Contacts of the strand formed by residues 116 - 122 (chain M) 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 GLN 116 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6M  LYS*     3.9    25.6    +      -       +      +
      7M  TYR      2.9    14.0    +      -       -      +
      8M  ASP      2.9    29.5    +      -       -      -
      9M  ASN*     4.4     1.1    -      -       -      +
     10M  GLY*     3.3    30.6    -      -       -      +
     11M  VAL*     3.9    11.4    -      -       +      -
    109M  GLY      3.8     4.5    -      -       -      -
    110M  VAL*     4.6     2.5    -      -       -      +
    111M  GLN*     5.2     1.2    -      -       -      +
    114M  GLY      4.9     4.9    -      -       -      +
    115M  ASP*     1.3    80.4    -      -       -      +
    117M  PHE*     1.3    59.6    +      -       -      +
    118M  LEU      4.2     0.2    -      -       -      -
    153M  GLU*     5.8     0.2    -      -       -      +
    156M  ILE*     3.6    15.0    -      -       -      +
    193M  LYS*     6.1     0.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 117 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11M  VAL*     4.0     3.8    -      -       -      +
     80M  PRO*     3.8    24.2    -      -       +      -
     81M  SER*     3.7    27.6    -      -       -      -
     84M  PHE*     3.6    34.3    -      +       +      -
    107M  VAL*     3.7    20.0    -      -       +      -
    108M  ALA*     3.4     5.0    -      -       -      -
    109M  GLY      2.6    43.1    +      -       -      +
    111M  GLN*     4.1    16.6    -      -       +      +
    115M  ASP      3.6     0.2    +      -       -      -
    116M  GLN*     1.3    74.9    -      -       -      +
    118M  LEU*     1.3    63.0    +      -       -      +
    119M  ARG*     3.7    33.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 118 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4M  SER*     3.6    29.2    -      -       -      +
      5M  MET*     4.1    12.3    -      -       -      +
      6M  LYS*     3.7    19.9    -      -       +      +
     11M  VAL*     4.7     9.6    -      -       +      -
    106M  ILE*     3.9     8.1    -      -       +      -
    107M  VAL      3.4     1.1    -      -       -      -
    108M  ALA*     3.6    28.9    -      -       +      -
    116M  GLN      4.2     0.8    +      -       -      -
    117M  PHE*     1.3    76.4    -      -       -      +
    119M  ARG*     1.3    59.8    +      -       -      +
    129M  SER*     2.5    32.6    +      -       -      -
    130M  SER      3.3    21.5    +      -       -      +
    131M  PRO      4.0    14.1    -      -       -      +
    133M  LEU*     3.7    16.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 119 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31L  GLU*     2.7    30.5    +      -       -      -
     53L  ASP*     4.6     5.5    +      -       -      -
     84M  PHE*     3.4    44.4    -      -       +      -
    105M  ILE      3.9     0.2    -      -       -      +
    106M  ILE*     3.3     3.6    -      -       -      +
    107M  VAL      2.8    37.9    +      -       -      -
    117M  PHE*     3.7    21.8    -      -       +      -
    118M  LEU*     1.3    76.1    -      -       -      +
    120M  TYR*     1.3    68.3    +      -       -      +
    127M  THR*     2.9    25.8    +      -       -      -
    128M  TYR*     3.3    13.9    -      -       -      +
    129M  SER*     3.2    27.0    -      -       -      +
    133M  LEU*     3.6     4.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 120 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84M  PHE*     3.6     3.6    -      -       -      -
    104M  ALA*     3.8    10.9    -      -       +      +
    105M  ILE      3.2    13.5    -      -       -      -
    106M  ILE*     4.0     6.7    -      -       +      +
    119M  ARG*     1.3    73.2    -      -       -      +
    121M  VAL*     1.3    61.3    +      -       -      +
    122M  ASN*     2.9    47.5    +      -       +      +
    126M  VAL      3.9     4.0    -      -       -      -
    127M  THR*     3.0    29.1    -      -       -      -
    128M  TYR*     2.9    63.1    +      +       +      +
    133M  LEU*     3.8    13.5    -      -       +      -
    134M  ALA      4.5     8.1    -      -       -      -
    135M  THR*     3.7    30.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 121 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84M  PHE*     3.9    18.2    -      -       +      -
     87M  LEU*     4.7     4.5    -      -       +      -
     88M  ALA*     3.8    23.6    -      -       -      +
     91M  MET*     3.8    26.5    -      -       +      -
    104M  ALA*     3.6     0.2    -      -       -      -
    105M  ILE*     2.6    60.5    +      -       +      +
    120M  TYR*     1.3    78.4    -      -       -      +
    122M  ASN*     1.3    70.0    +      -       -      +
    125M  GLY*     4.1     5.2    -      -       -      -
    126M  VAL      3.2     7.6    -      -       -      +
    127M  THR*     3.8    18.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 122 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91M  MET*     3.6    15.3    -      -       -      +
    103M  ASN      3.4    13.7    -      -       -      +
    104M  ALA*     4.0     3.8    -      -       +      -
    120M  TYR*     2.9    36.7    +      -       +      +
    121M  VAL*     1.3    78.6    -      -       -      +
    123M  LEU*     1.3    66.2    +      -       +      +
    124M  LEU*     2.7    28.0    +      -       -      +
    125M  GLY*     2.7    31.0    +      -       -      -
    126M  VAL*     3.4    18.4    +      -       -      +
    128M  TYR*     5.2     0.6    +      -       -      -
----------------------------------------------------------
 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