Contacts of the strand formed by residues 47 - 53 (chain H) 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 LEU 47 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42F  TYR*     5.4     0.9    -      -       +      -
     50F  PRO*     3.7    32.8    -      -       +      -
     93F  TYR*     3.7    37.8    -      -       +      -
    104F  PHE*     3.5    49.8    +      -       +      +
    105F  GLY      4.9     2.4    +      -       -      +
     39H  VAL*     3.8    19.7    -      -       +      -
     40H  LYS      3.8     1.3    -      -       -      -
     41H  GLN*     3.5    35.2    -      -       +      +
     45H  GLN      5.0     0.6    -      -       -      +
     46H  GLY*     1.3    71.7    -      -       -      -
     48H  GLU*     1.3    57.6    +      -       -      +
     97H  TYR*     4.5     5.2    -      -       +      -
    114H  TRP*     4.3     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 48 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104F  PHE*     4.9     0.2    -      -       -      -
     39H  VAL*     3.7     3.0    -      -       -      +
     40H  LYS*     2.7    63.4    +      -       +      +
     42H  ARG*     4.9    11.9    +      -       -      +
     45H  GLN*     5.3     6.4    -      -       -      +
     46H  GLY      4.6     3.0    -      -       -      +
     47H  LEU*     1.3    74.9    -      -       -      +
     49H  TRP*     1.3    64.6    +      -       -      +
     50H  ILE*     4.1     0.3    -      -       -      +
     63H  ASP*     6.2     0.2    -      -       -      +
     65H  LYS*     4.8    14.5    -      -       +      +
     66H  PHE*     3.4    31.8    -      -       +      -
    802H   NA      4.2     9.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100F  TYR*     3.5    26.0    -      +       +      -
    101F  PRO*     3.6    27.8    -      -       +      -
    102F  LEU*     3.3    39.4    +      -       +      +
    104F  PHE*     4.2    14.2    -      -       +      -
     37H  GLN*     2.8    25.4    +      -       +      -
     38H  TRP      3.9    12.3    -      -       -      -
     39H  VAL*     4.3     7.6    -      -       +      +
     47H  LEU      4.2     0.6    -      -       -      -
     48H  GLU*     1.3    72.9    -      -       -      +
     50H  ILE*     1.3    59.4    +      -       -      +
     51H  GLY*     3.4    31.9    +      -       -      -
     52H  ARG*     3.8    14.6    -      -       +      -
     61H  LYS*     4.1    10.5    -      -       +      -
     62H  TYR      3.9     5.8    -      -       -      -
     63H  ASP*     3.7    34.4    -      -       +      +
     66H  PHE*     3.5    12.1    -      -       -      -
    111H  MET*     3.9    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 50 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  TRP*     2.8    22.9    +      -       +      +
     40H  LYS*     3.9     9.6    -      -       +      +
     48H  GLU      4.1     4.9    -      -       -      +
     49H  TRP*     1.3    74.2    -      -       -      +
     51H  GLY*     1.3    57.3    +      -       -      +
     62H  TYR*     3.5     5.7    -      -       +      +
     63H  ASP*     2.9    26.8    +      -       -      +
     66H  PHE*     3.7    36.6    -      -       +      +
     70H  ALA*     3.4    31.9    -      -       +      -
     72H  ILE*     4.3     6.5    -      -       +      -
     83H  LEU*     3.9    21.1    -      -       +      -
     85H  LEU*     4.8     1.8    -      -       +      -
     96H  TYR*     3.6    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 51 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  TRP      3.0    24.4    +      -       -      -
     49H  TRP*     3.4    21.0    +      -       -      -
     50H  ILE*     1.3    82.0    -      -       -      +
     52H  ARG*     1.3    62.2    +      -       -      +
     61H  LYS      3.1    14.4    -      -       -      -
     62H  TYR*     3.9     0.7    -      -       -      -
     72H  ILE*     3.4    14.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 52 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100F  TYR*     3.3    20.8    +      -       +      -
     35H  TYR*     3.9    33.0    -      -       -      -
     36H  MET      3.2    12.6    -      -       -      +
     37H  GLN*     3.3    26.9    -      -       -      +
     49H  TRP*     3.8    11.7    -      -       +      -
     51H  GLY*     1.3    73.9    -      -       -      +
     53H  ILE*     1.3    60.5    +      -       -      +
     54H  ASP*     3.7     9.9    -      -       -      +
     59H  LYS      3.1    26.1    +      -       -      -
     60H  THR*     3.3     6.9    -      -       -      +
     61H  LYS*     2.8    49.1    +      -       +      +
     72H  ILE*     3.7     7.0    -      -       -      +
    178I  GLU*     3.0    20.2    +      -       -      -
    179I  GLU*     2.6    33.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 53 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35H  TYR*     3.4     4.5    -      -       -      -
     36H  MET*     2.9    49.5    +      -       +      +
     52H  ARG*     1.3    79.1    -      -       -      +
     54H  ASP*     1.3    71.3    +      -       -      +
     55H  PRO*     3.2    13.0    -      -       +      +
     58H  ASP*     4.1    17.5    -      -       +      +
     59H  LYS      3.4     5.6    -      -       -      +
     60H  THR*     3.7    20.2    -      -       +      -
     72H  ILE*     3.6    22.0    -      -       +      +
     73H  THR*     3.6    17.9    -      -       -      +
     74H  ALA*     3.6    31.6    -      -       +      +
     81H  ALA*     4.7     2.5    -      -       +      -
----------------------------------------------------------
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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