Contacts of the strand formed by residues 211 - 219 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199D  SER*     5.6     1.6    +      -       -      -
    200D  TYR*     3.9    17.3    +      -       -      +
    205D  LYS*     3.7    27.9    -      -       +      +
    209D  PRO      3.6     0.5    -      -       -      -
    210D  ASN*     1.3    96.4    +      -       -      +
    212D  PHE*     1.3    66.7    +      -       -      +
    213D  ASP*     4.5     6.9    -      -       -      +
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Residues in contact with PHE 212 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167D  ALA*     4.0    15.7    -      -       +      -
    168D  ALA*     4.3     9.9    -      -       +      -
    171D  VAL*     3.6    42.0    -      -       +      -
    200D  TYR*     3.5    47.3    -      +       -      -
    201D  TYR*     3.8    16.8    -      +       -      +
    209D  PRO*     3.2    38.6    -      -       +      -
    210D  ASN      4.5     2.0    -      -       -      -
    211D  GLU*     1.3    77.2    -      -       -      +
    213D  ASP*     1.3    68.0    +      -       -      +
    214D  VAL*     4.0     7.5    +      -       +      +
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Residues in contact with ASP 213 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197D  THR*     2.8    56.7    +      -       -      +
    198D  GLY*     4.3    10.8    -      -       -      -
    199D  SER      5.6     0.7    -      -       -      -
    200D  TYR*     5.9     0.2    -      -       -      +
    201D  TYR*     3.8     5.2    -      -       -      -
    211D  GLU*     4.5     7.4    -      -       -      +
    212D  PHE*     1.3    84.2    +      -       -      +
    214D  VAL*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 214 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171D  VAL*     5.5     0.4    -      -       +      -
    175D  VAL*     4.1    24.9    -      -       +      -
    194D  GLN*     3.6    32.3    -      -       +      +
    195D  LEU      3.9     1.6    -      -       -      -
    196D  ASN*     3.8    14.6    -      -       -      +
    197D  THR*     5.0     0.2    -      -       -      -
    201D  TYR*     4.5    10.3    -      -       -      +
    212D  PHE*     4.0     9.2    +      -       +      +
    213D  ASP*     1.3    80.1    -      -       -      +
    215D  MET*     1.3    63.7    +      -       -      +
    216D  PHE*     3.7    23.4    +      -       +      -
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Residues in contact with MET 215 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193D  GLU      3.3     5.9    -      -       -      +
    194D  GLN*     3.4     2.8    -      -       -      -
    195D  LEU*     2.8    68.5    +      -       +      +
    197D  THR*     4.4    18.4    +      -       +      +
    213D  ASP      4.2     0.4    -      -       -      -
    214D  VAL*     1.3    71.5    -      -       -      +
    216D  PHE*     1.3    64.8    +      -       -      +
    217D  LYS*     3.6     9.3    +      -       +      +
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Residues in contact with PHE 216 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175D  VAL*     4.2    13.5    -      -       +      -
    178D  LEU*     4.2    10.3    -      -       +      -
    179D  LEU*     3.8    46.9    -      -       +      -
    182D  MET*     4.2    15.7    -      -       +      -
    192D  VAL*     3.6    24.8    -      -       +      +
    193D  GLU      3.5     3.8    -      -       -      -
    194D  GLN*     4.8     2.9    -      -       +      -
    214D  VAL*     3.7    26.0    +      -       +      -
    215D  MET*     1.3    77.7    -      -       -      +
    217D  LYS*     1.3    59.3    +      -       -      +
    218D  LEU      4.1     1.0    +      -       -      -
    266D  PHE*     3.5    38.7    -      +       +      -
    270D  ILE*     5.6     2.9    -      -       +      -
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Residues in contact with LYS 217 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191D  GLY      4.2     1.0    -      -       -      +
    192D  VAL*     3.4     3.2    -      -       -      -
    193D  GLU*     2.6    82.1    +      -       -      +
    194D  GLN      4.6     3.4    -      -       -      -
    195D  LEU*     3.8    34.5    -      -       +      -
    215D  MET*     4.7    13.5    -      -       +      +
    216D  PHE*     1.3    73.2    -      -       -      +
    218D  LEU*     1.3    60.3    +      -       -      +
    219D  GLU*     4.1     6.0    +      -       -      +
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Residues in contact with LEU 218 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188D  GLU      3.6    21.8    -      -       -      +
    189D  PHE*     4.4     8.3    -      -       +      +
    190D  LYS      4.0    11.2    -      -       -      +
    191D  GLY*     3.9    27.4    -      -       -      +
    192D  VAL*     4.0    12.8    -      -       +      +
    216D  PHE      4.1     1.6    +      -       -      +
    217D  LYS*     1.3    74.6    -      -       -      +
    219D  GLU*     1.3    75.4    +      -       -      +
    220D  VAL*     3.3    15.0    +      -       +      +
    248D  LEU*     4.1    12.8    -      -       +      -
    262D  MET*     4.0    27.4    -      -       +      -
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Residues in contact with GLU 219 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191D  GLY      5.2     2.4    +      -       -      -
    193D  GLU*     5.9     3.1    -      -       -      +
    217D  LYS*     4.1     5.7    +      -       -      +
    218D  LEU*     1.3    81.3    -      -       -      +
    220D  VAL*     1.3    62.6    +      -       -      +
    221D  PRO*     3.4    33.3    -      -       -      +
----------------------------------------------------------
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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