Contacts of the strand formed by residues 211 - 219 (chain A) in PDB entry 4LEY


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 GLU 211 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  TYR*     3.8    18.9    +      -       -      +
    205A  LYS*     3.6    27.7    -      -       +      +
    209A  PRO*     3.7     1.7    -      -       -      +
    210A  ASN*     1.3    88.7    +      -       -      +
    212A  PHE*     1.3    66.1    +      -       -      +
    213A  ASP*     4.2     9.9    +      -       -      +
    305A  SER*     3.4    15.6    +      -       -      +
    307A  ASP*     5.5     4.3    -      -       -      +
    406A  GLU*     5.2     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  ILE      5.4     0.4    -      -       -      -
    167A  ALA*     4.0    15.0    -      -       +      -
    168A  ALA*     4.5     7.6    -      -       +      -
    171A  VAL*     3.6    31.4    -      -       +      -
    200A  TYR*     3.4    49.6    -      +       -      -
    201A  TYR*     3.5    24.2    -      +       +      +
    209A  PRO*     3.4    29.8    -      -       +      -
    211A  GLU*     1.3    74.8    -      -       -      +
    213A  ASP*     1.3    64.5    +      -       -      +
    214A  VAL*     4.8     2.2    -      -       +      -
    304A  ILE*     3.5    26.5    -      -       +      -
    305A  SER      2.9    11.4    +      -       -      +
    306A  VAL*     3.4    10.1    -      -       +      +
    307A  ASP      2.9    26.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  ASN*     3.8     0.3    -      -       -      -
    197A  THR*     2.9    54.7    +      -       -      +
    198A  GLY*     4.1    12.6    -      -       -      -
    199A  SER      5.4     1.1    -      -       -      -
    200A  TYR*     5.9     0.2    -      -       -      +
    201A  TYR*     3.8     7.0    -      -       -      -
    211A  GLU*     4.7    10.0    -      -       -      +
    212A  PHE*     1.3    79.0    +      -       -      +
    214A  VAL*     1.3    63.3    +      -       -      +
    307A  ASP*     3.8    22.1    -      -       -      +
    309A  ILE*     4.3    12.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  VAL*     5.4     0.9    -      -       +      -
    175A  VAL*     4.0    23.3    -      -       +      -
    194A  GLN*     3.7    22.7    -      -       +      +
    195A  LEU      4.0     2.2    -      -       -      -
    196A  ASN*     3.6    21.3    -      -       -      +
    197A  THR*     4.8     0.2    -      -       -      -
    201A  TYR*     4.8     5.4    -      -       -      +
    212A  PHE*     4.4     7.9    -      -       +      +
    213A  ASP*     1.3    79.0    -      -       -      +
    215A  MET*     1.3    64.2    +      -       -      +
    216A  PHE*     3.7    18.7    +      -       +      -
    306A  VAL*     4.3    13.2    -      -       +      -
    307A  ASP      2.9     9.3    +      -       -      +
    308A  ILE*     3.5     8.4    -      -       +      +
    309A  ILE*     2.9    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  GLU      3.1     5.2    -      -       -      +
    194A  GLN*     3.3     3.8    -      -       -      -
    195A  LEU*     2.9    58.5    +      -       +      +
    197A  THR*     4.3    18.4    -      -       -      +
    214A  VAL*     1.3    73.4    -      -       -      +
    216A  PHE*     1.3    65.9    +      -       -      +
    217A  LYS*     4.8     2.9    -      -       +      +
    309A  ILE*     3.5    25.1    -      -       +      +
    311A  ALA*     4.5    15.5    -      -       +      -
    346A  TYR*     4.7    18.6    -      -       +      -
    348A  VAL*     4.8     6.1    -      -       +      -
    366A  SER*     3.3    33.0    -      -       -      +
    368A  SER*     3.6    20.4    -      -       -      +
    369A  HIS      5.6     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  VAL*     4.1    15.7    -      -       +      -
    178A  LEU*     4.2    15.5    -      -       +      -
    179A  LEU*     3.9    48.7    -      -       +      -
    182A  MET*     4.3     8.5    -      -       +      -
    192A  VAL*     3.4    25.8    -      -       +      +
    193A  GLU      3.4     3.4    -      -       -      -
    194A  GLN*     4.5     3.1    -      -       +      -
    214A  VAL*     3.7    23.7    +      -       +      -
    215A  MET*     1.3    80.3    -      -       -      +
    217A  LYS*     1.3    59.2    +      -       -      +
    266A  PHE*     3.8    32.5    -      +       +      -
    308A  ILE*     3.9    20.6    -      -       +      -
    309A  ILE      2.9    10.4    +      -       -      +
    310A  LEU*     3.8     4.5    -      -       -      +
    311A  ALA*     2.9    25.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  GLY      4.4     1.0    -      -       -      +
    192A  VAL*     3.3     2.8    -      -       -      +
    193A  GLU*     2.5    82.9    +      -       -      +
    194A  GLN      4.9     1.6    -      -       -      -
    195A  LEU*     3.7    26.9    -      -       +      -
    215A  MET*     5.1     4.5    -      -       +      -
    216A  PHE*     1.3    73.6    -      -       -      +
    218A  LEU*     1.3    60.8    +      -       -      +
    219A  GLU*     4.4     1.0    +      -       -      +
    311A  ALA*     3.4    10.5    -      -       +      -
    313A  GLU*     2.7    28.7    +      -       +      +
    346A  TYR*     3.4    42.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  GLU      4.1    18.6    -      -       -      +
    189A  PHE*     4.4    12.8    -      -       +      -
    190A  LYS      3.8    23.3    -      -       -      +
    191A  GLY      4.2     4.0    -      -       -      +
    192A  VAL*     4.0    22.4    -      -       +      +
    216A  PHE      5.2     0.2    -      -       -      +
    217A  LYS*     1.3    73.4    -      -       -      +
    219A  GLU*     1.3    73.1    +      -       -      +
    220A  VAL*     3.5     4.6    +      -       +      +
    248A  LEU*     4.3    12.3    -      -       +      -
    262A  MET*     4.2    23.6    -      -       +      -
    310A  LEU*     5.7     1.8    -      -       +      -
    311A  ALA      2.9    14.0    +      -       -      +
    312A  LEU*     3.3     9.8    -      -       +      -
    313A  GLU*     2.9    18.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  GLY      5.7     1.0    +      -       -      -
    193A  GLU*     6.1     0.7    -      -       -      +
    217A  LYS*     4.3     1.2    -      -       -      +
    218A  LEU*     1.3    80.0    -      -       -      +
    220A  VAL*     1.3    63.9    +      -       -      +
    221A  PRO*     3.3    29.7    -      -       +      +
    313A  GLU*     3.3    30.5    -      -       -      +
    314A  SER*     5.5     0.2    -      -       -      -
    315A  LYS*     3.5    46.3    +      -       +      +
----------------------------------------------------------
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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