Contacts of the strand formed by residues 161 - 168 (chain E) in PDB entry 1SID


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 GLN 161 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  LEU*     5.3     0.7    -      -       -      -
    159E  GLY      3.1    11.3    +      -       -      +
    160E  SER*     1.3    73.9    -      -       -      +
    162E  TYR*     1.3    64.4    +      -       -      +
    163E  HIS*     4.2     8.8    +      -       +      +
    242E  ASN*     4.1     0.4    -      -       -      +
    243E  TYR*     3.6     3.2    -      -       -      -
    244E  THR*     2.7    47.2    +      -       +      +
    249E  THR*     3.0    19.6    +      -       -      +
    250E  PRO      3.0    13.1    +      -       -      -
    251E  PRO*     2.9    38.3    -      -       -      +
    252E  VAL*     3.6    15.5    +      -       -      +
    285E  ILE*     3.0    17.3    -      -       -      +
    286E  MET*     3.4    21.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 162 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  SER      4.3     0.2    -      -       -      -
    133D  GLY*     3.6    16.7    -      -       -      -
    136D  LEU*     4.0    21.8    -      -       +      -
    255D  PHE*     3.3    30.2    -      +       -      -
     98E  TRP*     4.5     5.7    -      +       -      -
    161E  GLN*     1.3    76.6    -      -       -      +
    163E  HIS*     1.3    67.9    +      -       -      +
    164E  VAL*     3.3    15.2    -      -       +      +
    224E  VAL*     3.2    34.2    -      -       +      +
    227E  TRP      4.4     3.1    +      -       -      -
    228E  HIS*     3.8    13.2    +      -       -      -
    229E  PRO*     4.7     1.6    -      -       -      +
    242E  ASN      3.5    15.7    -      -       -      -
    243E  TYR*     4.2    15.3    -      +       +      -
    283E  VAL*     3.1    34.6    -      -       +      +
    285E  ILE*     2.7    50.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 163 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129E  VAL*     4.6     4.5    -      -       +      +
    161E  GLN*     4.2     9.8    +      -       +      +
    162E  TYR*     1.3    79.1    +      -       -      +
    164E  VAL*     1.3    63.3    +      -       -      +
    241E  GLY*     2.8    20.4    -      -       -      -
    242E  ASN*     2.9    26.9    +      -       -      +
    252E  VAL      5.1     4.2    +      -       -      -
    253E  LEU*     5.0     8.4    -      -       +      +
    283E  VAL      2.8     6.7    -      -       -      -
    284E  ASP*     2.8    39.9    +      -       +      +
    285E  ILE      3.5    24.3    +      -       -      -
    286E  MET*     3.6    28.5    -      -       -      +
    304E  ARG*     4.4     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 164 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255D  PHE*     3.8    13.2    -      -       +      -
     98E  TRP*     3.7    22.7    -      -       +      -
    162E  TYR*     3.3    35.7    -      -       +      +
    163E  HIS*     1.3    83.9    -      -       -      +
    165E  PHE*     1.3    80.2    +      -       -      +
    229E  PRO*     4.8     4.7    -      -       +      -
    239E  TYR*     4.6    11.9    -      -       +      -
    240E  PHE      2.9    25.4    -      -       -      +
    241E  GLY*     3.7     6.7    -      -       -      -
    242E  ASN      4.3     0.2    -      -       -      +
    282E  CYS*     3.0     3.4    -      -       -      +
    283E  VAL*     2.9    26.6    +      -       +      +
    304E  ARG*     4.2     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 165 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98E  TRP*     4.7     2.5    -      -       -      -
    125E  VAL*     5.1    10.5    -      -       +      -
    127E  THR*     4.1    20.2    -      -       +      -
    164E  VAL*     1.3    83.3    -      -       -      +
    166E  ALA*     1.3    80.4    +      -       -      +
    167E  VAL*     4.4    10.8    -      -       +      -
    239E  TYR*     2.9     4.0    -      -       -      +
    240E  PHE*     2.7    77.8    +      +       +      -
    261E  THR*     6.0     5.6    -      -       +      -
    263E  LEU*     6.1     0.2    -      -       +      -
    281E  SER      2.9    16.2    -      -       -      +
    282E  CYS*     3.2    11.4    -      -       +      +
    304E  ARG*     3.8    28.0    -      -       -      +
    306E  PHE*     4.2    13.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with ALA 166 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165E  PHE*     1.3    81.0    -      -       -      +
    167E  VAL*     1.3    70.4    +      -       -      +
    172E  LEU*     4.8    10.5    -      -       +      -
    237E  THR*     4.0    13.7    -      -       +      -
    238E  ARG      2.7    22.0    -      -       -      +
    239E  TYR*     3.2    12.3    -      -       +      -
    279E  TYR      3.5     1.5    -      -       -      +
    280E  LEU*     3.5     0.5    -      -       -      -
    281E  SER*     2.7    39.5    +      -       -      +
    306E  PHE*     4.5     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 167 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122E  ALA*     4.7     6.7    -      -       +      -
    125E  VAL*     4.6    13.5    -      -       +      -
    165E  PHE*     4.4    11.2    -      -       +      -
    166E  ALA*     1.3    83.1    -      -       -      +
    168E  GLY*     1.3    61.6    +      -       -      +
    237E  THR*     3.2     4.4    -      -       -      -
    238E  ARG*     2.8    30.2    +      -       -      +
    240E  PHE*     6.1     0.2    -      -       +      -
    263E  LEU*     4.3    27.6    -      -       +      -
    271E  PRO*     3.9     7.2    -      -       +      +
    278E  LEU*     4.0    10.8    -      -       +      -
    279E  TYR      3.2     3.6    -      -       -      -
    280E  LEU*     4.0    23.6    -      -       +      -
    306E  PHE*     4.4    15.5    -      -       +      -
    308E  ILE*     4.5     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 168 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122E  ALA*     6.4     0.2    -      -       -      -
    167E  VAL*     1.3    76.4    -      -       -      +
    169E  GLY*     1.3    59.5    +      -       -      -
    170E  GLU      3.4     4.7    -      -       -      -
    236E  ASN      3.2     9.0    -      -       -      -
    237E  THR*     3.0    17.5    -      -       -      +
    271E  PRO*     4.2     6.7    -      -       -      -
    273E  CYS*     5.5     0.9    -      -       -      -
    278E  LEU*     3.6     8.0    -      -       -      +
    279E  TYR*     2.8    42.6    +      -       -      -
----------------------------------------------------------
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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