Contacts of the strand formed by residues 549 - 555 (chain A) in PDB entry 4N7E


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 ASN 549 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  TRP*     5.9     0.6    -      -       +      -
    117A  TYR*     3.6    28.4    -      -       +      +
    119A  LYS*     3.2    11.9    -      -       -      -
    495A  LEU*     3.9     3.8    -      -       -      +
    541A  SER*     3.7    16.6    -      -       -      -
    542A  GLU      4.6     0.3    +      -       -      -
    547A  SER*     3.2    15.8    +      -       -      +
    548A  MET*     1.3    80.2    -      -       -      +
    550A  ILE*     1.3    59.3    +      -       -      +
    568A  THR*     4.5     6.3    -      -       +      -
    569A  ILE      3.4     3.7    -      -       -      +
    570A  ASP*     2.9    25.0    -      -       -      +
      1C  NAG      1.4    62.1    +      -       -      +
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Residues in contact with ILE 550 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493A  THR*     3.8    22.9    -      -       +      +
    495A  LEU*     4.2     9.2    -      -       +      -
    502A  VAL*     4.4     8.1    -      -       +      -
    514A  ILE*     4.3    13.5    -      -       +      -
    539A  LEU*     3.8    34.8    -      -       +      -
    540A  ALA      3.6    17.3    -      -       -      +
    541A  SER*     3.8     9.0    -      -       -      -
    548A  MET      4.0     0.2    +      -       -      -
    549A  ASN*     1.3    73.8    -      -       -      +
    551A  SER*     1.3    61.5    +      -       -      +
    552A  ILE*     4.9     1.1    -      -       +      +
    567A  TYR      3.7     1.6    -      -       -      +
    568A  THR*     3.1     3.0    -      -       -      -
    569A  ILE*     2.8    50.3    +      -       +      +
    571A  PHE*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 551 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  TRP*     5.6     0.7    -      -       -      -
     91A  ILE*     5.0     2.6    -      -       -      +
    117A  TYR      3.6    14.9    +      -       -      -
    118A  GLY*     4.3     3.5    -      -       -      -
    539A  LEU*     3.3     6.8    -      -       -      -
    540A  ALA*     2.9    44.8    +      -       -      +
    550A  ILE*     1.3    71.9    -      -       -      +
    552A  ILE*     1.3    63.4    +      -       -      +
    553A  TRP*     3.5    22.8    -      -       -      -
    566A  SER*     5.3     2.2    -      -       -      -
    567A  TYR      3.6     0.9    -      -       -      -
    568A  THR*     2.5    25.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 552 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    504A  ILE*     4.0     7.2    -      -       +      -
    514A  ILE*     3.6    29.8    -      -       +      -
    529A  PHE*     3.5    44.2    -      -       +      -
    534A  ILE*     4.0    13.1    -      -       +      +
    536A  PHE*     2.7    40.4    -      -       +      -
    539A  LEU*     4.4     5.4    -      -       +      -
    550A  ILE*     4.9     3.4    -      -       +      +
    551A  SER*     1.3    71.2    -      -       -      +
    553A  TRP*     1.3    59.6    +      -       -      +
    565A  VAL      3.9     0.5    -      -       -      +
    566A  SER*     3.2     4.2    -      -       -      -
    567A  TYR*     2.8    48.4    +      -       +      +
    569A  ILE*     4.2     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 553 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  PHE*     3.6    38.4    -      +       -      -
     79A  VAL*     5.5     3.6    -      -       +      -
     81A  LEU*     3.6    19.5    -      -       +      +
     91A  ILE*     6.3     0.2    -      -       +      -
     93A  VAL*     3.6    28.5    -      -       +      -
    121A  PHE*     4.2    11.7    -      +       -      -
    534A  ILE*     4.4     1.6    -      -       -      -
    536A  PHE*     2.8    28.0    -      -       -      -
    537A  THR*     3.2    15.0    +      -       -      +
    538A  GLY      2.8    21.0    +      -       -      +
    540A  ALA*     3.6    24.7    -      -       +      +
    551A  SER*     3.5    25.5    -      -       -      -
    552A  ILE*     1.3    75.8    -      -       -      +
    554A  GLY*     1.3    59.0    +      -       -      +
    564A  TRP*     5.1    11.9    -      +       +      -
    565A  VAL      3.7     8.3    -      -       -      -
    566A  SER*     3.7    15.7    -      -       -      -
    806A  PGE      3.4    32.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 554 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534A  ILE*     4.4     5.9    -      -       -      +
    535A  TYR      3.0    14.1    -      -       -      -
    536A  PHE*     4.3     0.7    -      -       -      -
    537A  THR*     4.3     4.3    -      -       -      -
    552A  ILE      4.2     0.2    +      -       -      -
    553A  TRP*     1.3    77.4    -      -       -      +
    555A  PHE*     1.3    56.8    +      -       -      -
    564A  TRP*     3.5    17.7    -      -       -      -
    565A  VAL*     2.7    42.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 555 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  LEU*     4.3    18.4    -      -       +      -
    534A  ILE*     3.6     4.3    -      -       -      -
    535A  TYR*     2.8    66.2    +      +       +      +
    537A  THR*     4.2    20.2    -      -       +      -
    554A  GLY*     1.3    74.6    -      -       -      +
    556A  THR*     1.3    79.5    +      -       -      +
    562A  SER*     4.2     5.2    -      -       -      +
    563A  GLN      3.5    17.9    -      -       -      +
    564A  TRP*     3.8    33.0    -      +       +      +
    565A  VAL*     4.4     1.1    -      -       -      +
----------------------------------------------------------
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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