Contacts of the strand formed by residues 97 - 103 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  LEU*     3.8     1.6    -      -       -      -
     88B  HIS*     3.3    15.5    +      -       -      -
     90B  HIS*     2.4    44.3    +      -       +      -
     96B  ALA*     1.3    73.7    -      -       -      +
     98B  VAL*     1.3    68.0    +      -       -      +
     99B  TYR*     3.2    30.0    +      -       +      -
    129B  TYR*     3.9     3.5    -      -       -      -
    130B  VAL*     2.9    39.6    +      -       +      +
    136B  HIS*     3.6    10.8    -      -       -      -
    150B  ALA*     4.4     0.3    -      -       -      +
    151B  ILE      3.5    10.5    -      -       -      +
    152B  TYR*     3.5    33.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  LEU*     3.9    26.7    -      -       +      +
     68A  PHE*     4.3    20.6    -      -       +      -
    149A  LEU*     5.5     0.2    -      -       +      -
    151A  ILE*     4.5    23.3    -      -       +      -
     97B  GLU*     1.3    80.4    -      -       -      +
     99B  TYR*     1.3    67.9    +      -       -      +
    100B  VAL*     4.6     4.7    -      -       +      -
    127B  VAL*     3.4    28.0    -      -       +      -
    128B  VAL      3.3     6.5    -      -       -      +
    129B  TYR*     4.7     8.1    -      -       +      -
    150B  ALA*     3.4     1.7    -      -       -      -
    151B  ILE*     2.9    36.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  HIS*     3.7     9.9    +      -       -      -
     97B  GLU*     3.2    25.2    +      -       +      -
     98B  VAL*     1.3    80.5    -      -       -      +
    100B  VAL*     1.3    61.7    +      -       -      +
    108B  MET*     3.7    22.2    -      -       +      -
    122B  MET*     3.9    17.3    -      -       +      -
    126B  THR      4.4     0.9    -      -       -      -
    127B  VAL*     3.0    13.0    -      -       -      +
    128B  VAL*     2.9    31.4    +      -       +      +
    130B  VAL*     3.9     6.3    -      -       +      -
    136B  HIS*     2.5    43.9    +      +       -      -
    138B  THR*     4.3    12.0    +      -       +      -
    148B  PHE*     3.5    40.8    -      +       -      -
    149B  LEU      3.3     4.0    -      -       -      -
    150B  ALA*     3.9    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PHE*     3.9    19.7    -      -       +      -
    100A  VAL*     6.2     2.7    -      -       +      -
    102A  LEU*     6.2     1.3    -      -       +      -
    149A  LEU*     3.5    32.3    -      -       +      -
     98B  VAL*     4.6     4.0    -      -       +      -
     99B  TYR*     1.3    78.5    -      -       -      +
    101B  ALA*     1.3    63.0    +      -       -      +
    102B  LEU*     3.6    23.2    +      -       +      +
    122B  MET*     4.9     0.7    -      -       -      -
    125B  GLY      5.9     0.4    -      -       -      -
    126B  THR      3.6     4.9    -      -       -      -
    127B  VAL*     3.9    15.5    -      -       +      -
    148B  PHE*     3.5     2.2    -      -       -      +
    149B  LEU*     2.9    50.3    +      -       +      +
    151B  ILE*     5.2     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PHE*     4.2     2.4    -      -       -      -
    100B  VAL*     1.3    75.7    -      -       -      +
    102B  LEU*     1.3    63.2    +      -       -      +
    103B  LYS      3.9     0.4    -      -       -      +
    122B  MET*     4.2    15.5    -      -       +      -
    123B  GLU      3.5    25.8    -      -       -      +
    124B  PRO*     3.4     2.7    -      -       +      +
    125B  GLY      3.2    21.3    +      -       -      -
    126B  THR*     3.0    18.1    +      -       -      +
    146B  PHE*     4.2    16.8    -      -       +      -
    148B  PHE*     4.1     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PHE*     4.0    20.3    -      -       +      -
     10B  VAL*     4.6     2.9    -      -       +      -
     11B  ASP      4.8     0.7    -      -       -      +
     12B  PHE*     3.7    58.9    -      -       +      +
     70B  THR*     4.4    15.0    -      -       +      -
    100B  VAL*     3.7    33.0    -      -       +      +
    101B  ALA*     1.3    75.5    -      -       -      +
    103B  LYS*     1.3    62.0    +      -       -      +
    124B  PRO*     3.9    14.7    -      -       -      +
    147B  ILE*     3.0    21.5    +      -       +      +
    148B  PHE*     4.2     6.5    -      -       -      -
    149B  LEU*     4.4    17.3    -      -       +      -
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Residues in contact with LYS 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  PHE      4.1     6.7    -      -       -      +
     13B  GLU*     3.0    56.6    +      -       -      +
    101B  ALA      3.9     0.4    -      -       -      -
    102B  LEU*     1.3    78.6    +      -       -      +
    104B  GLY*     1.3    67.3    +      -       -      +
    124B  PRO*     4.2     9.5    -      -       +      +
    145B  PRO*     4.2     5.8    -      -       +      +
    146B  PHE*     3.5     6.9    -      -       -      -
    147B  ILE*     3.2    44.4    +      -       +      +
----------------------------------------------------------
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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