Contacts of the strand formed by residues 148 - 152 (chain B) in PDB entry 3SPD


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 LEU 148 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B  LEU*     3.4     4.4    -      -       -      -
     74B  LEU*     2.8    56.4    +      -       +      +
    100B  LEU*     4.2    29.2    -      -       +      +
    101B  VAL*     5.6     0.4    -      -       -      +
    104B  VAL*     4.7     5.4    -      -       +      -
    135B  VAL*     3.6    24.2    -      -       +      -
    136B  GLY*     3.5    33.4    -      -       -      +
    137B  PHE*     3.7    31.0    -      -       +      -
    147B  HIS*     1.3    70.7    -      -       -      +
    149B  HIS*     1.3    62.9    +      -       -      +
    150B  ILE*     3.6     2.1    +      -       +      +
    177B  ILE*     4.0    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 149 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  ASP*     4.6     2.9    -      -       -      -
     71B  HIS*     2.9    31.1    +      +       -      +
     72B  LEU      3.5     4.3    -      -       -      -
     73B  LEU*     3.5     6.6    -      -       +      +
    134B  LYS      3.7     0.6    -      -       -      +
    135B  VAL*     3.2     6.1    -      -       -      +
    136B  GLY      2.8    41.4    +      -       -      +
    138B  HIS*     3.8    31.8    +      +       -      -
    147B  HIS*     3.8    33.8    +      +       -      -
    148B  LEU*     1.3    73.8    -      -       -      +
    150B  ILE*     1.3    60.8    +      -       -      +
    151B  MET*     4.1     6.3    -      -       -      -
    169B  PHE*     3.6    23.5    -      +       -      -
    174B  PHE*     3.8    15.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with ILE 150 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LEU*     3.8    17.7    -      -       +      -
     70B  MET*     4.0    11.3    -      -       +      +
     71B  HIS*     3.7     0.5    -      -       -      -
     72B  LEU*     2.8    45.7    +      -       +      +
     74B  LEU*     3.8    26.5    -      -       +      +
    104B  VAL*     3.8    24.9    -      -       +      -
    108B  LEU*     5.9     0.2    -      -       +      -
    112B  ILE*     4.2    23.3    -      -       +      -
    133B  ILE*     4.1    18.8    -      -       +      -
    134B  LYS      3.5     4.0    -      -       -      -
    135B  VAL*     4.2    19.3    -      -       +      -
    148B  LEU*     4.1     3.1    -      -       +      +
    149B  HIS*     1.3    77.4    -      -       -      +
    151B  MET*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 151 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  LYS*     4.0     6.3    -      -       +      -
     68B  SER*     3.9     7.9    -      -       -      +
     70B  MET*     3.2    20.9    -      -       -      +
     71B  HIS*     3.8    28.7    -      -       +      +
    133B  ILE*     3.3     2.3    -      -       -      -
    134B  LYS*     2.8    55.6    +      -       +      +
    149B  HIS*     4.3    11.0    -      -       -      -
    150B  ILE*     1.3    78.1    -      -       -      +
    152B  THR*     1.3    68.3    +      -       -      +
    155B  HIS*     3.7    19.7    -      -       +      -
    169B  PHE*     3.3    39.9    -      -       +      -
    174B  PHE*     4.4     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 152 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  SER*     2.8    22.2    +      -       -      -
     70B  MET*     3.1    36.7    +      -       +      -
    116B  ALA*     4.6     5.8    -      -       +      -
    120B  LEU*     3.8    27.7    -      -       +      +
    129B  LEU*     5.4     1.1    -      -       +      -
    132B  TYR*     3.1    19.1    -      -       +      +
    133B  ILE*     4.1    12.8    -      -       +      -
    134B  LYS*     4.2     1.7    -      -       -      -
    151B  MET*     1.3    82.1    -      -       -      +
    153B  LEU*     1.3    62.3    +      -       -      +
    154B  ASP*     2.6    23.5    +      -       -      -
----------------------------------------------------------
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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