Contacts of the strand formed by residues 207 - 214 (chain E) in PDB entry 3GTL


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 ARG 207 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    867A  ILE*     5.6     1.4    -      -       -      +
    942A  PHE*     3.6    30.9    -      -       +      -
   1013A  ASP*     3.3    52.3    +      -       +      +
   1014A  ALA*     4.9     0.3    -      -       -      -
   1016A  THR*     4.6     6.4    +      -       -      +
    152E  LYS*     5.3     2.0    -      -       -      +
    199E  ILE*     4.3    21.2    -      -       +      +
    200E  ARG      3.7     4.7    -      -       -      +
    201E  LYS*     3.3    29.7    -      -       -      +
    202E  SER*     5.0     0.2    -      -       -      -
    205E  SER*     2.6    27.6    +      -       -      -
    206E  GLY*     1.3    77.5    -      -       -      +
    208E  TYR*     1.3    58.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 208 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    864A  ILE      4.3     2.9    +      -       -      -
    865A  GLN*     3.3    13.0    -      -       +      -
    866A  PHE*     2.7    34.2    +      -       +      -
    867A  ILE*     3.9    40.6    -      -       +      -
    870A  GLU*     3.2    42.8    -      -       +      +
   1013A  ASP*     5.8     0.9    -      -       -      -
    198E  ILE      2.8    25.8    -      -       -      +
    199E  ILE*     4.0     2.8    -      -       -      -
    200E  ARG*     3.1    46.7    +      -       +      +
    202E  SER*     4.8     0.9    -      -       -      -
    207E  ARG*     1.3    76.5    -      -       -      +
    209E  ALA*     1.3    71.2    +      -       -      +
    210E  SER*     3.5    21.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 209 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    866A  PHE*     3.4    13.1    -      -       +      +
    867A  ILE*     5.5     3.6    -      -       +      +
   1009A  ASN      5.9     0.9    -      -       -      +
   1010A  ALA*     5.3    15.5    -      -       +      -
   1013A  ASP*     5.6     7.2    +      -       +      +
    168E  TYR*     5.9     2.2    -      -       -      +
    197E  LYS*     4.8    10.3    -      -       -      +
    198E  ILE      4.1     2.5    -      -       -      -
    199E  ILE*     5.7     1.1    -      -       -      +
    208E  TYR*     1.3    92.1    -      -       -      +
    210E  SER*     1.3    58.8    +      -       -      +
    211E  TYR*     4.0    25.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 210 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    866A  PHE*     4.0     4.7    -      -       -      -
   1342A  GLU*     4.8     0.3    +      -       -      -
    176E  PRO*     5.9     1.4    -      -       -      +
    197E  LYS*     3.2     1.6    -      -       -      +
    198E  ILE*     2.6    60.8    +      -       -      +
    200E  ARG*     3.5    24.0    +      -       -      -
    208E  TYR*     3.5    22.0    +      -       -      -
    209E  ALA*     1.3    74.6    -      -       -      +
    211E  TYR*     1.3    68.3    +      -       -      +
    212E  ARG*     5.6     2.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 211 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    866A  PHE*     3.5    24.0    -      +       +      -
   1006A  ILE*     4.9     8.5    -      -       -      +
    156E  LEU*     4.3     9.2    -      -       +      -
    164E  LEU*     3.6    40.8    -      -       +      +
    168E  TYR*     4.8     8.5    -      +       -      -
    175E  LEU*     3.7    20.9    -      -       +      -
    176E  PRO*     3.4    23.0    -      -       -      +
    195E  VAL*     4.4     1.1    -      -       +      -
    196E  VAL      3.3    17.3    -      -       -      +
    197E  LYS*     2.8    52.1    +      -       +      -
    209E  ALA*     4.0    24.2    -      -       +      +
    210E  SER*     1.3    76.7    +      -       -      +
    212E  ARG*     1.3    70.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 212 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1341A  ILE*     3.5    22.3    -      -       -      +
   1342A  GLU*     3.2    32.6    +      -       -      +
   1376A  THR*     3.5    36.6    +      -       -      +
   1377A  THR*     3.7    15.4    +      -       -      +
    175E  LEU*     4.8     0.2    -      -       -      -
    176E  PRO*     2.7    28.5    +      -       -      +
    177E  ARG      3.4    18.8    +      -       -      -
    178E  ILE*     4.0    16.0    -      -       +      +
    194E  GLU      4.3     0.7    -      -       -      +
    195E  VAL*     3.1     5.1    -      -       -      -
    196E  VAL*     2.7    47.2    +      -       +      +
    198E  ILE*     3.6    24.5    -      -       +      -
    200E  ARG*     5.9     0.2    -      -       -      +
    210E  SER*     5.6     2.2    +      -       -      +
    211E  TYR*     1.3    76.6    +      -       -      +
    213E  ILE*     1.3    66.3    +      -       -      +
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Residues in contact with ILE 213 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161E  LYS*     4.6     2.2    -      -       -      +
    172E  GLU*     3.8    48.5    -      -       +      +
    175E  LEU*     3.7    26.5    -      -       +      +
    176E  PRO      3.3     2.0    +      -       -      -
    177E  ARG*     3.3    24.7    -      -       +      +
    178E  ILE*     2.8    25.7    +      -       -      +
    193E  GLY*     3.9    26.0    -      -       -      +
    195E  VAL*     3.8    18.4    -      -       +      +
    212E  ARG*     1.3    75.1    -      -       -      +
    214E  CYS*     1.3    72.9    +      -       -      +
    215E  MET*     5.6     0.4    -      -       -      -
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Residues in contact with CYS 214 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178E  ILE*     3.4    19.1    -      -       +      -
    179E  GLN      4.7     0.7    -      -       -      -
    180E  ARG*     4.4    12.8    -      -       -      -
    185E  ALA*     5.0     0.9    -      -       -      -
    190E  LEU*     3.8    22.2    -      -       -      -
    191E  LYS      3.1    29.6    -      -       -      +
    192E  ARG*     4.4     6.9    +      -       -      -
    193E  GLY*     4.1     8.5    +      -       -      +
    194E  GLU      3.6    13.7    +      -       -      +
    213E  ILE*     1.3    89.9    -      -       -      +
    215E  MET*     1.3    88.8    +      -       -      +
----------------------------------------------------------
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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