Contacts of the strand formed by residues 118 - 122 (chain D) in PDB entry 3Q3G


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 118 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  GLN*     3.2    22.7    +      -       -      +
      9D  SER*     2.8    23.9    +      -       -      +
     10D  GLY      3.4    26.5    -      -       -      +
     12D  GLU*     4.7     0.7    -      -       +      -
     22D  LEU*     3.9    33.9    -      -       +      +
     23D  SER      4.9     0.3    +      -       -      -
     94D  ALA      3.7     0.3    -      -       -      +
     95D  VAL*     3.4     4.7    -      -       -      +
     96D  TYR*     2.9    38.5    +      -       -      +
    117D  GLY*     1.3    70.8    +      -       -      -
    119D  THR*     1.3    69.2    +      -       -      +
    120D  VAL      3.6     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 119 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11D  ALA*     3.4    18.4    -      -       +      +
     12D  GLU      2.7    32.3    +      -       -      +
     94D  ALA      3.8     6.3    -      -       -      +
     95D  VAL*     4.0    12.5    -      -       +      +
    117D  GLY      4.3     0.4    -      -       -      -
    118D  THR*     1.3    71.9    -      -       -      +
    120D  VAL*     1.3    61.0    +      -       -      +
    121D  THR*     4.0    17.3    -      -       -      +
    800D   NA      3.6    17.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 120 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12D  GLU*     3.6     8.5    -      -       +      -
     14D  VAL*     4.0    24.5    -      -       +      -
     20D  VAL*     4.3    13.9    -      -       +      -
     22D  LEU*     3.8    29.8    -      -       +      -
     85D  LEU*     4.9     0.2    -      -       +      -
     88D  LEU*     4.9     2.7    -      -       +      -
     92D  ASP      4.3     5.8    -      -       -      +
     93D  THR*     3.4     5.8    -      -       -      +
     94D  ALA      3.0    28.2    +      -       -      +
     96D  TYR*     3.7    32.5    -      -       +      -
    118D  THR*     4.2     1.6    -      -       +      +
    119D  THR*     1.3    79.8    -      -       -      +
    121D  THR*     1.3    63.3    +      -       -      +
    122D  VAL*     4.2    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 121 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12D  GLU      2.9    12.5    +      -       -      -
     13D  LEU*     3.4    19.8    -      -       +      +
     14D  VAL*     3.0    27.3    +      -       -      +
     93D  THR*     3.9    13.9    -      -       +      +
    119D  THR*     4.0    14.6    -      -       -      +
    120D  VAL*     1.3    75.3    +      -       -      +
    122D  VAL*     1.3    67.7    +      -       -      +
    123D  SER*     4.0     1.1    -      -       -      -
    157D  PHE*     4.8     8.5    -      -       +      -
    186D  TYR*     3.7    23.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 122 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14D  VAL*     3.3    20.2    -      -       +      +
     15D  LYS      4.2     0.4    -      -       -      +
     16D  PRO*     3.7    32.1    -      -       +      -
     88D  LEU*     3.9    23.8    -      -       +      -
     89D  THR      3.4    36.8    -      -       -      +
     90D  SER*     4.2     9.3    -      -       -      +
     92D  ASP*     4.3     0.2    -      -       +      -
     93D  THR*     3.0    24.3    +      -       -      +
    120D  VAL*     4.2     7.4    -      -       +      -
    121D  THR*     1.3    75.5    -      -       -      +
    123D  SER*     1.3    65.4    +      -       -      +
    181D  LEU*     5.7     4.0    -      -       -      +
----------------------------------------------------------
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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