Contacts of the strand formed by residues 155 - 161 (chain E) in PDB entry 1OGA


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 VAL 155 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12E  TYR*     3.6    10.2    +      -       -      -
    123E  PRO*     4.8     0.4    -      -       +      -
    147E  ALA*     5.9     0.2    -      -       +      -
    150E  PHE*     3.6    47.3    -      -       +      -
    153E  ASP*     3.8     7.6    +      -       -      +
    154E  HIS*     1.3    80.2    -      -       -      +
    156E  GLU*     1.3    69.1    +      -       -      +
    176E  PRO*     5.7     0.2    -      -       +      -
    190E  LEU*     4.0    20.8    -      -       +      +
    212E  VAL*     3.8    23.1    -      -       +      -
    213E  GLN      3.2     8.7    -      -       -      +
    214E  PHE*     3.9    14.8    -      -       +      -
    215E  TYR*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 156 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  LYS*     2.9    29.7    +      -       -      +
     12E  TYR*     3.5    16.7    -      -       -      +
    155E  VAL*     1.3    79.2    -      -       -      +
    157E  LEU*     1.3    60.6    +      -       -      +
    158E  SER*     4.1     1.4    +      -       -      -
    211E  GLN*     3.6     2.3    +      -       -      +
    212E  VAL*     3.5     2.9    -      -       -      -
    213E  GLN*     2.8    42.5    +      -       +      +
    215E  TYR*     2.6    35.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 157 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145E  CYS*     4.0     7.0    -      -       +      +
    147E  ALA*     4.8     6.7    -      -       +      -
    155E  VAL*     4.2     1.4    -      -       +      +
    156E  GLU*     1.3    73.4    -      -       -      +
    158E  SER*     1.3    69.1    +      -       -      +
    159E  TRP*     4.0    10.5    -      -       +      +
    172E  THR*     4.0    14.8    +      -       +      +
    190E  LEU*     4.5    27.7    -      -       +      +
    191E  SER      5.0     0.4    -      -       -      -
    192E  SER*     3.7    38.6    -      -       -      +
    210E  CYS*     3.8    30.7    -      -       -      -
    211E  GLN      3.2     5.4    -      -       -      +
    212E  VAL*     4.0    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 158 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156E  GLU      5.1     1.5    +      -       -      -
    157E  LEU*     1.3    79.4    -      -       -      +
    159E  TRP*     1.3    64.5    +      -       -      +
    160E  TRP*     2.9    25.9    +      -       -      -
    165E  GLU*     3.4    26.0    -      -       -      -
    210E  CYS*     3.6     2.9    -      -       -      -
    211E  GLN*     2.8    51.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 159 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127E  VAL*     4.5     8.3    -      -       +      -
    143E  LEU*     4.0    28.9    -      -       +      -
    144E  VAL      4.1     2.7    -      -       -      -
    145E  CYS*     3.4    42.8    -      -       +      -
    157E  LEU*     4.0     8.4    -      -       +      +
    158E  SER*     1.3    72.9    -      -       -      +
    160E  TRP*     1.3    64.3    +      -       -      +
    165E  GLU*     3.3     7.4    -      -       -      +
    166E  VAL*     2.9    45.2    +      -       +      +
    170E  VAL*     3.6    29.4    -      -       +      -
    192E  SER*     2.9    29.0    +      -       -      -
    193E  ARG      3.8     4.6    +      -       -      -
    194E  LEU*     3.6    38.1    -      -       +      -
    208E  PHE*     5.0     2.9    -      -       +      -
    209E  ARG      3.5    21.8    -      -       -      -
    210E  CYS*     4.1    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 160 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158E  SER*     2.9    30.3    +      -       -      -
    159E  TRP*     1.3    79.6    -      -       -      +
    161E  VAL*     1.3    62.7    +      -       -      +
    162E  ASN      4.1     0.4    +      -       -      -
    163E  GLY*     3.6    26.2    -      -       -      +
    164E  LYS*     3.3     5.8    -      -       -      +
    165E  GLU*     3.4    45.8    -      -       +      -
    207E  HIS*     3.7     1.2    +      -       -      +
    208E  PHE*     3.4     5.2    -      -       -      -
    209E  ARG*     2.8    73.9    +      -       +      +
    211E  GLN*     3.7    26.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 161 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160E  TRP*     1.3    77.6    -      -       -      +
    162E  ASN*     1.3    78.3    +      -       -      +
    164E  LYS*     2.8    24.7    +      -       -      +
    166E  VAL*     4.0    32.3    -      -       +      +
    194E  LEU*     4.0    11.2    -      -       +      -
    196E  VAL*     5.8     1.6    -      -       +      -
    200E  PHE*     3.6    36.6    -      -       +      -
    206E  ASN*     5.4     0.2    -      -       +      -
    207E  HIS      3.4     7.9    -      -       -      +
    208E  PHE*     4.0    19.7    -      -       +      -
----------------------------------------------------------
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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