Contacts of the strand formed by residues 15 - 19 (chain B) in PDB entry 3UR9


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 GLY 15 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  LYS*     3.0    18.4    +      -       -      +
     12B  PHE      2.8    24.5    +      -       -      -
     13B  GLY      3.2     0.6    +      -       -      -
     14B  SER*     1.3    82.2    -      -       -      +
     16B  TRP*     1.3    66.0    +      -       -      -
     31B  VAL*     3.7     8.0    -      -       -      +
    137B  GLY      3.6    11.4    -      -       -      -
    139B  CYS      3.4    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  VAL*     4.0    18.8    -      -       +      -
     10B  THR*     3.2    10.8    -      -       -      +
     11B  LYS*     3.3    55.1    -      -       +      +
     12B  PHE*     3.6     6.7    +      -       -      +
     15B  GLY*     1.3    78.1    +      -       -      -
     17B  GLY*     1.3    58.8    +      -       -      +
     27B  THR*     2.7    26.5    +      -       -      -
     31B  VAL*     4.1     0.8    -      -       -      +
     88B  LYS*     3.2    55.0    +      -       +      -
     89B  ARG      4.0     9.9    -      -       -      -
     90B  ASP*     3.8    17.2    +      -       -      -
    137B  GLY      2.9    24.1    +      -       -      -
    138B  ASP*     4.1     9.4    -      -       -      +
    139B  CYS      2.9    12.4    +      -       -      +
    140B  GLY*     3.1    21.5    -      -       -      -
    141B  ALA*     4.2     4.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  VAL*     3.5     8.7    -      -       -      +
     10B  THR      2.8    30.5    +      -       -      -
     16B  TRP*     1.3    75.1    -      -       -      +
     18B  PHE*     1.3    61.6    +      -       -      +
     25B  PHE*     3.3    23.3    -      -       -      -
     26B  ILE      3.1    14.1    -      -       -      -
     27B  THR*     3.9     1.3    -      -       -      -
    140B  GLY      4.0     6.5    -      -       -      -
    142B  PRO*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  LEU*     3.8    18.4    -      -       +      -
      8B  ARG*     3.4    40.4    -      -       +      -
      9B  VAL*     4.0     8.3    -      -       +      -
     17B  GLY*     1.3    74.8    -      -       -      +
     19B  TRP*     1.3    72.9    +      -       -      +
     20B  VAL*     3.3    11.6    +      -       +      -
     25B  PHE*     3.4     6.6    -      -       -      -
     26B  ILE*     2.8    46.9    +      -       +      +
     71B  MET*     3.6    23.3    -      -       +      -
     86B  LEU*     4.7     1.8    -      -       +      -
    140B  GLY      4.8     2.5    -      -       -      +
    142B  PRO*     3.4    39.5    -      -       +      -
    144B  VAL*     4.5     2.9    -      -       +      -
    153B  VAL*     3.9    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  SER      4.6     3.2    +      -       -      -
      8B  ARG*     2.9    44.2    +      -       +      +
     10B  THR*     3.3    31.2    +      -       -      +
     18B  PHE*     1.3    71.7    -      -       -      +
     20B  VAL*     1.3    60.5    -      -       -      +
     21B  SER      3.5    17.0    -      -       -      +
     22B  PRO      4.0     6.7    -      -       -      -
     23B  THR      4.3     0.4    -      -       -      -
     24B  VAL      3.5    14.8    -      -       -      -
     25B  PHE*     3.4    22.5    -      +       +      -
     40B  PHE*     3.7    28.7    -      +       -      -
     60B  PHE*     3.7    28.3    -      +       -      -
     64B  MET*     3.4    33.9    -      -       +      -
     65B  ARG*     3.7    32.0    -      -       +      +
     68B  LEU*     3.5    18.8    -      -       +      -
----------------------------------------------------------
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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