Contacts of the strand formed by residues 145 - 149 (chain A) in PDB entry 1Q84


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 145 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  VAL*     4.2     9.2    -      -       +      -
    102A  TRP      3.4     9.4    -      -       -      +
    103A  THR*     4.2    11.0    -      -       +      -
    104A  PRO*     4.7     3.8    -      -       +      -
    108A  PRO*     4.8     1.6    -      -       +      -
    112A  THR*     4.2    14.1    -      -       +      +
    113A  PRO      3.4    11.0    +      -       -      +
    114A  VAL*     3.3     8.6    -      -       +      +
    115A  LEU*     2.9    27.5    +      -       -      +
    143A  GLY      3.9     0.2    +      -       -      -
    144A  ALA*     1.3    75.8    -      -       -      +
    146A  LEU*     1.3    62.2    +      -       -      +
    147A  VAL*     4.5     2.9    -      -       +      -
    187A  ILE*     3.9    33.0    -      -       +      -
    190A  PHE*     4.3     9.9    -      -       +      +
    191A  GLY      4.4     0.7    -      -       -      -
    192A  GLY*     3.9    24.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  ASN      3.8     0.2    -      -       -      +
    101A  VAL*     3.3     5.4    -      -       -      +
    102A  TRP*     2.9    63.1    +      -       +      +
    115A  LEU*     3.3    16.2    -      -       +      +
    117A  TRP*     4.6     7.2    -      -       +      -
    135A  GLY*     4.2    12.1    -      -       -      +
    138A  LEU*     3.4    41.3    -      -       +      -
    139A  ALA*     5.6     0.2    -      -       +      -
    144A  ALA*     3.8     4.4    +      -       +      +
    145A  VAL*     1.3    74.8    -      -       -      +
    147A  VAL*     1.3    75.0    +      -       -      +
    148A  SER*     4.6     2.0    -      -       -      +
    200A  PHE*     4.1     9.6    -      -       +      -
    455A  PHE*     4.0    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  LEU*     4.4    16.8    -      -       +      -
    100A  ASN      3.2    10.3    -      -       -      +
    101A  VAL*     4.2     5.6    -      -       +      -
    114A  VAL*     4.0    13.7    -      -       +      -
    115A  LEU      2.8     9.2    +      -       -      +
    116A  ILE*     3.2    15.8    -      -       +      +
    117A  TRP      2.8    25.6    +      -       -      -
    145A  VAL*     4.5     1.8    -      -       +      -
    146A  LEU*     1.3    82.8    -      -       -      +
    148A  SER*     1.3    69.2    +      -       -      +
    149A  MET*     5.7     1.1    -      -       +      -
    179A  ALA*     5.7     1.3    -      -       +      +
    183A  VAL*     3.8    24.2    -      -       +      -
    187A  ILE*     3.8    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  LEU*     3.2     4.2    -      -       -      +
    100A  ASN*     2.7    58.0    +      -       -      +
    102A  TRP*     3.8    11.9    -      -       -      -
    116A  ILE*     5.1     0.9    -      -       -      -
    117A  TRP*     3.7    28.0    -      -       -      -
    128A  ALA*     3.3    17.2    +      -       -      +
    133A  TYR*     5.4     2.4    +      -       -      -
    146A  LEU*     4.6     2.8    -      -       -      +
    147A  VAL*     1.3    76.8    -      -       -      +
    149A  MET*     1.3    61.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  PHE*     4.1     2.7    -      -       +      -
     98A  TYR      3.7     4.3    -      -       -      -
     99A  LEU*     3.9     8.7    -      -       +      -
    116A  ILE*     3.6    31.0    -      -       +      -
    117A  TRP      3.8    10.7    +      -       -      +
    118A  ILE*     4.0    20.2    -      -       +      -
    119A  TYR*     3.4    19.9    -      -       -      -
    128A  ALA*     3.9     3.2    -      -       -      +
    147A  VAL*     5.7     1.1    -      -       +      -
    148A  SER*     1.3    76.4    -      -       -      +
    150A  ASN*     1.3    75.6    +      -       -      +
    151A  TYR*     3.9     3.5    +      -       -      +
    176A  GLN*     4.2    25.6    -      -       +      +
    179A  ALA*     3.8    28.5    -      -       +      -
    180A  LEU*     4.0    16.8    -      -       +      -
----------------------------------------------------------
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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