Contacts of the strand formed by residues 26 - 34 (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 ALA 26 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20K  CYS*     3.1    27.2    -      -       -      +
     22K  ASP*     4.3     4.3    -      -       -      +
     24K  THR*     3.5    13.9    +      -       -      +
     25K  GLY*     1.3    80.0    +      -       -      +
     27K  ARG*     1.3    60.1    +      -       -      +
     29K  LEU*     4.2     3.4    -      -       +      -
     57K  VAL*     3.6    35.7    -      -       +      -
     59K  LYS      3.7     4.0    -      -       -      -
     64K  MET*     4.0     6.0    -      -       +      +
     97K  ILE*     3.9    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 27 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19K  THR*     3.8     7.8    -      -       -      +
     20K  CYS*     3.0    25.4    +      -       -      +
     25K  GLY      4.6     3.6    +      -       -      +
     26K  ALA*     1.3    75.9    -      -       -      +
     28K  GLU*     1.3    57.6    +      -       +      +
     59K  LYS*     2.6    23.5    +      -       +      +
     60K  GLY*     4.1    14.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 28 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17K  LEU*     3.6    33.6    -      -       +      +
     18K  ILE      3.5     9.1    -      -       -      +
     27K  ARG*     1.3    79.1    -      -       +      +
     29K  LEU*     1.3    70.5    +      -       -      +
     57K  VAL*     3.7     5.2    -      -       -      +
     58K  THR*     2.8    55.3    +      -       -      +
     59K  LYS*     3.1    45.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 29 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17K  LEU*     3.4     2.6    -      -       -      -
     18K  ILE*     2.8    51.7    +      -       +      +
     19K  THR      4.5     0.4    -      -       -      +
     20K  CYS*     3.6    35.9    -      -       +      -
     26K  ALA*     4.2    10.8    -      -       +      -
     28K  GLU*     1.3    81.4    -      -       -      +
     30K  LYS*     1.3    58.8    +      -       -      +
     55K  VAL*     3.3    23.3    -      -       +      -
     56K  SER      3.6     1.3    -      -       -      -
     57K  VAL*     3.6    29.8    -      -       +      -
     58K  THR*     4.6     0.2    -      -       -      -
     69K  LEU*     6.1     0.4    -      -       +      -
     71K  ALA*     4.6     6.5    -      -       +      -
     95K  ALA*     4.2    22.0    -      -       +      +
     97K  ILE*     4.3    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 30 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19920    U      3.3    14.8    +      -       -      -
   19930    C      2.7    46.9    +      -       +      +
   19940    A      5.7     0.6    -      -       -      +
     15K  GLY*     3.9    21.1    -      -       -      +
     16K  SER      3.3     3.6    -      -       -      -
     17K  LEU*     3.7    11.0    -      -       +      -
     29K  LEU*     1.3    72.1    -      -       -      +
     31K  VAL*     1.3    74.2    +      -       -      +
     32K  ILE*     3.5     2.3    +      -       +      +
     55K  VAL*     3.0    17.7    -      -       -      +
     56K  SER*     2.9    31.6    +      -       -      +
     58K  THR*     3.6    18.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      5.2     1.0    +      -       -      -
     12K  LEU*     4.7     9.6    -      -       +      -
     13K  GLU      3.4    24.9    -      -       -      +
     14K  LYS*     4.2     5.5    -      -       -      +
     15K  GLY*     2.7    29.3    +      -       -      -
     16K  SER*     2.9    22.2    +      -       -      +
     18K  ILE*     4.2    15.9    -      -       +      -
     30K  LYS*     1.3    75.0    -      -       -      +
     32K  ILE*     1.3    61.7    +      -       -      +
     33K  SER      4.2    15.3    -      -       -      +
     34K  VAL*     5.0     1.8    -      -       +      -
     47K  ALA*     4.7     8.7    -      -       +      -
     53K  ILE*     4.0    31.2    -      -       +      -
     54K  THR      4.0     2.9    -      -       -      -
     55K  VAL*     4.2     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 32 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      3.3    66.0    -      -       +      +
   25960    A      3.4    23.8    -      -       -      +
     14K  LYS*     2.6    41.7    +      -       -      +
     30K  LYS*     3.7    10.3    -      -       +      +
     31K  VAL*     1.3    80.4    -      -       -      +
     33K  SER*     1.3    60.7    +      -       -      +
     54K  THR*     3.0    11.5    +      -       +      +
     55K  VAL*     4.0     4.7    -      -       -      +
     56K  SER*     3.5    25.6    -      -       -      +
     68K  VAL*     4.6    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 33 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   25960    A      2.5    32.5    +      -       -      +
   25970    U      3.1    29.3    +      -       -      -
   88120   CL      3.3    14.5    -      -       -      +
     14K  LYS*     5.4     1.3    -      -       -      -
     31K  VAL*     4.2     3.1    -      -       -      +
     32K  ILE*     1.3    82.9    +      -       -      +
     34K  VAL*     1.3    66.8    +      -       -      +
     45K  PRO*     6.0     0.4    -      -       -      -
     53K  ILE*     3.2     9.9    -      -       -      +
     54K  THR*     2.8    29.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 34 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   25970    U      2.9    18.7    +      -       -      -
     13K  GLU      6.3     0.2    -      -       -      -
     14K  LYS*     6.1     0.9    -      -       +      +
     31K  VAL*     5.0     4.0    -      -       +      -
     33K  SER*     1.3    79.0    -      -       -      +
     35K  HIS*     1.3    72.8    +      -       -      +
     37K  TYR*     3.1    31.8    +      -       +      +
     45K  PRO*     4.8     8.6    -      -       +      +
     46K  LYS*     3.3    32.5    -      -       -      +
     47K  ALA*     3.3    18.6    -      -       +      -
     51K  ASP*     4.2    28.9    -      -       +      +
     52K  LYS      4.0     2.2    -      -       -      +
     53K  ILE*     4.3     0.9    -      -       +      -
----------------------------------------------------------
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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