Contacts of the strand formed by residues 115 - 119 (chain A) in PDB entry 3Q29


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 SER 115 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  ALA      3.7     1.4    +      -       -      -
    114A  LEU*     1.3    74.7    +      -       -      +
    116A  LEU*     1.3    64.1    +      -       -      +
    117A  ILE*     3.6     1.9    +      -       -      +
    227A  ILE*     3.6     5.5    -      -       -      +
    228A  ASN      3.1    31.1    +      -       -      +
    233A  TRP*     5.8     0.7    -      -       -      -
    245A  VAL*     3.4    27.9    -      -       -      +
    246A  THR      3.5     2.5    -      -       -      -
    248A  LEU*     3.7     6.5    -      -       -      -
    321A  THR*     3.5    25.6    +      -       -      -
    324A  ASN*     2.8    23.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  SER*     1.3    71.8    -      -       -      +
    117A  ILE*     1.3    63.3    +      -       -      +
    118A  TYR*     5.1     0.7    -      -       +      -
    126A  PRO*     4.3    11.7    -      -       +      -
    127A  PRO      4.4     7.0    -      -       -      +
    133A  ILE*     6.2     0.4    -      -       +      -
    148A  LEU*     4.7     4.3    -      -       +      -
    225A  MET*     3.9    37.7    -      -       +      -
    226A  THR      3.8    13.2    -      -       -      +
    227A  ILE*     4.4    12.6    -      -       +      -
    244A  GLY      3.8     0.2    -      -       -      +
    245A  VAL*     3.4     3.5    -      -       -      -
    246A  THR*     2.8    62.7    +      -       +      +
    247A  VAL      3.9     9.4    -      -       -      +
    248A  LEU*     3.6    12.3    -      -       +      +
    249A  PRO*     4.1    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  SER      4.0     8.1    -      -       -      +
    116A  LEU*     1.3    77.9    -      -       -      +
    118A  TYR*     1.3    63.6    +      -       -      +
    218A  PHE*     3.6    25.0    -      -       +      -
    225A  MET*     3.2     5.5    -      -       -      +
    226A  THR*     2.9    46.0    +      -       +      +
    228A  ASN*     3.9    31.6    -      -       +      +
    232A  ALA*     5.0     0.9    -      -       +      -
    233A  TRP*     4.0    26.7    -      -       +      +
    236A  ILE*     3.9    18.8    -      -       +      -
    243A  TYR*     3.9     9.4    -      -       +      -
    244A  GLY      3.4     9.4    -      -       -      +
    245A  VAL*     4.4    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  LEU*     5.1     1.3    -      -       +      -
    117A  ILE*     1.3    75.0    -      -       -      +
    119A  ASN*     1.3    62.3    +      -       -      +
    120A  LYS*     3.5    34.2    -      -       +      +
    123A  LEU*     3.3    29.4    -      -       +      -
    124A  PRO      3.9     6.7    +      -       -      -
    126A  PRO*     3.7    42.2    -      -       +      +
    218A  PHE*     3.5     6.3    -      -       -      -
    224A  ALA      3.3     8.7    -      -       -      +
    225A  MET*     4.0    12.6    -      -       +      -
    243A  TYR*     3.1     6.4    -      -       -      +
    244A  GLY*     2.9    56.8    +      -       -      -
    245A  VAL      4.8     0.2    -      -       -      -
    246A  THR*     4.0    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  TYR*     1.3    70.6    -      -       -      +
    120A  LYS*     1.3    60.0    +      -       -      +
    121A  ASP*     3.0    23.5    +      -       -      +
    122A  LEU*     3.3    34.5    +      -       +      +
    123A  LEU*     2.8    30.7    +      -       -      +
    218A  PHE*     3.5    14.6    +      -       +      -
    221A  GLY*     4.1    16.2    -      -       -      -
    223A  THR      4.4     1.4    +      -       -      +
    224A  ALA*     2.9    16.3    +      -       -      +
    241A  VAL*     3.8    20.7    -      -       -      +
    242A  ASN      3.7     6.9    +      -       -      +
----------------------------------------------------------
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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