Contacts of the strand formed by residues 194 - 199 (chain D) in PDB entry 1UU1


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 LEU 194 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160D  ILE*     5.3     1.8    -      -       +      -
    164D  LEU*     3.9    19.3    -      -       +      -
    169D  PHE*     3.6     8.0    -      -       -      -
    170D  VAL*     3.4    30.7    -      -       +      +
    172D  LEU*     3.9    21.8    -      -       +      -
    184D  TYR*     3.9    14.1    -      -       +      +
    187D  PHE*     3.9    29.2    -      -       +      +
    188D  LEU*     3.7    35.3    -      -       +      +
    191D  TYR*     4.6     7.6    -      -       +      +
    192D  GLU      3.3     3.6    +      -       -      +
    193D  ASN*     1.3    79.5    -      -       -      +
    195D  ALA*     1.3    72.1    +      -       -      +
    196D  VAL*     4.7     2.5    -      -       +      -
    216D  ALA*     3.7     8.0    -      -       -      +
    217D  SER      4.4     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 195 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92D  MET*     4.1    10.5    -      -       +      -
    169D  PHE*     3.4    22.9    -      -       +      -
    170D  VAL      2.8    10.0    +      -       -      +
    171D  ALA*     3.6     2.6    -      -       -      -
    172D  LEU*     2.9    25.6    +      -       -      +
    194D  LEU*     1.3    79.6    -      -       -      +
    196D  VAL*     1.3    64.0    +      -       -      +
    197D  ILE*     3.9     1.6    +      -       -      +
    214D  VAL*     4.1    14.1    -      -       +      -
    215D  VAL      3.5     5.6    -      -       -      +
    216D  ALA*     3.9    12.8    -      -       +      -
    220D  PHE*     4.4     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 196 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172D  LEU*     3.5    14.8    -      -       +      -
    174D  GLU*     3.5    41.5    -      -       +      +
    184D  TYR      4.2     5.2    -      -       -      +
    185D  VAL*     3.9    38.4    -      -       +      +
    188D  LEU*     4.8     1.8    -      -       +      -
    194D  LEU*     4.7     9.2    -      -       +      -
    195D  ALA*     1.3    75.7    -      -       -      +
    197D  ILE*     1.3    63.4    +      -       -      +
    198D  ARG*     3.9    11.2    -      -       +      +
    213D  TYR      3.9     0.5    -      -       -      +
    214D  VAL*     3.2     5.6    -      -       -      -
    215D  VAL*     2.9    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 197 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85D  ALA*     3.6    31.6    -      -       +      +
     88D  ILE*     3.8    25.8    -      -       +      -
     89D  ILE*     4.3    15.9    -      -       +      -
     92D  MET*     3.9    24.7    -      -       +      -
    143D  PHE*     5.0     1.1    -      -       +      -
    171D  ALA*     4.2    20.9    -      -       +      -
    172D  LEU      3.1     6.1    +      -       -      -
    173D  ASP*     4.2    24.2    -      -       +      +
    174D  GLU*     2.8    34.8    +      -       -      +
    175D  ALA      3.6     1.1    +      -       -      -
    195D  ALA      4.5     1.8    -      -       -      +
    196D  VAL*     1.3    76.8    -      -       -      +
    198D  ARG*     1.3    63.2    +      -       -      +
    213D  TYR      3.6     7.9    -      -       -      +
    214D  VAL*     4.1     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 198 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68D  TYR*     4.4     2.4    -      -       -      -
     69D  LEU*     3.7    19.1    -      -       -      +
     85D  ALA*     4.1     7.3    -      -       -      +
    174D  GLU*     2.8    44.0    +      -       -      +
    175D  ALA*     5.2     0.4    -      -       -      -
    177D  TYR*     3.5    36.5    +      -       -      +
    178D  GLU*     4.3     4.5    +      -       -      +
    183D  SER*     3.2    28.7    +      -       -      -
    185D  VAL*     4.0     9.7    -      -       -      +
    196D  VAL*     3.9     9.4    -      -       +      +
    197D  ILE*     1.3    74.3    -      -       -      +
    199D  THR*     1.3    64.3    +      -       -      +
    212D  GLY*     3.1     4.3    -      -       -      -
    213D  TYR*     2.8    79.4    +      -       +      +
    215D  VAL*     5.1     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 199 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85D  ALA*     4.2     4.9    -      -       -      -
    174D  GLU      5.1     0.2    +      -       -      -
    175D  ALA*     3.5    37.2    -      -       +      +
    178D  GLU*     4.6    10.3    +      -       -      +
    198D  ARG*     1.3    78.3    -      -       -      +
    200D  PHE*     1.3    72.7    +      -       -      +
    201D  SER*     2.8    14.1    +      -       -      +
    202D  LYS*     4.1    19.3    +      -       +      +
    203D  ALA*     5.5     1.4    +      -       -      +
    204D  PHE*     4.2    11.4    -      -       -      -
    211D  VAL      3.6     7.9    +      -       -      -
    212D  GLY*     4.0     0.4    -      -       -      -
    213D  TYR*     4.7     3.8    +      -       -      -
   1335D  PMP      2.8    31.2    +      -       -      +
----------------------------------------------------------
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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