Contacts of the strand formed by residues 214 - 220 (chain A) in PDB entry 4TR8


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 GLU 214 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  SER*     4.1    12.8    +      -       -      -
    130A  ILE*     3.4    26.3    +      -       -      -
    131A  ALA*     3.4    22.4    +      -       -      +
    132A  GLN*     3.0    17.9    +      -       -      +
    210A  GLU*     4.8     0.4    +      -       -      +
    212A  ASP      4.8     4.9    -      -       -      +
    213A  GLY*     1.3    77.5    -      -       -      +
    215A  VAL*     1.3    60.9    +      -       -      +
    227A  THR      4.4     0.4    -      -       -      +
    228A  THR*     3.9    11.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  SER*     3.3     4.6    -      -       -      -
    130A  ILE*     2.8    61.5    +      -       +      +
    132A  GLN*     3.8    21.8    -      -       +      -
    135A  LEU*     4.0    10.3    -      -       +      -
    208A  LEU*     4.0    14.6    -      -       +      -
    214A  GLU*     1.3    74.2    -      -       -      +
    216A  GLY*     1.3    72.6    +      -       -      +
    217A  ILE*     3.9     4.3    +      -       +      -
    226A  ALA*     3.9    15.3    -      -       +      -
    227A  THR      3.5    17.7    -      -       -      +
    228A  THR*     3.7    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  PHE      3.7     5.6    -      -       -      -
    129A  SER*     4.4     5.8    -      -       -      -
    215A  VAL*     1.3    71.5    -      -       -      +
    217A  ILE*     1.4    59.3    +      -       -      +
    218A  VAL*     5.5     2.5    -      -       -      -
    225A  ARG      3.6     1.0    -      -       -      +
    226A  ALA*     3.2     6.8    -      -       -      -
    227A  THR*     2.8    42.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  LEU      3.9     0.3    -      -       -      +
    127A  ASN*     3.2     7.1    -      -       -      +
    128A  PHE*     2.7    80.8    +      -       +      +
    130A  ILE*     4.3    12.1    -      -       +      -
    135A  LEU*     3.6    28.5    -      -       +      -
    204A  LEU*     5.3     0.4    -      -       +      -
    215A  VAL*     3.9     6.5    -      -       +      +
    216A  GLY*     1.4    75.8    -      -       -      +
    218A  VAL*     1.3    66.1    +      -       -      +
    219A  LEU*     3.8    20.9    -      -       +      -
    224A  ILE*     4.2    14.1    -      -       +      -
    225A  ARG      3.3     4.0    -      -       -      +
    226A  ALA*     3.7    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  GLY*     3.8    26.9    -      -       -      +
    126A  LEU      3.5     5.6    -      -       -      +
    127A  ASN*     4.2    15.7    -      -       +      +
    216A  GLY      5.5     1.8    -      -       -      -
    217A  ILE*     1.3    78.8    -      -       -      +
    219A  LEU*     1.3    65.0    +      -       -      +
    220A  GLY*     3.8     1.6    +      -       -      +
    223A  HIS      4.6     0.2    -      -       -      -
    224A  ILE*     3.3     8.3    -      -       -      +
    225A  ARG*     2.9    74.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  GLY      3.5     0.5    -      -       -      -
    125A  SER*     2.8    34.4    +      -       -      -
    126A  LEU*     2.7    45.7    +      -       +      +
    128A  PHE*     4.2    12.3    -      -       +      -
    160A  LEU*     5.5     7.4    -      -       +      +
    162A  VAL*     4.1    16.8    -      -       +      -
    167A  LEU*     6.0     1.1    -      -       +      -
    192A  HIS*     4.5    14.1    -      -       +      +
    194A  VAL*     3.9    33.2    -      -       +      -
    217A  ILE*     3.8     9.2    -      -       +      -
    218A  VAL*     1.3    73.2    -      -       -      +
    220A  GLY*     1.3    55.2    +      -       -      +
    223A  HIS      4.1     1.6    -      -       -      -
    224A  ILE*     3.8    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  GLY      5.4     2.0    -      -       -      -
    123A  PRO      4.0    15.0    -      -       -      -
    124A  GLY*     4.3     2.9    -      -       -      -
    125A  SER*     4.1     5.7    -      -       -      -
    194A  VAL*     4.1     7.3    -      -       -      +
    218A  VAL*     3.8     3.0    +      -       -      +
    219A  LEU*     1.3    76.5    -      -       -      +
    221A  GLN*     1.3    64.0    +      -       -      -
    222A  HIS      3.3     3.1    -      -       -      -
    223A  HIS*     2.7    24.1    +      -       -      +
    237A  LEU*     3.5     9.5    -      -       -      +
----------------------------------------------------------
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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