Contacts of the strand formed by residues 23 - 31 (chain D) in PDB entry 1U3H


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 ARG 23 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  ILE*     4.8     4.2    -      -       -      +
      2C  GLU*     3.1    33.1    +      -       -      +
     16D  TYR*     3.7     2.5    -      -       -      +
     17D  PHE*     3.8     0.7    -      -       -      -
     18D  THR*     2.9    61.6    +      -       +      +
     20D  GLY      4.5     0.7    -      -       -      +
     21D  THR      2.9     0.4    -      -       -      -
     22D  GLN*     1.3    84.0    -      -       +      +
     24D  ILE*     1.3    70.5    +      -       -      +
     25D  ARG*     4.2    33.9    -      -       -      +
     43D  ASP*     4.9     5.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 24 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16D  TYR      3.4     8.7    -      -       -      +
     17D  PHE*     3.9    21.1    -      -       +      -
     21D  THR*     4.0    15.5    +      -       +      +
     23D  ARG*     1.3    88.4    +      -       -      +
     25D  ARG*     1.3    70.1    +      -       -      +
     42D  SER*     4.3     1.7    +      -       -      -
     43D  ASP*     5.4     1.4    -      -       -      +
     75D  LEU*     3.9    36.7    -      -       +      +
     79D  CYS*     4.0    15.0    -      -       +      -
     80D  ARG*     3.8    53.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 25 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  ILE*     3.6    44.7    -      -       -      +
     14D  PHE      3.5     1.9    -      -       -      +
     15D  CYS*     3.8     1.2    -      -       -      -
     16D  TYR*     3.0    44.3    +      -       +      +
     23D  ARG*     4.2    20.3    -      -       -      +
     24D  ILE*     1.3    78.7    -      -       -      +
     26D  TYR*     1.3    61.1    +      -       -      +
     27D  VAL*     3.9    11.2    -      -       +      +
     41D  ASP*     2.6    35.5    +      -       -      +
     42D  SER*     3.4    11.2    -      -       -      +
     43D  ASP*     2.7    35.9    +      -       -      +
     44D  VAL*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 26 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11D  PHE*     5.3     0.2    -      -       -      -
     14D  PHE      3.3    20.6    -      -       -      -
     15D  CYS*     4.4     2.2    -      -       -      -
     25D  ARG*     1.3    72.8    -      -       -      +
     27D  VAL*     1.3    62.4    +      -       -      +
     28D  THR*     3.5    16.0    +      -       -      -
     40D  PHE*     3.8    21.3    -      +       -      -
     41D  ASP*     3.6     1.4    -      -       -      -
     42D  SER*     2.9    39.0    +      -       -      -
     71D  THR*     3.7    25.6    -      -       +      -
     74D  GLU*     2.8    40.0    +      -       +      +
     75D  LEU*     3.8    29.1    -      -       +      +
     78D  VAL*     5.5     0.4    -      -       +      -
     79D  CYS*     3.5    22.9    -      -       -      -
      2P  SER*     2.8    33.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 27 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  ILE*     4.8     4.5    -      -       +      -
     12D  GLN      3.7     1.0    -      -       -      +
     13D  PRO*     3.4     1.4    -      -       -      +
     14D  PHE*     2.6    42.0    +      -       +      +
     16D  TYR*     3.6    28.5    -      -       +      -
     25D  ARG*     3.9    22.2    -      -       +      +
     26D  TYR*     1.3    80.9    -      -       -      +
     28D  THR*     1.3    63.3    +      -       -      +
     29D  ARG*     3.8    39.5    -      -       +      +
     39D  ARG*     4.3     8.5    -      -       +      -
     40D  PHE      3.4     8.3    -      -       -      +
     41D  ASP*     4.0    10.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 28 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11D  PHE*     3.0    37.1    -      -       +      -
     12D  GLN      3.9     2.7    -      -       -      -
     13D  PRO*     4.4     1.8    -      -       -      +
     26D  TYR*     3.5    33.3    +      -       -      -
     27D  VAL*     1.3    72.1    +      -       -      +
     29D  ARG*     1.3    59.7    +      -       -      +
     30D  TYR*     3.1    23.9    -      -       +      +
     39D  ARG*     3.3     5.7    -      -       -      +
     40D  PHE*     2.9    47.7    +      -       +      +
     47D  TYR*     4.9     3.4    -      -       +      +
     71D  THR*     4.5     2.7    -      -       -      +
      3P  GLN      5.4     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 29 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  ILE*     3.4    23.8    -      -       -      +
    143C  TYR*     3.4    30.1    +      -       -      -
     10D  GLN      3.7     1.0    -      -       -      +
     11D  PHE*     3.6     9.0    -      -       -      -
     12D  GLN*     3.0    39.7    +      -       +      +
     14D  PHE*     3.6    23.4    -      -       +      -
     16D  TYR*     3.2    22.6    +      -       -      -
     27D  VAL*     3.8    16.3    -      -       +      +
     28D  THR*     1.3    76.1    -      -       -      +
     30D  TYR*     1.3    61.1    +      -       -      +
     31D  ILE*     3.6    12.5    -      -       +      +
     36D  GLU*     3.3    23.4    +      -       -      +
     38D  LEU      3.9     3.1    -      -       -      -
     39D  ARG*     3.5    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 30 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69C  ASN*     5.1     0.4    -      -       -      -
     10D  GLN      3.8     2.9    -      -       -      -
     11D  PHE*     3.7    11.8    -      +       -      -
     28D  THR*     3.1    29.3    -      -       +      +
     29D  ARG*     1.3    75.1    -      -       -      +
     31D  ILE*     1.3    62.7    +      -       -      +
     36D  GLU*     3.6     1.1    -      -       -      +
     37D  TYR*     2.9    57.3    +      -       +      -
     38D  LEU*     2.9    33.8    +      -       +      +
     39D  ARG      4.7     0.2    -      -       -      -
     47D  TYR*     4.0    14.5    +      +       -      -
     61D  TYR*     3.8    16.8    -      +       -      -
      3P  GLN      4.1     0.5    +      -       -      -
      4P  TYR*     3.5    30.3    -      +       -      -
      5P  ARG*     3.1    50.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 31 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143C  TYR*     4.0    29.6    -      -       +      -
      9D  VAL*     3.6     5.5    -      -       -      +
     10D  GLN*     2.8    54.3    +      -       +      +
     12D  GLN*     4.8     6.1    -      -       -      +
     29D  ARG*     3.6    31.2    -      -       +      +
     30D  TYR*     1.3    80.2    -      -       -      +
     32D  TYR*     1.3    64.3    +      -       -      +
     33D  ASN      3.7     6.5    -      -       -      +
     34D  ARG*     3.6    15.3    -      -       -      +
     35D  GLU      3.2    22.9    -      -       -      +
     36D  GLU*     3.8    17.0    -      -       +      -
     37D  TYR*     3.7     7.9    +      -       -      -
      4P  TYR*     4.8     1.0    +      -       -      -
----------------------------------------------------------
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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