Contacts of the strand formed by residues 415 - 425 (chain A) in PDB entry 4U7C


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 SER 415 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413A  ARG*     3.1    21.4    +      -       -      +
    414A  LYS*     1.3    81.8    -      -       -      +
    416A  MET*     1.3    63.2    +      -       -      +
    417A  SER*     5.3     0.2    +      -       -      -
    512A  ARG*     3.2    42.4    +      -       -      -
    513A  ILE      3.3    12.1    -      -       -      -
    514A  SER*     4.1     3.8    -      -       -      -
    516A  PHE*     3.6     6.2    -      -       -      -
      8D    G      3.6    16.5    +      -       -      +
      9D    A      3.0    14.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 416 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413A  ARG*     3.5    38.4    -      -       -      +
    415A  SER*     1.3    74.6    -      -       -      +
    417A  SER*     1.3    67.6    +      -       -      +
    442A  LEU*     3.8    10.0    -      -       +      +
    445A  ASP*     3.4    39.9    -      -       +      +
    446A  LEU*     3.6    28.0    -      -       +      -
    449A  GLU*     3.9     3.6    -      -       +      +
    451A  LEU*     3.7    17.0    -      -       +      -
    512A  ARG*     3.4     0.7    -      -       -      +
    513A  ILE*     2.9    35.3    +      -       +      +
    516A  PHE*     4.6     1.8    -      -       +      -
      8D    G      3.3    16.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416A  MET*     1.3    81.4    -      -       -      +
    418A  VAL*     1.3    68.7    +      -       -      +
    419A  GLU*     5.0     8.3    +      -       -      -
    442A  LEU*     3.8     2.2    -      -       -      -
    445A  ASP*     5.4     0.3    -      -       -      +
    511A  VAL      3.3    12.3    -      -       -      -
    512A  ARG*     3.6    28.5    +      -       -      -
      7D    T      3.9    29.2    +      -       -      +
      8D    G      2.9    19.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    417A  SER*     1.3    80.7    -      -       -      +
    419A  GLU*     1.3    65.8    +      -       -      +
    420A  ARG*     3.8    11.0    -      -       -      +
    438A  LEU*     3.8    26.3    -      -       +      +
    441A  GLU*     3.4    26.5    -      -       +      +
    442A  LEU*     3.9    23.3    -      -       +      +
    445A  ASP*     3.7    22.9    -      -       -      +
    509A  MET      4.3     0.2    -      -       -      +
    510A  GLY*     3.2     1.7    -      -       -      -
    511A  VAL*     2.9    32.5    +      -       +      +
      7D    T      3.7    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 419 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    417A  SER*     5.0     7.8    +      -       -      -
    418A  VAL*     1.3    81.7    -      -       -      +
    420A  ARG*     1.3    67.9    +      -       -      +
    438A  LEU*     4.7     0.9    -      -       -      -
    459A  LYS*     3.3    36.8    +      -       +      +
    508A  LEU*     3.8    21.9    -      -       +      +
    509A  MET      3.3    13.0    -      -       -      +
    510A  GLY*     3.6     8.2    -      -       -      -
    603A  PEG      5.7     0.5    -      -       -      +
      6D    C      3.5    24.7    +      -       +      +
      7D    T      2.9    47.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 420 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418A  VAL*     3.8    10.9    -      -       -      +
    419A  GLU*     1.3    75.9    +      -       -      +
    421A  THR*     1.3    72.9    +      -       -      +
    422A  PHE*     3.4    17.0    -      -       +      -
    434A  LEU*     5.2     1.6    -      -       +      -
    438A  LEU*     4.4    15.8    -      -       +      +
    441A  GLU*     2.5    44.1    +      -       -      -
    508A  LEU*     3.2     4.0    -      -       -      -
    509A  MET      2.9    31.9    +      -       -      +
    170B  ASN*     5.9     0.2    -      -       -      +
    172B  ASP*     2.7    41.8    +      -       -      -
      6D    C      3.9     6.7    -      -       -      +
      7D    T      5.7     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 421 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420A  ARG*     1.3    81.4    -      -       -      +
    422A  PHE*     1.3    70.8    +      -       -      +
    461A  LYS*     5.5     0.2    +      -       -      -
    507A  ARG*     3.3    35.2    +      -       -      +
    508A  LEU*     3.2    14.8    -      -       -      +
    170B  ASN*     3.5     8.3    -      -       -      +
      4D    G      4.4     9.0    -      -       -      +
      5D  VKJ      3.6    18.1    +      -       -      +
      6D    C      2.6    36.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 422 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420A  ARG*     3.4    26.0    -      -       +      -
    421A  THR*     1.3    81.4    -      -       -      +
    423A  SER*     1.3    78.8    +      -       -      +
    424A  GLU      3.8     0.2    +      -       -      -
    425A  ILE*     3.5    28.7    -      -       +      -
    434A  LEU*     3.8    31.2    -      -       +      -
    506A  LEU*     3.9    17.0    -      -       +      -
    507A  ARG*     2.9    39.5    +      -       -      +
    508A  LEU      3.7    18.2    -      -       -      -
    509A  MET*     3.8    11.7    -      -       +      -
    170B  ASN*     3.3    20.9    -      -       +      +
    172B  ASP*     6.1     1.3    -      -       +      -
    173B  LYS*     3.9     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 423 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422A  PHE*     1.3    86.9    -      -       -      +
    424A  GLU*     1.3    70.6    +      -       -      +
    425A  ILE*     3.6     0.7    -      -       -      +
    116B  GLU*     2.6    28.8    +      -       -      -
    119B  ASP*     4.7     8.6    -      -       -      +
    120B  ASN*     5.3     9.0    -      -       -      -
    170B  ASN*     3.4    11.0    +      -       -      +
    173B  LYS*     3.1    22.9    +      -       -      -
      3D    T      6.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 424 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  ARG*     4.5     6.2    +      -       -      -
    422A  PHE      3.8     0.4    +      -       -      -
    423A  SER*     1.3    80.1    -      -       -      +
    425A  ILE*     1.3    60.7    +      -       -      +
    426A  ASN*     3.1    28.9    +      -       -      +
    463A  VAL*     3.7    25.7    -      -       +      +
    505A  ARG*     2.6    47.6    +      -       +      +
    506A  LEU      3.3     9.6    -      -       -      +
    507A  ARG*     5.1     1.5    -      -       -      +
    119B  ASP*     3.2    33.7    +      -       +      +
    173B  LYS*     3.2    13.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 425 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422A  PHE*     3.5    30.5    -      -       +      -
    423A  SER      3.6     8.1    -      -       -      +
    424A  GLU*     1.3    79.2    -      -       -      +
    426A  ASN*     1.3    63.6    +      -       -      +
    427A  LYS      4.2     1.1    -      -       -      +
    430A  GLU*     3.8    29.4    -      -       +      +
    431A  GLN*     2.9    41.9    +      -       +      +
    434A  LEU*     3.8    22.9    -      -       +      -
    504A  LEU      3.1     6.8    -      -       -      +
    506A  LEU*     3.1    16.7    +      -       +      +
    119B  ASP*     5.4     1.1    -      -       -      -
    173B  LYS*     3.6    29.2    -      -       +      +
----------------------------------------------------------
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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