Contacts of the strand formed by residues 68 - 75 (chain K) 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 VAL 68 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      3.8    38.4    -      -       -      +
   25960    A      4.5    17.7    -      -       -      +
   25970    U      5.6     0.4    -      -       -      +
     32K  ILE*     4.6     3.1    -      -       +      -
     54K  THR*     3.7    26.2    -      -       +      -
     55K  VAL      3.2     7.0    -      -       -      +
     56K  SER*     4.6     2.0    -      -       -      -
     66K  ARG      3.7     3.8    +      -       -      +
     67K  GLN*     1.3    72.4    -      -       -      +
     69K  LEU*     1.3    68.8    +      -       -      +
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Residues in contact with LEU 69 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29K  LEU*     6.5     0.2    -      -       +      -
     54K  THR*     3.5     4.1    -      -       -      +
     55K  VAL*     2.6    47.7    +      -       +      +
     57K  VAL*     4.2     9.6    -      -       +      -
     64K  MET*     3.9    28.3    -      -       +      -
     67K  GLN*     3.7    34.3    -      -       +      +
     68K  VAL*     1.3    82.5    -      -       -      +
     70K  GLU*     1.3    67.0    +      -       -      +
     97K  ILE*     4.1    23.6    -      -       +      -
     98K  VAL      5.4     0.9    -      -       -      +
    105K  ARG*     4.7    12.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 70 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   25970    U      5.0     6.2    +      -       -      +
     35K  HIS*     5.9     2.7    -      -       -      -
     52K  LYS*     3.6    35.4    +      -       +      +
     53K  ILE      3.4     9.4    -      -       -      +
     54K  THR*     4.4    12.6    -      -       +      +
     69K  LEU*     1.3    77.0    -      -       -      +
     71K  ALA*     1.3    64.4    +      -       -      +
     97K  ILE*     3.5     6.8    -      -       -      +
     98K  VAL*     2.9    38.0    +      -       +      +
     99K  ASP      4.1    14.7    -      -       -      +
    100K  GLU*     5.1     7.2    -      -       -      +
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Residues in contact with ALA 71 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29K  LEU*     4.6     7.0    -      -       +      -
     52K  LYS*     3.3     7.9    -      -       -      +
     53K  ILE*     2.8    40.2    +      -       +      +
     55K  VAL*     4.4    10.8    -      -       +      -
     70K  GLU*     1.3    77.4    -      -       -      +
     72K  VAL*     1.3    65.6    +      -       -      +
     95K  ALA*     4.2    14.4    -      -       +      -
     96K  VAL      3.3    20.4    -      -       -      +
     97K  ILE*     3.9     3.8    -      -       +      +
     98K  VAL*     4.0     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 72 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50K  GLY      4.7     0.9    -      -       -      +
     51K  ASP      3.6     7.4    -      -       -      +
     52K  LYS*     4.7     6.3    -      -       +      -
     71K  ALA*     1.3    80.0    -      -       -      +
     73K  VAL*     1.3    74.2    +      -       -      +
     74K  VAL*     3.3     6.8    +      -       +      +
     95K  ALA*     3.1     5.0    -      -       -      -
     96K  VAL*     2.9    33.3    +      -       +      +
     98K  VAL*     3.9    23.6    -      -       +      -
    117K  VAL*     4.0     9.6    -      -       +      -
    121K  PHE*     3.3    55.9    -      -       +      -
    124K  VAL*     4.9     6.1    -      -       +      -
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Residues in contact with VAL 73 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12K  LEU*     4.1    22.7    -      -       +      -
     18K  ILE*     5.6     0.2    -      -       +      -
     47K  ALA*     5.0     1.6    -      -       +      -
     48K  GLY      3.4    29.8    -      -       -      +
     49K  LEU*     3.8     9.6    -      -       -      -
     50K  GLY      3.0    18.9    +      -       -      +
     51K  ASP      3.1    14.3    +      -       -      +
     53K  ILE*     4.0    31.4    -      -       +      -
     72K  VAL*     1.3    74.3    -      -       -      +
     74K  VAL*     1.3    61.6    +      -       -      +
     75K  ARG      3.8    13.7    -      -       -      +
     76K  GLN*     4.9     1.6    -      -       +      -
     94K  ALA      3.6    13.0    -      -       -      +
     95K  ALA*     4.0     3.4    -      -       +      -
    117K  VAL*     3.7     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 74 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21K  ALA*     5.7     1.1    -      -       +      -
     49K  LEU*     4.0     6.2    -      -       -      +
     72K  VAL*     3.3    15.5    +      -       +      +
     73K  VAL*     1.3    75.2    -      -       -      +
     75K  ARG*     1.3    67.4    +      -       +      +
     90K  PHE*     4.5     0.7    -      -       -      -
     94K  ALA*     2.8    15.4    +      -       +      +
     96K  VAL*     3.7    27.4    -      -       +      +
    112K  PRO      3.9     0.9    -      -       -      +
    113K  ILE*     3.0    50.0    -      -       +      -
    114K  ALA*     3.7    21.0    +      -       -      +
    117K  VAL*     4.2    14.9    -      -       +      +
    124K  VAL*     4.7     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 75 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19K  THR*     4.7     5.1    -      -       -      +
     21K  ALA*     3.9    10.3    -      -       -      +
     49K  LEU*     4.8     1.8    -      -       -      -
     73K  VAL*     3.8     8.4    -      -       -      +
     74K  VAL*     1.3    85.1    -      -       +      +
     76K  GLN*     1.3    64.7    +      -       -      +
     90K  PHE*     3.6    31.9    -      -       +      -
     92K  ASP*     2.9    40.2    +      -       -      +
     93K  ASN*     3.2     2.1    -      -       -      +
     94K  ALA*     2.9    50.2    +      -       +      +
    110K  LYS*     2.9    27.5    +      -       -      +
    111K  GLY*     3.5    10.5    +      -       -      -
    112K  PRO*     2.9    42.0    +      -       -      +
    113K  ILE*     5.4     0.8    -      -       -      +
     24U  LYS*     5.8     1.2    -      -       -      +
----------------------------------------------------------
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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