Contacts of the strand formed by residues 20 - 28 (chain L) in PDB entry 4G7Z


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 20 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14L  ARG*     5.3     1.1    -      -       +      -
     15L  THR*     3.8     4.5    -      -       -      -
     16L  GLN*     3.3    50.9    +      -       +      +
     17L  GLY      4.0     3.6    -      -       -      +
     19L  GLU*     1.3    80.8    -      -       +      +
     21L  GLY*     1.3    77.9    +      -       -      +
     22L  GLU*     3.1    41.6    +      -       +      +
    198L  ARG*     3.2    20.8    +      -       +      -
    199L  ILE      3.4    13.0    -      -       -      -
    200L  TRP*     3.3    49.9    -      +       +      -
    207L  PRO*     3.2    15.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 21 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14L  ARG      3.2    12.3    -      -       -      -
     15L  THR*     4.3     2.5    -      -       -      -
     20L  TYR*     1.3    85.5    -      -       -      +
     22L  GLU*     1.3    63.2    +      -       -      +
     23L  PHE*     3.5    18.2    -      -       -      -
    198L  ARG*     3.5     4.9    -      -       -      -
    199L  ILE      3.2    28.8    +      -       -      -
    207L  PRO*     3.7     3.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 22 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12L  THR      3.7     0.7    -      -       -      +
     13L  VAL*     3.3     5.4    -      -       -      -
     14L  ARG*     2.7    82.6    +      -       +      +
     20L  TYR*     3.1    34.8    +      -       +      +
     21L  GLY*     1.3    70.7    -      -       -      -
     23L  PHE*     1.3    62.8    +      -       -      +
    196L  THR*     4.0    14.0    -      -       +      +
    197L  LEU      3.4     2.9    -      -       -      +
    198L  ARG*     3.9    15.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 23 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225K  PHE*     6.3     0.2    -      -       +      -
     11L  PHE*     3.8    32.8    -      +       +      -
     12L  THR      3.3     4.7    -      -       -      -
     13L  VAL*     3.7    27.6    -      -       +      -
     15L  THR*     5.3     1.3    -      -       +      -
     21L  GLY*     3.5    22.9    -      -       -      -
     22L  GLU*     1.3    74.8    -      -       -      +
     24L  VAL*     1.3    62.9    +      -       -      +
    195L  LEU      3.4     2.6    -      -       -      +
    196L  THR*     3.5     0.9    -      -       -      -
    197L  LEU*     2.7    59.0    +      -       +      +
    199L  ILE*     3.8    26.2    -      -       +      -
    207L  PRO*     3.7    30.5    -      -       +      -
    208L  LEU*     3.7    20.9    -      -       +      -
    211L  LEU*     4.2    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 24 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10L  VAL      3.3     5.1    -      -       -      +
     11L  PHE*     3.6     3.8    -      -       -      -
     12L  THR*     2.9    43.8    +      -       -      +
     14L  ARG*     3.4    32.5    -      -       -      +
     22L  GLU      5.1     0.2    -      -       -      -
     23L  PHE*     1.3    78.0    -      -       -      +
     25L  LEU*     1.3    62.9    +      -       -      +
     26L  GLU*     4.0    12.6    -      -       +      +
    194L  LYS*     3.6    35.9    -      -       +      +
    195L  LEU      3.1     7.9    -      -       -      +
    196L  THR*     4.2    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 25 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221K  HIS      5.1     0.2    -      -       -      +
    224K  TYR*     3.5    31.4    -      -       +      +
    225K  PHE*     3.9    31.9    -      -       +      -
      9L  PRO*     3.7    23.1    -      -       +      -
     10L  VAL      3.8    10.1    -      -       -      +
     11L  PHE*     4.1    15.5    -      -       +      -
     23L  PHE      4.3     0.2    -      -       -      -
     24L  VAL*     1.3    72.3    -      -       -      +
     26L  GLU*     1.3    59.7    +      -       -      +
     28L  LEU*     3.7    32.0    -      -       +      +
     36L  LEU*     4.0     9.6    -      -       +      -
    194L  LYS*     3.9     0.3    -      -       -      -
    195L  LEU*     3.0    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 26 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9L  PRO*     4.2     1.3    -      -       -      -
     10L  VAL*     3.1    40.5    +      -       +      +
     24L  VAL*     4.0     8.6    -      -       +      +
     25L  LEU*     1.3    75.3    -      -       -      +
     27L  PRO*     1.3    76.0    -      -       +      +
    184L  THR*     3.5    27.0    +      -       +      +
    193L  ASP      4.0     0.4    -      -       -      +
    194L  LYS*     3.5    44.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 27 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  LEU*     3.8    25.1    -      -       +      +
      7L  LYS*     5.7     6.3    -      -       +      +
      8L  ALA      5.5     1.1    -      -       -      +
      9L  PRO*     3.3    31.2    -      -       +      +
     10L  VAL*     5.0     1.6    -      -       +      +
     26L  GLU*     1.3    89.3    -      -       +      +
     28L  LEU*     1.3    60.6    +      -       -      +
    184L  THR*     4.7     9.6    -      -       +      -
    186L  LEU*     4.9    11.2    -      -       +      -
    192L  LEU*     3.7    28.5    -      -       +      -
    193L  ASP      3.5     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 28 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221K  HIS*     4.6    12.8    -      -       +      -
    224K  TYR*     5.0     0.9    -      -       +      -
      6L  LEU*     3.9     6.3    -      -       -      -
      9L  PRO*     4.1    12.3    -      -       +      -
     25L  LEU*     3.7    44.6    -      -       +      +
     27L  PRO*     1.3    80.4    -      -       -      +
     29L  GLU*     1.3    63.1    +      -       -      +
     32L  PHE*     3.7    25.8    -      -       +      +
     33L  GLY*     3.8    11.9    -      -       -      -
     36L  LEU*     4.3    12.6    -      -       +      -
    192L  LEU*     3.5     9.9    -      -       -      +
    193L  ASP*     2.8    41.2    +      -       +      +
    195L  LEU*     4.1    12.6    -      -       +      -
----------------------------------------------------------
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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