Contacts of the strand formed by residues 33 - 38 (chain H) in PDB entry 5U0A


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 LYS 33 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307D  SER*     3.6    35.4    +      -       -      +
     29H  VAL*     4.2     1.3    -      -       -      -
     30H  TYR      2.9    28.7    +      -       -      +
     31H  GLY      3.2     4.6    -      -       -      +
     32H  GLY*     1.3    80.3    -      -       -      +
     34H  GLU*     1.3    67.3    +      -       -      +
     35H  ARG*     3.3     5.1    -      -       -      +
    196H  GLY*     3.5    30.1    -      -       -      +
    303H  ALA*     3.8    26.9    +      -       +      +
    304H  LEU      4.7     7.9    +      -       -      -
    305H  TYR*     5.3    10.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 34 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27H  THR*     3.2    39.5    +      -       +      +
     28H  VAL      3.4     8.3    -      -       -      +
     29H  VAL*     4.1    16.1    -      -       +      +
     32H  GLY      4.4     0.2    +      -       -      -
     33H  LYS*     1.3    74.7    -      -       +      +
     35H  ARG*     1.3    60.1    +      -       -      +
    196H  GLY*     3.3     8.3    -      -       -      -
    197H  THR      3.1    34.2    +      -       -      +
    198H  THR*     5.4     2.6    -      -       -      -
    199H  VAL*     4.3    10.9    -      -       -      +
    168J  ASN*     3.1    29.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 35 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27H  THR*     4.2     2.5    -      -       -      -
     28H  VAL*     2.7    41.0    +      -       +      +
     30H  TYR*     3.1    43.4    +      -       -      -
     31H  GLY*     4.3     1.8    +      -       -      -
     33H  LYS*     3.3     6.7    +      -       -      +
     34H  GLU*     1.3    80.4    -      -       -      +
     36H  THR*     1.3    65.9    +      -       -      +
     37H  ARG*     4.4     0.2    -      -       -      +
    192H  PHE*     4.0     7.1    -      -       +      +
    193H  THR*     3.0    36.5    +      -       -      +
    194H  VAL      3.6     9.2    +      -       -      -
    195H  HIS      3.9     7.2    -      -       -      +
    196H  GLY*     4.2     2.2    -      -       -      -
    197H  THR*     3.9     2.2    -      -       -      +
    300H  PHE      2.2    27.5    +      -       -      -
    301H  GLU      2.4    29.0    +      -       -      -
    303H  ALA*     3.0    34.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 36 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25H  PRO*     3.7    18.7    -      -       -      +
     26H  LYS      3.3    12.2    +      -       -      -
     27H  THR*     4.0    11.3    -      -       -      +
     34H  GLU      4.4     0.2    -      -       -      -
     35H  ARG*     1.3    72.1    -      -       -      +
     37H  ARG*     1.3    63.1    +      -       -      +
    192H  PHE*     3.5     0.9    -      -       -      -
    193H  THR*     3.1    42.3    +      -       +      +
    197H  THR*     3.0    21.9    +      -       +      +
    199H  VAL*     6.0     2.0    -      -       -      -
    227H  SER*     3.5    23.4    +      -       -      +
    228H  ALA      4.9     1.1    -      -       -      +
    231H  PHE*     3.8    16.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 37 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14D  TYR*     2.7    40.3    +      -       -      -
    200D  GLU*     6.0     0.6    -      -       -      +
    201D  VAL      4.2     5.3    +      -       -      -
    202D  ASP*     2.8    36.2    +      -       -      +
     18H  ASN*     4.7     4.2    -      -       -      +
     25H  PRO*     5.5     0.2    -      -       -      +
     26H  LYS*     2.5    66.1    +      -       -      +
     27H  THR      3.9     9.9    +      -       -      +
     28H  VAL*     3.3    28.8    -      -       +      +
     36H  THR*     1.3    78.5    +      -       -      +
     38H  VAL*     1.3    66.4    +      -       -      +
     39H  SER*     3.7     5.7    -      -       -      -
    190H  HIS*     3.6    27.1    +      -       +      -
    191H  ALA      3.1    12.8    -      -       -      +
    192H  PHE*     4.1     5.4    -      -       +      -
    231H  PHE*     5.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 38 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17H  ILE*     3.4    21.8    -      -       +      -
     18H  ASN*     4.0    13.7    -      -       +      +
     37H  ARG*     1.3    75.3    -      -       -      +
     39H  SER*     1.3    66.1    +      -       -      +
     40H  SER*     3.6     0.5    +      -       -      -
     42H  SER*     3.4    22.4    -      -       -      +
     43H  TRP*     3.7    25.7    -      -       +      -
    190H  HIS*     3.8     2.7    -      -       -      -
    191H  ALA*     2.7    33.6    +      -       +      +
    231H  PHE*     3.4    32.5    -      -       +      -
    268H  PRO*     4.0     9.2    -      -       +      -
----------------------------------------------------------
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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