Contacts of the strand formed by residues 467 - 475 (chain C) 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 ILE 467 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328C  LEU*     4.5    11.1    +      -       +      -
    333C  ILE*     3.8    28.9    -      -       +      -
    410C  ILE*     4.4     4.7    -      -       +      -
    437C  ARG*     3.0    39.0    +      -       +      +
    438C  ILE*     3.9    28.7    -      -       +      -
    455C  LEU*     3.6    23.3    -      -       +      -
    459C  ALA*     3.6    26.2    -      -       +      -
    460C  ARG      3.5    11.2    -      -       -      +
    461C  VAL*     4.5     3.6    -      -       +      +
    466C  PHE*     1.3    73.9    -      -       -      +
    468C  ARG*     1.3    66.7    +      -       -      +
    487C  THR*     4.1     0.5    -      -       -      -
    488C  ALA*     3.8     9.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 468 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    437C  ARG*     4.4     1.1    -      -       -      +
    458C  TYR      4.2     0.5    -      -       -      +
    459C  ALA*     3.2     6.3    -      -       -      +
    460C  ARG*     2.7    39.9    +      -       +      +
    462C  ASP*     2.9    39.9    +      -       -      +
    464C  LEU*     6.0     0.4    -      -       -      +
    466C  PHE*     4.3     5.6    -      -       +      +
    467C  ILE*     1.3    79.9    -      -       -      +
    469C  THR*     1.3    60.0    +      -       -      +
    485C  TYR*     2.9    43.0    +      -       +      +
    486C  MET      3.3    18.4    -      -       -      +
    487C  THR*     3.8    31.1    -      -       -      +
    490C  GLU*     3.9     7.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 469 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435C  TYR      4.5     1.3    -      -       -      +
    436C  GLY*     3.5    28.7    +      -       -      -
    437C  ARG*     3.5    29.6    -      -       -      +
    468C  ARG*     1.3    74.3    -      -       -      +
    470C  PRO*     1.3    73.3    +      -       -      +
    471C  TYR*     3.5    29.1    -      -       +      +
    484C  VAL      3.8     0.5    -      -       -      +
    485C  TYR*     3.7     3.4    -      -       -      -
    486C  MET*     3.0    21.4    +      -       -      -
    538C  GLN*     3.3    17.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 470 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13C  ILE*     4.6     1.8    -      -       +      -
    458C  TYR*     3.5    35.4    -      -       +      +
    469C  THR*     1.3    91.9    +      -       -      +
    471C  TYR*     1.3    66.6    +      -       -      +
    483C  VAL*     4.4     9.6    -      -       +      -
    484C  VAL      3.7     5.8    -      -       -      +
    485C  TYR*     3.3    40.6    -      -       +      +
    534C  VAL*     3.2    17.8    -      -       +      +
    538C  GLN*     2.8    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 471 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    435C  TYR*     3.4    13.6    -      +       -      -
    469C  THR*     3.5    29.7    -      -       +      +
    470C  PRO*     1.3    80.1    -      -       -      +
    472C  ARG*     1.3    61.2    +      -       -      +
    483C  VAL*     3.3     4.3    -      -       -      -
    484C  VAL*     2.7    36.4    +      -       -      +
    486C  MET*     3.8    21.5    -      -       +      -
    491C  GLU*     3.7    18.3    +      -       +      -
    496C  ILE*     3.4    39.9    -      -       +      -
    516C  ARG*     2.7    26.4    +      -       -      -
    531C  PHE*     4.0    17.9    -      -       +      -
    532C  MET      3.5     3.1    -      -       -      +
    533C  ASP*     3.4    21.5    -      -       -      -
    534C  VAL*     3.7     8.1    -      -       -      -
    538C  GLN*     4.3     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 472 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  ILE*     6.2     0.6    -      -       -      +
     10C  ARG*     3.8    38.8    +      -       -      +
     12C  VAL*     3.3    49.6    -      -       +      +
    471C  TYR*     1.3    75.4    -      -       -      +
    473C  ARG*     1.3    63.6    +      -       -      +
    474C  VAL*     3.6     0.3    -      -       -      +
    479C  VAL*     3.6    26.6    -      -       +      +
    480C  THR      3.5    16.2    -      -       -      +
    481C  ASP*     3.9     6.2    +      -       -      +
    482C  GLU      3.7     6.1    -      -       -      +
    483C  VAL*     4.5     2.7    -      -       +      -
    499C  ALA*     5.6     2.2    +      -       -      +
    503C  LEU*     4.6     9.5    -      -       -      +
    531C  PHE*     3.0     9.8    -      -       -      -
    532C  MET*     2.6    59.9    +      -       +      +
    533C  ASP      4.0     9.3    +      -       -      -
    534C  VAL*     4.3    10.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 473 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471C  TYR      3.8     0.8    +      -       -      -
    472C  ARG*     1.3    72.2    -      -       -      +
    474C  VAL*     1.3    56.7    +      -       -      +
    475C  VAL*     3.6    27.8    -      -       +      -
    479C  VAL*     3.6     1.0    -      -       -      +
    480C  THR*     2.7    36.3    +      -       -      +
    482C  GLU*     3.1    54.7    +      -       +      +
    484C  VAL*     4.1    14.8    -      -       +      +
    530C  GLU      4.7     2.9    -      -       -      -
    531C  PHE*     3.5    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 474 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472C  ARG      3.6    10.3    -      -       -      +
    473C  ARG*     1.3    77.1    -      -       -      +
    475C  VAL*     1.3    62.4    +      -       -      +
    476C  GLY      4.5     5.1    +      -       -      +
    477C  GLY      4.3     9.6    -      -       -      +
    478C  VAL      3.1    21.3    -      -       -      +
    479C  VAL*     3.8    21.8    -      -       +      -
    508C  ILE*     4.6     4.5    -      -       +      -
    529C  VAL*     3.4    36.3    -      -       +      +
    530C  GLU*     3.1    18.5    +      -       -      +
    531C  PHE      3.6    17.5    -      -       -      -
    532C  MET*     3.7    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 475 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473C  ARG*     3.6    27.0    +      -       +      -
    474C  VAL*     1.3    77.5    -      -       -      +
    476C  GLY*     1.3    65.6    +      -       -      +
    478C  VAL*     3.0    31.8    +      -       -      +
    480C  THR*     4.4     8.9    +      -       -      +
    482C  GLU*     5.6     0.4    -      -       -      +
----------------------------------------------------------
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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