Contacts of the strand formed by residues 97 - 103 (chain A) in PDB entry 1X8E


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 97 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  HIS*     4.2     6.8    -      -       -      -
     90A  HIS*     2.7    35.1    +      -       +      -
     96A  ALA*     1.3    78.3    -      -       -      +
     98A  VAL*     1.3    68.4    +      -       -      +
     99A  TYR*     3.1    29.3    +      -       +      -
    128A  VAL      3.6     0.3    -      -       -      +
    129A  TYR*     3.7     1.6    -      -       -      -
    130A  VAL*     3.0    47.2    +      -       +      +
    136A  HIS*     3.1    23.5    -      -       +      +
    150A  ALA*     4.7     0.2    -      -       -      +
    151A  ILE      3.4     6.9    -      -       -      +
    152A  TYR*     3.7    33.1    +      -       +      +
     66B  LEU*     3.8     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  GLU*     1.3    79.3    -      -       -      +
     99A  TYR*     1.3    64.5    +      -       -      +
    100A  VAL*     4.3     5.8    -      -       +      -
    127A  VAL*     3.6    26.9    -      -       +      -
    128A  VAL      3.4     4.9    -      -       -      +
    129A  TYR*     4.6     8.5    -      -       +      -
    151A  ILE*     2.9    42.4    +      -       +      +
     66B  LEU*     3.9    21.3    -      -       +      +
     68B  PHE*     3.8    23.6    -      -       +      -
    149B  LEU*     6.1     0.2    -      -       +      -
    151B  ILE*     4.1    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  HIS*     3.6    21.5    +      +       -      -
     97A  GLU*     3.1    29.1    +      -       +      -
     98A  VAL*     1.3    77.0    -      -       -      +
    100A  VAL*     1.3    69.2    +      -       -      +
    108A  MET*     3.4    27.4    -      -       +      -
    122A  MET*     4.3     9.9    -      -       +      -
    126A  THR      4.8     0.2    -      -       -      -
    127A  VAL*     3.3     4.3    -      -       -      +
    128A  VAL*     2.9    32.5    +      -       +      +
    130A  VAL*     4.1     8.7    -      -       +      -
    136A  HIS*     2.9    32.4    +      +       -      -
    138A  THR*     4.0    13.1    -      -       +      +
    148A  PHE*     3.5    41.5    -      +       -      -
    149A  LEU      3.4     3.4    -      -       -      -
    150A  ALA*     3.8    15.1    -      -       +      +
    152A  TYR*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  VAL*     4.3     8.1    -      -       +      -
     99A  TYR*     1.3    82.3    -      -       -      +
    101A  ALA*     1.3    66.8    +      -       -      +
    102A  LEU*     3.7    21.2    +      -       +      +
    122A  MET*     4.6     1.1    -      -       -      -
    126A  THR      3.8     4.0    -      -       -      +
    127A  VAL*     3.7    23.1    -      -       +      -
    148A  PHE*     3.3     6.7    -      -       -      +
    149A  LEU*     2.8    44.7    +      -       +      +
    151A  ILE*     4.6     8.1    -      -       +      -
     12B  PHE*     4.1    13.9    -      -       +      -
    100B  VAL*     6.2     2.2    -      -       +      -
    149B  LEU*     4.0    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  VAL*     1.3    75.4    -      -       -      +
    102A  LEU*     1.3    65.5    +      -       -      +
    122A  MET*     4.1    21.5    -      -       +      +
    123A  GLU      3.0    31.9    -      -       -      +
    124A  PRO*     4.0     0.4    -      -       +      -
    125A  GLY      3.3    17.2    +      -       -      +
    126A  THR*     3.0    18.1    +      -       -      +
    146A  PHE*     4.7     7.2    -      -       +      -
    147A  ILE      4.1     4.0    -      -       -      -
    148A  PHE*     4.4     1.1    -      -       -      -
     12B  PHE*     3.8     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  VAL*     4.7     3.4    -      -       +      -
     11A  ASP      5.2     0.2    -      -       -      +
     12A  PHE*     4.0    57.4    -      -       +      +
     15A  GLY*     5.4     0.2    -      -       -      -
     70A  THR*     4.6    11.9    -      -       +      -
    100A  VAL*     3.7    26.9    -      -       +      +
    101A  ALA*     1.3    80.6    -      -       -      +
    103A  LYS*     1.3    65.4    +      -       -      +
    124A  PRO*     4.0    14.4    -      -       -      +
    147A  ILE*     3.0    22.5    +      -       +      +
    148A  PHE*     4.2     4.5    -      -       -      -
    149A  LEU*     4.2    20.9    -      -       +      +
     12B  PHE*     4.2    17.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PHE      3.7    10.8    -      -       -      +
     13A  GLU*     2.7    54.9    +      -       -      +
    102A  LEU*     1.3    84.4    -      -       -      +
    104A  GLY*     1.3    58.0    +      -       -      +
    124A  PRO*     4.2     6.9    -      -       +      +
    144A  GLU*     4.1    19.7    -      -       -      +
    145A  PRO*     3.3     7.6    -      -       +      +
    146A  PHE*     3.5     3.7    -      -       -      -
    147A  ILE*     2.8    40.3    +      -       +      +
----------------------------------------------------------
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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