Contacts of the strand formed by residues 199 - 207 (chain B) in PDB entry 4YLO


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 ASP 199 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  PRO      3.8     0.9    -      -       -      -
     31B  LEU*     2.7    67.7    +      -       -      +
     32B  GLU      3.2    15.3    -      -       -      +
     33B  ARG*     4.0     4.9    +      -       -      -
     34B  GLY      5.0     2.9    +      -       -      -
     36B  GLY*     3.5    22.4    +      -       -      -
     37B  HIS*     5.7     1.2    -      -       -      -
    187B  VAL*     3.7    18.3    -      -       -      +
    188B  GLU      3.9     2.2    -      -       -      +
    189B  ALA*     3.6    15.7    -      -       +      +
    190B  ALA*     3.1    11.7    +      -       -      +
    197B  ASP      4.6     2.2    -      -       -      +
    198B  LEU*     1.3    76.4    -      -       -      +
    200B  LYS*     1.3    60.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  VAL*     4.9     4.2    -      -       -      +
     27B  THR*     4.5    22.0    +      -       +      +
     28B  LEU      3.7     4.9    -      -       -      +
     29B  GLU*     3.6    42.7    +      -       +      -
     31B  LEU*     5.4     0.2    -      -       -      -
    186B  ASN      3.6     0.5    -      -       -      +
    187B  VAL*     3.4    28.9    -      -       -      +
    188B  GLU*     2.7    24.2    +      -       +      +
    189B  ALA      4.9     0.4    -      -       -      -
    190B  ALA*     3.1    22.8    -      -       +      +
    199B  ASP*     1.3    75.6    -      -       -      +
    201B  LEU*     1.3    60.2    +      -       -      +
    202B  VAL*     4.0    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  VAL      3.6     2.1    -      -       -      +
     27B  THR*     3.5     2.4    -      -       -      -
     28B  LEU*     2.9    53.2    +      -       +      +
     31B  LEU*     3.9    22.6    -      -       +      +
     36B  GLY*     3.2    31.2    -      -       -      +
     39B  LEU*     4.5    12.6    -      -       +      -
     40B  GLY      4.7     2.5    -      -       -      +
     43B  LEU*     5.5     3.6    -      -       +      -
    185B  TYR*     4.6    12.1    -      -       +      -
    187B  VAL*     3.5    20.2    -      -       +      -
    199B  ASP      4.1     0.4    +      -       -      -
    200B  LYS*     1.3    73.6    -      -       -      +
    202B  VAL*     1.3    62.0    +      -       -      +
    203B  ILE*     3.9    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  LYS*     6.2     2.2    -      -       +      -
     26B  VAL      3.6     4.7    -      -       -      +
     27B  THR*     3.9    27.4    -      -       +      -
    184B  ALA      4.0     0.5    -      -       -      +
    185B  TYR*     3.3     4.0    -      -       -      -
    186B  ASN*     2.9    50.4    +      -       +      +
    188B  GLU*     5.7     5.6    -      -       +      +
    200B  LYS*     4.6    17.3    -      -       +      -
    201B  LEU*     1.3    78.5    -      -       -      +
    203B  ILE*     1.3    63.3    +      -       -      +
    204B  GLU*     4.0    18.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  ALA      3.8     1.7    -      -       -      +
     25B  LYS*     3.5     3.1    -      -       -      -
     26B  VAL*     2.9    44.5    +      -       +      +
     40B  GLY*     4.8     4.0    -      -       -      +
     43B  LEU*     4.3    20.2    -      -       +      -
     47B  LEU*     6.5     0.7    -      -       +      -
    183B  ILE*     5.4     5.8    -      -       +      -
    184B  ALA*     3.4    11.2    -      -       -      +
    185B  TYR*     3.7    20.4    -      -       +      -
    201B  LEU*     3.9    31.2    -      -       +      -
    202B  VAL*     1.3    79.4    -      -       -      +
    204B  GLU*     1.3    72.2    +      -       -      +
    205B  MET*     3.9     7.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  HIS*     5.5     5.7    +      -       +      -
     24B  ALA      3.9     3.4    -      -       -      +
     25B  LYS*     4.5    32.3    +      -       +      +
    182B  ARG*     3.9    20.7    +      -       +      +
    183B  ILE*     3.6     3.6    -      -       -      -
    184B  ALA*     2.9    36.3    +      -       +      +
    186B  ASN*     5.5     5.7    +      -       -      +
    202B  VAL*     4.8    16.5    -      -       +      +
    203B  ILE*     1.3    78.8    -      -       -      +
    205B  MET*     1.3    62.7    +      -       -      +
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Residues in contact with MET 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  THR      3.7     1.0    -      -       -      +
     23B  HIS*     3.5     8.2    +      -       -      -
     24B  ALA*     2.9    46.1    +      -       +      +
     47B  LEU*     3.9    15.5    -      -       +      -
    180B  VAL*     3.2    35.0    -      -       +      -
    182B  ARG*     3.5     4.3    -      -       -      +
    183B  ILE*     3.3    29.4    -      -       +      -
    203B  ILE*     5.1     8.5    -      -       +      +
    204B  GLU*     1.3    75.3    -      -       -      +
    206B  GLU*     1.3    68.1    +      -       -      +
    207B  THR*     4.3    12.8    -      -       +      +
    213B  PRO*     5.1     8.7    -      -       +      +
    216B  ALA*     5.2     5.8    -      -       -      -
    217B  ILE*     4.8    17.5    -      -       -      -
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Residues in contact with GLU 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  THR*     3.4    23.8    +      -       +      +
     23B  HIS*     4.5    13.6    +      -       -      +
    180B  VAL*     3.8     1.0    -      -       -      -
    181B  GLU*     2.8    47.2    +      -       +      +
    182B  ARG*     2.9    44.7    +      -       +      +
    205B  MET*     1.3    77.0    -      -       -      +
    207B  THR*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  SER      4.1     2.0    -      -       -      +
     22B  THR*     2.6    39.8    +      -       -      +
    179B  PRO*     3.5    15.1    +      -       -      +
    180B  VAL*     4.7     1.5    -      -       -      +
    181B  GLU*     4.9     3.1    -      -       -      -
    205B  MET*     4.6    12.8    -      -       +      -
    206B  GLU*     1.3    79.5    -      -       -      +
    208B  ASN*     1.3    66.0    +      -       -      +
    209B  GLY      3.0     8.5    +      -       -      +
    211B  ILE*     3.3    33.6    +      -       -      +
    213B  PRO*     3.8    26.5    -      -       +      -
    216B  ALA*     5.5     2.7    -      -       -      +
----------------------------------------------------------
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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