Contacts of the strand formed by residues 97 - 104 (chain I) 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 VAL 97 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -5I  SER*     4.9     2.2    +      -       -      -
     45I  ILE*     3.6    20.4    -      -       +      -
     46I  THR      3.1     9.4    -      -       -      +
     47I  GLY*     4.3     0.7    -      -       -      -
     48I  LEU      4.4     2.0    -      -       -      +
     51I  ASP*     3.6    29.6    -      -       +      -
     52I  VAL      4.2     1.6    -      -       -      +
     55I  LEU*     3.5    26.9    -      -       +      -
     87I  LEU*     4.2     7.6    -      -       +      -
     95I  TYR*     3.1    13.8    +      -       +      +
     96I  PHE*     1.3    80.7    -      -       -      +
     98I  GLY*     1.3    59.8    +      -       -      +
     99I  PRO*     3.8    14.7    -      -       +      +
    114I  ASP*     5.0     0.2    -      -       -      -
    115I  LEU*     3.5    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 98 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44I  GLY      4.0     0.5    -      -       -      +
     45I  ILE*     3.8     1.5    -      -       -      -
     46I  THR*     2.7    30.2    +      -       -      +
     97I  VAL*     1.3    73.8    -      -       -      +
     99I  PRO*     1.3    65.4    -      -       -      +
    100I  VAL*     3.9     1.2    +      -       -      +
    113I  PHE      4.1     8.3    -      -       -      -
    114I  ASP*     5.7     0.2    -      -       -      -
    127I  SER*     3.0    28.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 99 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43I  LEU*     3.9    17.5    -      -       +      -
     44I  GLY      3.3     6.3    -      -       -      +
     45I  ILE*     4.4     7.9    -      -       +      -
     55I  LEU*     5.1     2.9    -      -       +      -
     59I  PHE*     6.0     1.3    -      -       +      -
     83I  VAL*     4.3     6.3    -      -       +      -
     87I  LEU*     4.1    19.7    -      -       +      -
     97I  VAL*     3.8    24.0    -      -       +      +
     98I  GLY*     1.3    88.2    -      -       -      +
    100I  VAL*     1.3    64.6    -      -       -      +
    112I  GLY*     3.5     0.7    -      -       -      -
    113I  PHE*     3.3    54.6    +      -       +      +
    114I  ASP      4.7     0.2    -      -       -      +
    127I  SER*     5.3     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 100 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3I  VAL*     3.8    25.6    -      -       +      +
      5I  ALA*     3.6    32.1    -      -       +      +
     14I  ILE*     3.9     6.8    -      -       +      +
     42I  PHE      3.9     0.3    -      -       -      +
     43I  LEU*     3.3     4.5    -      -       -      +
     44I  GLY      2.7    37.5    +      -       -      -
     98I  GLY      4.4     1.3    -      -       -      +
     99I  PRO*     1.3    79.7    -      -       -      +
    101I  VAL*     1.3    66.0    +      -       -      +
    111I  ALA      3.4    11.4    -      -       -      +
    125I  ILE*     3.8    23.6    -      -       +      +
    126I  VAL      4.8     0.4    -      -       -      -
    127I  SER*     3.8    24.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 101 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41I  VAL*     4.4     7.0    -      -       +      -
     42I  PHE      3.4     6.3    -      -       -      +
     43I  LEU*     3.7    23.8    -      -       +      -
     76I  PRO*     4.1     9.0    -      -       +      +
     79I  PHE*     3.7    23.8    -      -       +      -
     80I  THR*     3.6    21.1    -      -       -      +
     83I  VAL*     4.5     0.9    -      -       +      -
    100I  VAL*     1.3    74.7    -      -       -      +
    102I  ALA*     1.3    65.3    +      -       -      +
    109I  PHE*     4.0    11.9    -      -       +      -
    110I  ILE*     3.0     8.5    -      -       -      +
    111I  ALA*     2.9    35.4    +      -       +      +
    113I  PHE*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 102 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5I  ALA*     4.3     3.6    -      -       +      -
     12I  VAL*     4.2    13.7    -      -       +      -
     13I  ALA      4.7     0.4    -      -       -      +
     14I  ILE*     4.1    32.7    -      -       +      +
     41I  VAL*     3.9     1.9    -      -       -      +
     42I  PHE*     2.8    38.4    +      -       +      +
     76I  PRO*     5.2     0.9    -      -       -      -
    100I  VAL      4.2     0.4    +      -       -      -
    101I  VAL*     1.3    79.2    -      -       -      +
    103I  GLY*     1.3    58.2    +      -       -      +
    109I  PHE      3.4     4.9    -      -       -      -
    110I  ILE*     4.1    14.4    -      -       +      -
    178I  ILE*     4.6     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 103 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12I  VAL*     3.8    11.8    -      -       -      +
     40I  HIS      4.1    11.9    -      -       -      -
     42I  PHE*     5.4     0.2    -      -       -      -
     76I  PRO*     3.9    14.2    -      -       -      +
    102I  ALA*     1.3    76.4    -      -       -      +
    104I  ILE*     1.3    65.2    +      -       -      -
    108I  PRO*     3.8     1.2    -      -       -      +
    109I  PHE*     2.9    35.3    +      -       -      +
    178I  ILE*     5.0     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 104 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10I  ASP      3.7    21.1    -      -       -      +
     11I  CYS*     3.9     7.9    -      -       -      -
     12I  VAL*     4.5     3.6    -      -       +      -
     40I  HIS*     3.2    23.8    +      -       -      -
     76I  PRO*     4.0     3.1    -      -       -      +
    103I  GLY*     1.3    76.1    -      -       -      +
    105I  ASN*     1.3    72.0    +      -       -      +
    106I  GLY*     3.3    35.2    -      -       -      +
    107I  LYS      3.7     6.7    -      -       -      +
    108I  PRO*     4.3     3.4    -      -       +      -
    178I  ILE*     3.7    26.2    -      -       +      +
    179I  LYS      3.7     4.9    -      -       -      +
    181I  LYS*     3.6    39.9    -      -       +      +
----------------------------------------------------------
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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