Contacts of the strand formed by residues 41 - 47 (chain L) in PDB entry 3SDI


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 ILE 41 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36L  ASP*     3.8     3.4    +      -       -      +
     37L  CYS*     2.8    29.6    +      -       +      +
     38L  GLY      3.4    12.0    +      -       -      +
     39L  ASP*     3.2     8.9    -      -       +      +
     40L  ASN*     1.3    84.8    -      -       -      +
     42L  VAL*     1.3    74.8    +      -       -      +
     43L  MET*     5.3     0.2    -      -       +      -
     59L  PHE*     4.3    24.5    -      -       +      -
     63L  VAL*     5.3     1.1    -      -       +      -
     74L  LEU*     3.6    28.3    -      -       +      +
     75L  SER      4.6     2.2    -      -       -      +
     76L  ILE*     4.0    27.6    -      -       +      +
     79L  ALA*     3.8    22.4    -      -       +      -
    101L  ILE*     4.4     9.4    -      -       +      -
    102L  ALA      3.6     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 42 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14L  LEU*     3.6    31.4    -      -       +      +
     34L  VAL*     4.7     0.2    -      -       +      -
     35L  PHE      3.2     7.9    -      -       -      +
     36L  ASP*     4.3     3.4    -      -       -      -
     41L  ILE*     1.3    78.6    -      -       -      +
     43L  MET*     1.3    62.1    +      -       -      +
    101L  ILE*     3.2     8.7    -      -       -      +
    102L  ALA*     3.0    48.0    +      -       +      +
    176L  LEU*     3.7    30.5    -      -       +      -
    178L  VAL*     3.7    24.5    -      -       +      -
    184L  VAL*     4.1    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 43 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14L  LEU*     3.8     4.2    -      -       -      +
     33L  LYS      3.8     0.9    -      -       -      +
     34L  VAL*     3.4     1.0    -      -       -      -
     35L  PHE*     2.8    40.0    +      -       -      -
     37L  CYS*     3.5    17.3    -      -       -      -
     41L  ILE*     5.3     0.2    -      -       +      -
     42L  VAL*     1.3    77.0    -      -       -      +
     44L  SER*     1.3    67.3    +      -       -      +
     45L  ALA*     5.1     1.1    -      -       +      -
     55L  LEU*     4.1    28.0    -      -       +      -
     56L  VAL*     4.1    21.1    -      -       +      -
     59L  PHE*     3.7    32.3    -      -       +      -
     83L  ILE*     3.7    26.5    -      -       +      -
     99L  THR*     4.0    16.2    -      -       -      +
    100L  ILE      3.5     5.4    -      -       -      +
    101L  ILE*     3.5    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 44 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3L  ILE*     3.2    38.0    -      -       -      +
     14L  LEU*     3.7    13.9    -      -       -      +
     33L  LYS*     2.5    26.3    +      -       -      +
     34L  VAL*     4.1     4.5    -      -       -      -
     43L  MET*     1.3    76.3    -      -       -      +
     45L  ALA*     1.3    61.4    +      -       -      +
     46L  ASN      4.1     0.7    -      -       -      -
     56L  VAL*     5.1     1.6    -      -       -      -
     98L  HIS      4.0     0.3    -      -       -      +
     99L  THR*     3.3     4.7    +      -       -      -
    100L  ILE      2.9    34.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 45 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33L  LYS*     4.2     7.4    +      -       -      +
     43L  MET*     5.1     0.9    -      -       +      -
     44L  SER*     1.3    76.8    +      -       -      +
     46L  ASN*     1.3    61.7    +      -       -      +
     47L  GLY      4.1     0.7    +      -       -      -
     48L  PHE      5.2     0.2    -      -       -      +
     49L  ALA*     5.5     2.3    -      -       -      -
     52L  GLY*     3.6    34.7    -      -       -      +
     55L  LEU*     4.3     9.0    -      -       +      -
     56L  VAL*     4.5     9.3    -      -       +      +
     97L  VAL*     3.6    22.7    -      -       +      +
     98L  HIS      3.6     5.4    -      -       -      -
     99L  THR*     3.9    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 46 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -1L  GLY      3.1    18.6    +      -       -      +
      1L  GLY      3.0    12.3    -      -       -      +
      2L  THR*     4.3     0.9    -      -       -      -
      3L  ILE*     3.9    28.9    -      -       +      -
     33L  LYS*     2.9    37.1    -      -       -      +
     44L  SER*     4.1     0.4    -      -       -      -
     45L  ALA*     1.3    73.1    -      -       -      +
     47L  GLY*     1.3    61.1    +      -       -      +
     97L  VAL*     3.3     3.1    -      -       -      -
     98L  HIS*     2.9    37.7    +      -       -      +
    128L  GLY*     3.0    32.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 47 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -4L  GLY      4.7     1.1    -      -       -      -
     -3L  ASP*     4.6     8.5    -      -       -      -
     -2L  ASN*     3.1    28.7    +      -       -      +
     -1L  GLY      4.1     4.2    +      -       -      +
     45L  ALA      4.1     1.2    +      -       -      -
     46L  ASN*     1.3    84.8    -      -       -      +
     48L  PHE*     1.3    62.2    +      -       -      -
     49L  ALA*     3.3     3.8    +      -       -      +
     96L  TYR      3.8     5.8    -      -       -      -
     97L  VAL*     4.3     0.2    -      -       -      +
     98L  HIS*     6.3     0.2    -      -       -      -
    128L  GLY*     6.1     1.1    -      -       -      -
----------------------------------------------------------
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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