Contacts of the strand formed by residues 204 - 216 (chain B) in PDB entry 3RT0


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 ASP 204 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199B  ARG*     5.6     0.2    +      -       -      -
    202B  MET*     3.8    29.3    -      -       +      +
    203B  GLU*     1.3    82.3    -      -       -      +
    205B  ALA*     1.3    61.6    +      -       -      +
    241B  VAL*     5.7     0.2    -      -       -      -
    242B  TYR      3.4     4.9    -      -       -      +
    243B  ASP*     3.2    27.6    -      -       -      +
    252B  ASP*     4.7     4.3    -      -       -      +
    255B  ARG*     5.2     1.6    +      -       -      -
    431B  SER*     2.8    25.7    +      -       -      -
    492B  ASP*     5.2     0.9    -      -       -      +
    493B  ASN*     3.4    25.1    +      -       -      +
    495B  SER*     2.8    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194B  SER*     4.8     5.2    -      -       -      -
    204B  ASP*     1.3    76.9    -      -       -      +
    206B  PHE*     1.3    60.8    +      -       -      +
    241B  VAL*     3.7     4.5    -      -       -      +
    242B  TYR*     2.8    34.4    +      -       +      +
    251B  ALA*     3.6    33.2    -      -       +      +
    252B  ASP*     3.9    11.7    -      -       -      +
    255B  ARG*     4.0    19.5    -      -       +      +
    495B  SER*     4.9     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  THR*     3.7    32.8    -      -       +      -
    194B  SER*     3.6    33.0    -      -       -      +
    205B  ALA*     1.3    77.4    -      -       -      +
    207B  ALA*     1.3    67.2    +      -       -      +
    208B  VAL*     4.1    19.1    -      -       +      -
    240B  GLY      3.2    14.1    -      -       -      +
    241B  VAL*     4.4    11.4    -      -       +      -
    242B  TYR*     4.1     4.9    -      -       -      -
    255B  ARG*     3.3    23.6    -      -       -      +
    495B  SER*     5.2     3.4    -      -       -      -
    497B  ILE*     4.6     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  PHE*     1.3    76.6    -      -       -      +
    208B  VAL*     1.3    65.5    +      -       -      +
    238B  PHE*     3.8    19.7    -      -       +      +
    239B  PHE*     3.4     2.8    -      -       -      -
    240B  GLY      2.8    37.7    +      -       -      +
    242B  TYR*     4.0     7.4    -      -       +      -
    255B  ARG*     3.7    23.3    -      -       +      +
    259B  HIS*     4.5     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  TRP*     3.5    46.7    -      -       +      +
    192B  THR*     4.1     7.0    -      -       -      +
    206B  PHE*     4.1    13.3    -      -       +      -
    207B  ALA*     1.3    80.9    -      -       -      +
    209B  SER*     1.3    66.0    +      -       -      +
    210B  PRO*     3.9     9.3    -      -       +      +
    238B  PHE      3.2     3.1    -      -       -      -
    239B  PHE*     3.7    30.1    -      -       +      -
    497B  ILE*     3.9    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 209 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207B  ALA      4.3     0.2    -      -       -      -
    208B  VAL*     1.3    76.7    -      -       -      +
    210B  PRO*     1.3    65.4    +      -       -      +
    212B  PHE*     3.0    44.8    -      -       -      +
    237B  HIS*     5.1     0.2    -      -       -      -
    238B  PHE*     2.7    38.8    +      -       -      -
    259B  HIS*     4.4    15.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 210 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188B  PRO*     3.8    25.6    -      -       +      -
    190B  TRP*     3.8    24.2    -      -       +      -
    208B  VAL*     3.9    13.6    -      -       +      +
    209B  SER*     1.3    85.5    +      -       -      +
    211B  HIS*     1.3    77.4    +      -       +      +
    212B  PHE*     3.0     5.3    +      -       -      -
    237B  HIS*     3.7    10.1    -      -       +      +
    239B  PHE*     6.0     0.7    -      -       +      -
    467B  GLY      4.5     5.2    -      -       -      +
    468B  LYS      5.3     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 211 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  CYS      4.0     6.7    -      -       -      -
    187B  ILE*     5.2     1.1    -      -       +      -
    188B  PRO*     3.6    19.8    -      -       +      +
    210B  PRO*     1.3    83.8    -      -       +      +
    212B  PHE*     1.3    62.6    +      -       -      +
    213B  LEU      3.5     3.3    +      -       -      +
    214B  LYS*     5.9     2.3    +      -       -      +
    235B  THR*     3.5    30.5    +      -       +      +
    236B  GLY      3.9     0.7    -      -       -      -
    237B  HIS*     2.9    31.0    +      +       -      -
    467B  GLY*     4.3     9.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 212 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209B  SER*     3.0    38.8    -      -       -      +
    210B  PRO      3.0     2.0    +      -       -      -
    211B  HIS*     1.3    80.3    -      -       -      +
    213B  LEU*     1.3    91.0    +      -       +      +
    214B  LYS*     4.3     0.7    +      -       -      +
    236B  GLY      3.1     5.4    +      -       -      +
    238B  PHE*     4.3    15.3    -      +       +      -
    259B  HIS*     3.2    49.6    -      +       +      -
    260B  PHE*     3.8    31.4    -      +       -      -
    262B  LEU*     5.8     0.2    -      -       +      -
    263B  ALA*     4.1     8.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 213 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211B  HIS      4.8     0.4    -      -       -      -
    212B  PHE*     1.3   110.9    -      -       +      +
    214B  LYS*     1.3    64.5    +      -       -      +
    215B  LEU*     4.0    20.2    -      -       +      -
    235B  THR*     3.3     8.5    +      -       -      -
    236B  GLY*     2.7    41.0    +      -       -      +
    238B  PHE*     5.3     2.2    -      -       +      -
    262B  LEU*     4.0    12.8    -      -       +      -
    263B  ALA*     4.1    20.2    -      -       +      +
    266B  ILE*     4.0    14.8    -      -       +      -
    333B  LEU*     3.8    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 214 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211B  HIS      5.9     1.9    +      -       -      +
    212B  PHE      4.3     1.0    +      -       -      +
    213B  LEU*     1.3    75.3    -      -       -      +
    215B  LEU*     1.3    64.5    +      -       -      +
    216B  PRO*     3.6     8.0    -      -       -      +
    233B  HIS*     3.9    31.4    -      -       +      -
    234B  LEU      3.7     4.0    -      -       -      +
    235B  THR*     5.5     4.7    -      -       -      +
    266B  ILE*     4.4     6.6    -      -       -      +
    270B  LYS*     4.1    10.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 215 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  LEU*     4.0    18.6    -      -       +      -
    214B  LYS*     1.3    72.4    -      -       -      +
    216B  PRO*     1.3    73.6    -      -       +      +
    217B  ILE*     3.1     1.4    +      -       -      -
    220B  LEU*     4.2    26.2    -      -       +      +
    233B  HIS*     3.3     4.4    -      -       -      -
    234B  LEU*     2.7    39.8    +      -       -      +
    236B  GLY*     4.1    19.3    -      -       -      -
    266B  ILE*     3.5    31.6    -      -       +      -
    286B  TRP*     3.9    25.8    -      -       +      -
    333B  LEU*     4.8    10.5    -      -       +      -
    334B  VAL      5.7     0.2    -      -       -      +
    335B  CYS*     4.4    11.7    -      -       +      -
    340B  VAL*     6.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214B  LYS      3.6     8.3    -      -       -      +
    215B  LEU*     1.3    85.4    -      -       +      +
    217B  ILE*     1.3    65.8    +      -       -      +
    218B  LYS*     3.1     4.3    -      -       +      +
    219B  MET*     2.9    41.5    +      -       +      +
    220B  LEU*     4.1     2.6    +      -       -      +
    232B  THR      3.9     6.3    -      -       -      +
    233B  HIS*     3.9     6.7    -      -       +      +
    266B  ILE*     4.0    11.0    -      -       +      +
    269B  ILE*     5.3     0.4    -      -       +      -
    270B  LYS*     3.3    32.1    -      -       +      +
    272B  GLU*     3.6    24.2    -      -       -      +
----------------------------------------------------------
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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