Contacts of the strand formed by residues 171 - 176 (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 TYR 171 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115D  LEU*     3.7    15.3    -      -       +      -
    131D  TRP*     3.8    15.7    -      -       +      -
    132D  PHE      3.2    10.8    -      -       -      +
    133D  ARG*     3.8    25.5    +      -       +      -
    138D  GLU*     5.5     0.2    -      -       -      -
    161D  LEU*     3.6    31.4    -      -       +      -
    163D  MET*     3.6    40.6    -      -       +      +
    164D  THR      3.8     4.9    +      -       -      -
    165D  PRO*     4.9     1.1    -      -       +      -
    169D  GLU*     2.9    46.1    +      -       +      -
    170D  VAL*     1.3    76.4    -      -       -      +
    172D  THR*     1.3    62.7    +      -       -      +
    187D  GLU*     3.3     5.0    -      -       -      +
    188D  TRP*     2.9    52.1    +      +       +      +
----------------------------------------------------------
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Residues in contact with THR 172 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130D  ARG      3.7     1.0    -      -       -      +
    131D  TRP*     3.1    12.6    -      -       -      -
    132D  PHE*     2.8    48.8    +      -       +      +
    135D  GLY      6.3     0.4    -      -       -      -
    170D  VAL*     4.3     6.5    +      -       -      +
    171D  TYR*     1.3    78.8    +      -       -      +
    173D  CYS*     1.3    72.1    +      -       -      +
    174D  HIS*     4.4     1.3    -      -       +      +
    185D  THR*     4.0    23.1    -      -       +      -
    186D  VAL      3.1     9.9    -      -       -      +
    187D  GLU*     3.5    17.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 173 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99D  VAL*     4.1     9.3    -      -       +      +
    101D  ILE*     3.9    17.0    -      -       +      +
    117D  CYS*     2.0    51.8    -      -       +      -
    129D  VAL*     3.7    21.8    -      -       -      -
    130D  ARG      3.5     4.9    -      -       -      -
    131D  TRP*     4.4     6.3    -      -       +      -
    172D  THR*     1.3    72.8    -      -       -      +
    174D  HIS*     1.3    59.4    +      -       -      +
    175D  VAL*     4.2     2.6    -      -       -      +
    184D  ILE      3.4     1.4    -      -       -      +
    185D  THR*     3.1     6.4    -      -       -      -
    186D  VAL*     2.8    33.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 174 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128D  LYS*     3.5     2.2    -      -       +      +
    129D  VAL*     3.2     5.4    -      -       -      -
    130D  ARG*     2.8    56.0    +      -       +      +
    132D  PHE*     3.8    26.1    -      +       +      -
    172D  THR*     4.0     1.1    -      -       +      -
    173D  CYS*     1.3    72.7    -      -       -      +
    175D  VAL*     1.3    65.2    +      -       -      +
    176D  GLU*     3.0    32.7    +      -       +      -
    183D  PRO*     3.5    25.7    -      -       +      +
    184D  ILE      3.4     1.3    +      -       -      -
    185D  THR*     3.1    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 175 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97D  PRO*     4.4    11.9    -      -       +      -
     99D  VAL*     3.9    24.7    -      -       +      -
    119D  VAL*     3.9    19.7    -      -       +      -
    127D  ILE*     3.9    28.3    -      -       +      -
    128D  LYS      3.2     4.3    -      -       -      +
    129D  VAL*     3.8    20.6    -      -       +      -
    173D  CYS*     4.2     2.5    -      -       -      -
    174D  HIS*     1.3    79.4    -      -       -      +
    176D  GLU*     1.3    68.9    +      -       -      +
    180D  LEU*     4.1     6.6    -      -       +      +
    183D  PRO*     3.3     5.8    -      -       -      +
    184D  ILE*     2.8    39.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 176 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127D  ILE*     3.5     4.9    -      -       -      +
    128D  LYS*     2.9    62.4    +      -       +      +
    130D  ARG*     3.4    10.7    +      -       -      -
    174D  HIS*     3.0    24.8    +      -       +      +
    175D  VAL*     1.3    73.6    -      -       -      +
    177D  HIS*     1.3    62.5    +      -       -      +
    183D  PRO*     3.5    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