Contacts of the strand formed by residues 149 - 155 (chain A) in PDB entry 1UA4


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 ILE 149 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ALA*     3.7    19.7    -      -       +      +
    119A  ASN*     3.7    19.1    -      -       -      +
    122A  GLY*     4.1     0.7    -      -       -      -
    123A  GLY*     3.9    17.9    -      -       -      +
    129A  VAL*     3.7    19.1    -      -       +      -
    131A  VAL*     4.1    16.2    -      -       +      -
    144A  PHE*     3.9    21.3    -      -       +      -
    145A  LEU      3.4    24.2    -      -       -      +
    147A  GLY      2.7    10.9    +      -       -      +
    148A  PRO*     1.3    74.6    -      -       -      +
    150A  TYR*     1.3    66.4    +      -       -      +
    163A  HIS*     3.3    33.4    +      -       +      +
    164A  PRO*     4.0    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  PRO*     4.7     9.0    -      -       +      -
    129A  VAL      2.8    23.9    +      -       -      +
    130A  ILE*     3.3     8.3    -      -       +      -
    131A  VAL*     2.9    28.9    +      -       -      +
    147A  GLY      5.4     0.2    -      -       -      -
    148A  PRO*     3.5    34.1    -      -       +      +
    149A  ILE*     1.3    78.4    -      -       -      +
    151A  VAL*     1.3    65.5    +      -       -      +
    161A  LEU*     3.9    52.7    -      -       +      -
    162A  ILE*     3.3    10.1    -      -       -      +
    163A  HIS*     5.1     1.8    -      -       +      -
    164A  PRO*     4.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  VAL*     3.6    22.4    -      -       +      +
    133A  VAL*     4.1    13.0    -      -       +      -
    136A  LEU*     4.2    19.1    -      -       +      -
    150A  TYR*     1.3    76.8    -      -       -      +
    152A  PRO*     1.3    71.9    -      -       +      +
    153A  THR*     4.7     5.6    -      -       +      -
    160A  LYS      3.8     0.3    -      -       -      +
    161A  LEU*     3.7     4.0    -      -       -      -
    162A  ILE*     2.8    50.5    +      -       +      +
    164A  PRO*     3.8    30.5    -      -       +      -
    167A  PHE*     5.2     1.1    -      -       +      -
    212A  ARG*     6.5     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  ILE*     4.1    12.8    -      -       +      -
    131A  VAL      4.3     2.0    -      -       -      +
    151A  VAL*     1.3    88.6    -      -       +      +
    153A  THR*     1.3    65.6    +      -       -      +
    159A  VAL*     4.1     5.4    -      -       +      -
    160A  LYS      3.9     3.8    -      -       -      +
    161A  LEU*     3.9    11.9    -      -       +      -
    212A  ARG*     5.3     5.9    +      -       -      -
    214A  GLU*     3.4    29.8    -      -       +      +
    215A  PHE*     3.4    34.8    -      -       +      -
    222A  VAL*     3.9    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  VAL*     4.3     3.4    -      -       +      +
    152A  PRO*     1.3    80.4    -      -       -      +
    154A  LEU*     1.3    63.4    +      -       -      +
    155A  GLU*     4.7     4.6    -      -       -      +
    159A  VAL*     3.4     9.5    -      -       -      +
    160A  LYS*     2.9    50.4    +      -       -      +
    162A  ILE*     3.6    32.4    -      -       +      +
    167A  PHE*     4.4    20.6    -      -       +      -
    214A  GLU*     4.3    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  THR*     1.3    79.0    -      -       -      +
    155A  GLU*     1.3    65.3    +      -       -      +
    156A  ASN      4.3     4.0    -      -       -      +
    157A  GLY*     3.9    35.0    -      -       -      +
    158A  GLU      3.7     8.1    -      -       -      +
    159A  VAL*     5.4     3.8    -      -       +      -
    214A  GLU*     5.0    10.1    +      -       +      +
    218A  SER*     5.7     9.6    -      -       -      +
    221A  GLU*     6.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  THR*     4.7     3.8    -      -       -      +
    154A  LEU*     1.3    76.9    -      -       -      +
    156A  ASN*     1.3    79.1    +      -       -      +
    157A  GLY      3.6     0.2    -      -       -      -
    158A  GLU*     3.1    20.7    +      -       -      +
    160A  LYS*     4.0    31.3    -      -       +      +
----------------------------------------------------------
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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