Contacts of the strand formed by residues 5 - 13 (chain A) in PDB entry 3U53


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 5 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ARG*     1.3    75.3    -      -       -      +
      6A  CYS*     1.3    66.4    +      -       -      +
     42A  LYS*     4.6     4.9    -      -       +      -
     43A  GLY*     3.0    26.7    -      -       -      +
     44A  HIS*     4.2    10.5    -      -       +      +
     45A  VAL      4.5     0.4    -      -       -      +
     90A  THR      2.9    12.1    +      -       -      +
     91A  VAL*     3.1    21.0    -      -       +      -
     92A  ILE*     2.9    22.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 6 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ARG*     5.1     1.3    -      -       -      -
      5A  ALA*     1.3    80.7    -      -       -      +
      7A  GLY*     1.3    59.8    +      -       -      +
     42A  LYS*     3.2     5.4    -      -       -      -
     43A  GLY      2.8    27.8    +      -       -      +
     45A  VAL*     4.2     9.2    -      -       -      -
     51A  ASP*     3.5    58.1    -      -       -      +
     54A  THR*     3.8    10.3    -      -       -      +
     55A  ALA*     3.9    11.0    -      -       +      +
     58A  GLU*     4.1     3.1    -      -       -      +
     91A  VAL*     4.6     0.2    -      -       -      -
     92A  ILE*     3.2    20.0    -      -       +      +
     94A  TRP*     4.6     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 7 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  CYS*     1.3    76.6    -      -       -      +
      8A  LEU*     1.3    74.8    +      -       -      +
     41A  PRO      3.1    15.0    -      -       -      -
     42A  LYS*     3.8     6.0    -      -       -      +
     55A  ALA*     3.4    12.1    -      -       -      +
     92A  ILE      2.8     9.3    +      -       -      +
     93A  TYR*     3.4    12.0    -      -       -      -
     94A  TRP*     3.3    14.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 8 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  GLY*     1.3    83.3    -      -       -      +
      9A  ILE*     1.3    60.7    +      -       -      +
     10A  ILE*     3.1    17.2    +      -       +      +
     40A  PRO*     3.2    15.2    -      -       -      +
     41A  PRO*     3.1    16.7    +      -       -      +
     52A  LEU*     4.4     0.2    -      -       +      -
     55A  ALA*     3.7    19.3    -      -       +      +
     56A  LEU*     4.1    13.2    -      -       +      -
     59A  THR*     3.4    23.9    +      -       +      +
     70A  LEU*     3.9    25.8    -      -       +      -
     72A  ILE*     3.9    13.5    -      -       +      -
     93A  TYR*     3.6     4.2    -      -       -      -
     94A  TRP*     3.4    30.7    -      -       +      +
     96A  ALA*     3.9    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 9 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  LEU*     1.3    70.0    -      -       -      +
     10A  ILE*     1.3    60.2    +      -       -      +
     26A  PHE*     3.8    29.8    -      -       +      -
     40A  PRO*     4.0    13.0    -      -       +      -
     76A  PHE*     4.4    16.2    -      -       +      -
     78A  ARG*     5.6     0.2    -      -       +      -
     93A  TYR*     3.9    32.5    -      -       +      -
     94A  TRP      2.8    12.0    +      -       -      +
     95A  LEU*     3.5    16.5    -      -       +      +
     96A  ALA      3.0    23.0    +      -       -      +
    131A  MET*     5.6     1.1    -      -       -      -
    134A  ALA*     4.1    30.7    -      -       +      +
    135A  LEU*     4.0    18.6    -      -       +      -
    138A  GLY*     5.4     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 10 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  LEU*     3.1    16.6    +      -       +      +
      9A  ILE*     1.3    74.7    -      -       -      +
     11A  PHE*     1.3    61.8    +      -       -      +
     26A  PHE*     3.3     7.6    -      -       -      +
     27A  LEU*     3.0    43.0    +      -       +      +
     40A  PRO*     4.7     3.0    -      -       -      +
     41A  PRO*     4.0    17.9    -      -       +      -
     59A  THR*     4.1    15.5    -      -       +      -
     65A  ILE*     4.3     4.5    -      -       +      -
     70A  LEU*     3.4    31.0    -      -       +      -
     96A  ALA*     3.5    14.6    -      -       +      +
     98A  VAL*     3.6    23.6    -      -       +      -
    116A  TRP*     3.8    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 11 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  ILE*     1.3    76.4    -      -       -      +
     12A  ARG*     1.3    72.5    +      -       -      +
     13A  ARG*     4.2    17.3    -      -       +      -
     24A  ILE*     4.2     7.4    -      -       +      -
     25A  GLU      2.9    13.2    -      -       -      +
     26A  PHE*     3.8    17.7    -      -       +      -
     73A  ILE*     4.0    11.9    -      -       +      -
     95A  LEU*     3.5    24.0    -      -       +      -
     96A  ALA      3.0    35.7    +      -       -      -
     97A  GLU*     3.4    36.0    -      -       +      -
     98A  VAL*     3.0    25.7    +      -       -      +
    116A  TRP*     3.7     4.7    -      -       -      -
    142A  LEU*     3.6    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 12 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     1.3    76.7    -      -       -      +
     13A  ARG*     1.3    64.3    +      -       -      +
     14A  CYS*     4.0     4.7    +      -       -      -
     24A  ILE*     3.3     5.7    -      -       -      -
     25A  GLU*     2.7    64.7    +      -       +      +
     97A  GLU*     5.1     0.2    -      -       -      -
     98A  VAL*     3.3    23.8    -      -       +      +
    101A  TYR*     2.9    68.6    +      -       +      -
    116A  TRP*     3.3    54.4    -      -       +      +
    159A  GOL      3.7     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 13 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     4.2    12.2    -      -       +      -
     12A  ARG*     1.3    77.9    -      -       -      +
     14A  CYS*     1.3    62.3    +      -       -      +
     15A  LEU*     3.9    27.7    +      -       +      +
     23A  ALA*     3.1    10.9    +      -       -      +
     24A  ILE*     4.2    11.8    -      -       +      +
     73A  ILE*     6.2     0.6    -      -       -      +
     97A  GLU*     3.0    33.1    +      -       -      +
    101A  TYR*     4.0     6.6    -      -       -      -
    142A  LEU*     4.5    19.8    +      -       -      +
    146A  GLU*     3.1    36.5    +      -       -      +
    159A  GOL      3.1    36.1    +      -       -      +
----------------------------------------------------------
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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