Contacts of the strand formed by residues 491 - 500 (chain A) in PDB entry 5FFO


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 LYS 491 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489A  PRO*     4.4     9.8    -      -       +      +
    490A  ARG*     1.3    83.5    -      -       +      +
    492A  LEU*     1.3    65.7    +      -       -      +
    493A  ASN*     4.0     6.3    +      -       -      +
    527A  THR*     4.1    23.3    -      -       +      -
    528A  ILE      3.8     2.0    -      -       -      -
    529A  SER*     3.5    27.2    +      -       -      +
    568A  THR*     4.5    11.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 492 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442A  ILE*     4.3    34.1    -      -       +      -
    482A  ALA*     4.4    11.0    -      -       +      -
    483A  ASP      5.2     0.4    -      -       -      +
    488A  LEU*     4.6    11.4    -      -       +      -
    489A  PRO*     4.2    17.5    -      -       +      +
    490A  ARG      3.3     7.4    +      -       -      +
    491A  LYS*     1.3    76.0    -      -       -      +
    493A  ASN*     1.3    62.0    +      -       -      +
    494A  PHE*     3.4    22.6    -      -       +      -
    528A  ILE*     2.9    34.0    +      -       +      +
    530A  ARG*     4.2    22.0    -      -       +      +
    564A  LEU*     4.3     9.0    -      -       +      -
    569A  ALA*     3.9    25.6    -      -       +      -
    577A  PRO*     5.7     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 493 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491A  LYS*     4.0     8.1    +      -       -      +
    492A  LEU*     1.3    71.2    -      -       -      +
    494A  PHE*     1.3    60.6    +      -       -      +
    495A  GLN*     5.7     0.4    -      -       -      -
    526A  MET      3.4     4.5    -      -       -      +
    527A  THR*     2.7    34.6    +      -       -      +
    564A  LEU*     3.1     6.9    -      -       -      +
    565A  ASP*     3.1    32.8    +      -       +      +
    568A  THR*     3.6    32.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 494 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442A  ILE*     5.0     6.7    -      -       +      -
    444A  VAL*     5.0    13.9    -      -       +      -
    480A  LEU*     4.2    21.8    -      -       +      -
    482A  ALA*     3.7    21.8    -      -       +      -
    492A  LEU*     3.4    31.2    -      -       +      -
    493A  ASN*     1.3    72.4    -      -       -      +
    495A  GLN*     1.3    62.6    +      -       -      +
    496A  VAL*     4.0     3.1    -      -       +      -
    525A  ASN*     3.6     2.1    -      -       -      +
    526A  MET*     2.4    63.3    +      -       +      +
    528A  ILE*     3.4    31.0    -      -       +      -
    562A  TYR*     5.1     8.1    -      +       +      -
    563A  ARG      3.2    24.5    -      -       -      +
    564A  LEU*     4.3    16.8    -      -       +      -
    579A  LEU*     5.6     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 495 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493A  ASN      4.3     0.6    +      -       -      +
    494A  PHE*     1.3    74.6    -      -       -      +
    496A  VAL*     1.3    61.6    +      -       -      +
    497A  GLU*     4.2    17.1    +      -       -      +
    524A  LYS      4.1     3.8    -      -       -      -
    525A  ASN*     4.0    17.3    -      -       -      +
    562A  TYR*     3.7     0.7    -      -       -      -
    563A  ARG*     2.9    46.6    +      -       +      +
    564A  LEU      5.3     4.9    -      -       -      -
    565A  ASP*     3.8    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 496 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    478A  PHE*     4.7    12.3    -      -       +      -
    480A  LEU*     4.0    27.8    -      -       +      -
    494A  PHE*     4.4     8.7    -      -       +      -
    495A  GLN*     1.3    75.7    -      -       -      +
    497A  GLU*     1.3    65.9    +      -       -      +
    498A  LEU*     3.6    22.6    -      -       +      +
    522A  HIS      3.9     1.6    -      -       -      +
    523A  SER*     3.8     1.4    -      -       -      -
    524A  LYS*     3.2    38.7    +      -       +      +
    526A  MET*     4.6    11.2    -      -       +      -
    560A  MET*     4.5    13.5    -      -       +      -
    561A  GLU      3.3    16.4    -      -       -      +
    562A  TYR*     4.2     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 497 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    495A  GLN*     4.3    18.1    +      -       +      +
    496A  VAL*     1.3    85.8    +      -       -      +
    498A  LEU*     1.3    63.1    +      -       -      +
    499A  LEU*     4.5     8.0    +      -       +      -
    521A  SER*     6.5     0.2    -      -       -      -
    522A  HIS      4.0     2.5    -      -       -      +
    523A  SER*     3.4    30.3    +      -       -      -
    559A  PHE*     5.3     0.2    -      -       -      -
    561A  GLU*     2.8    62.9    +      -       +      +
    563A  ARG*     6.2     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 498 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448A  LEU*     5.8     1.1    -      -       +      -
    476A  VAL*     4.3    16.6    -      -       +      -
    478A  PHE*     4.1    31.0    -      -       +      -
    496A  VAL*     3.6    23.1    -      -       +      -
    497A  GLU*     1.3    83.0    -      -       -      +
    499A  LEU*     1.3    63.1    +      -       -      +
    500A  LEU*     4.2     2.5    -      -       +      -
    514A  PHE*     4.1    28.3    -      -       +      -
    520A  PRO      4.0     0.6    -      -       -      +
    521A  SER*     3.2    28.6    -      -       -      -
    522A  HIS*     3.4    16.5    +      -       +      +
    558A  ILE*     5.6     5.4    -      -       +      -
    559A  PHE      3.5    10.1    -      -       -      +
    560A  MET*     3.8    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 499 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497A  GLU*     4.5     7.6    +      -       +      -
    498A  LEU*     1.3    76.4    -      -       -      +
    500A  LEU*     1.3    64.6    +      -       -      +
    501A  ASP      3.9     0.3    +      -       -      -
    502A  LYS*     4.1    30.8    +      -       +      +
    520A  PRO      4.0     2.2    -      -       -      +
    521A  SER*     3.6    25.8    -      -       -      -
    557A  THR      4.1     0.3    -      -       -      +
    558A  ILE*     5.6     0.2    -      -       -      -
    559A  PHE*     2.9    66.0    +      -       +      +
    561A  GLU*     5.0     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 500 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    474A  PHE*     4.8     5.4    -      -       +      -
    476A  VAL*     5.0     5.4    -      -       +      -
    498A  LEU*     6.2     1.6    -      -       +      -
    499A  LEU*     1.3    74.7    -      -       -      +
    501A  ASP*     1.3    71.6    +      -       -      +
    502A  LYS*     3.3     0.9    +      -       -      -
    510A  ARG*     3.8    13.2    +      -       -      +
    512A  ALA*     3.6    20.9    -      -       +      +
    513A  LEU*     3.6    28.5    -      -       -      +
    514A  PHE*     3.7    30.1    -      -       +      -
    520A  PRO*     3.3    17.8    +      -       -      +
    541A  ALA*     3.8    24.0    -      -       +      -
    556A  ILE*     5.5     0.7    -      -       +      -
    557A  THR      4.3     1.3    -      -       -      -
    558A  ILE*     3.8    33.4    -      -       +      -
----------------------------------------------------------
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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