Contacts of the strand formed by residues 40 - 47 (chain 1) 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 THR 40 (chain 1).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     351  PRO*     3.3     4.0    -      -       -      +
     361  VAL*     2.8    37.7    +      -       +      +
     381  ASP      3.9     0.6    -      -       -      -
     391  ASN*     1.3    93.1    +      -       -      +
     411  VAL*     1.3    71.2    +      -       -      +
     421  VAL*     4.2     6.5    -      -       +      -
     801  PRO*     3.3    20.8    -      -       +      +
     831  ILE*     3.7    23.8    -      -       +      +
    1071  VAL*     3.9    22.0    -      -       +      -
    1081  ALA      3.4    11.4    -      -       -      +
    1911  ILE*     4.9     0.2    -      -       -      -
    1971  LEU*     4.1     4.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 41 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     131  ILE*     3.8    26.8    -      -       +      +
     331  LEU*     3.9    15.0    -      -       +      -
     341  ILE      3.6    22.4    -      -       -      +
     351  PRO*     4.2     7.6    -      -       +      -
     401  THR*     1.3    79.4    -      -       -      +
     421  VAL*     1.3    66.9    +      -       -      +
     431  GLY      4.0     0.2    -      -       -      -
    1061  ILE      3.9     0.9    -      -       -      +
    1071  VAL*     3.7     1.0    -      -       -      -
    1081  ALA*     2.8    42.0    +      -       -      +
    1891  ALA*     4.1    13.9    -      -       +      -
    1911  ILE*     3.7    15.4    -      -       +      +
    1971  LEU*     3.7    22.0    -      -       +      -
    1991  PHE*     4.8     2.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 42 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     321  ARG      3.7     1.7    -      -       -      +
     331  LEU      3.7     0.2    -      -       -      -
     341  ILE*     2.7    47.6    +      -       +      +
     361  VAL*     4.2     2.9    -      -       +      -
     401  THR*     4.2     7.9    -      -       +      -
     411  VAL*     1.3    76.9    -      -       -      +
     431  GLY*     1.3    57.9    +      -       -      +
     441  ILE*     3.9    17.4    +      -       +      -
     581  LEU*     3.9    26.9    -      -       +      -
     831  ILE*     4.0    22.7    -      -       +      -
     871  LEU*     4.2     6.7    -      -       +      -
    1051  ILE*     3.8    26.2    -      -       +      -
    1061  ILE      3.4     3.6    -      -       -      +
    1071  VAL*     4.1     8.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 43 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      21  VAL*     3.8    11.7    -      -       -      +
     131  ILE*     3.8    10.9    -      -       -      +
     321  ARG      3.3     7.9    -      -       -      -
     331  LEU*     3.9    17.3    -      -       -      -
     421  VAL*     1.3    70.9    -      -       -      +
     441  ILE*     1.3    63.0    +      -       -      +
    1041  ALA      3.8     0.7    -      -       -      +
    1051  ILE*     3.5     4.7    -      -       -      -
    1061  ILE      2.9    38.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 44 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      21  VAL*     3.7     4.8    -      -       -      +
     321  ARG*     2.9    37.5    +      -       -      +
     341  ILE*     3.7    24.0    -      -       +      -
     421  VAL*     3.9    19.5    -      -       +      +
     431  GLY*     1.3    80.1    -      -       -      +
     451  SER*     1.3    64.4    +      -       -      +
     511  MET*     3.8    27.8    -      -       +      +
     541  ILE*     3.7    32.5    -      -       +      -
     581  LEU*     5.4     0.4    -      -       +      -
    1031  ASN*     3.4    34.5    -      -       +      +
    1041  ALA      3.7     3.1    -      -       -      +
    1051  ILE*     4.3     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 45 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -11  GLY*     3.7     4.5    -      -       -      -
      01  THR      3.0    27.8    -      -       -      -
      21  VAL*     3.9     2.3    -      -       -      +
     321  ARG*     3.7     4.3    -      -       -      +
     441  ILE*     1.3    74.1    -      -       -      +
     461  GLY*     1.3    62.4    +      -       -      +
     481  ILE*     6.1     0.7    -      -       -      -
     511  MET*     6.3     0.2    -      -       -      -
    1031  ASN*     2.9    19.0    +      -       -      +
    1041  ALA*     2.9    37.8    +      -       -      +
    1351  THR*     2.9    23.2    +      -       -      -
    1361  GLY*     5.3     0.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 46 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -21  THR*     3.3    13.4    -      -       -      -
     -11  GLY      2.9    32.4    +      -       -      -
     451  SER*     1.3    79.2    -      -       -      +
     471  ASP*     1.3    66.2    +      -       -      -
     481  ILE*     3.3     3.8    +      -       -      +
    1021  TRP*     3.4    11.2    -      -       -      -
    1031  ASN*     4.4     1.6    -      -       -      -
    1041  ALA      5.0     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 47 (chain 1). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -71  GLN*     4.8     1.6    +      -       -      -
     -61  GLN      4.2     2.4    -      -       -      +
     -51  PRO*     3.4    10.3    -      -       +      +
     -41  ILE*     3.2    28.4    +      -       -      +
     -31  VAL      3.5     8.3    -      -       -      -
     -21  THR*     4.1     4.3    -      -       -      +
     461  GLY*     1.3    68.3    -      -       -      -
     481  ILE*     1.3    58.0    +      -       -      +
     491  SER*     2.7    44.4    +      -       -      -
     501  ASP*     2.9    14.4    +      -       -      +
     511  MET*     3.0    14.0    +      -       -      +
    1021  TRP*     2.8    32.0    +      -       +      +
    1031  ASN*     2.9    22.0    +      -       -      -
     912  LYS*     4.4     6.5    +      -       -      -
    1162  GLY*     5.3     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page


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