N  ARG*     3.6    48.0    +      -       +      +
     61N  ALA*     1.3    76.1    -      -       -      +
     63N  SER*     1.3    63.4    +      -       -      +
     64N  SER*     2.8    38.3    +      -       -      +
     65N  ASP*     2.7    40.5    +      -       -      +
     66N  LEU*     3.7     3.8    +      -       -      +
     84N  THR*     4.0     3.4    -      -       -      -
     87N  LEU*     5.1     2.3    -      -       -      +
----------------------------------------------------------
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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