Contacts of the strand formed by residues 33 - 38 (chain L) in PDB entry 4OQT


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 33 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4L  MET*     3.7    29.6    -      -       +      -
     23L  CYS*     4.3     2.5    -      -       -      -
     29L  VAL*     4.3     7.2    -      -       +      -
     31L  SER      3.1     4.8    +      -       -      -
     32L  TYR*     1.3    76.1    -      -       -      +
     34L  ALA*     1.3    62.2    +      -       -      +
     35L  TRP*     3.5    34.0    -      -       +      +
     48L  ILE      4.4     0.3    -      -       -      +
     49L  TYR      3.6     0.2    -      -       -      -
     50L  ASP*     2.8     8.5    +      -       -      +
     51L  ALA*     2.6    35.2    +      -       -      +
     71L  PHE*     3.6    54.7    -      -       +      -
     88L  CYS*     4.2     7.4    -      -       +      -
     89L  GLN      3.5    11.7    -      -       -      +
     90L  GLN*     4.3     2.0    -      -       -      -
     91L  ARG*     5.5     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 34 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104H  ALA      4.1    17.7    -      -       -      +
     33L  LEU*     1.3    75.4    -      -       -      +
     35L  TRP*     1.3    62.4    +      -       -      +
     36L  TYR*     3.7    23.8    -      -       +      +
     46L  LEU*     4.4     2.7    -      -       +      -
     48L  ILE      3.3    13.7    -      -       -      +
     49L  TYR*     4.4     0.7    -      -       -      -
     87L  TYR      4.0     0.2    -      -       -      +
     88L  CYS*     3.3     5.0    -      -       -      +
     89L  GLN*     2.7    48.9    +      -       -      +
     91L  ARG*     4.6     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 35 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6L  GLN*     3.7    17.9    -      -       -      -
     21L  LEU*     4.2    10.1    -      -       +      -
     22L  SER      4.0    11.9    -      -       -      -
     23L  CYS*     3.5    32.1    -      -       +      -
     33L  LEU*     3.5    23.0    -      -       +      +
     34L  ALA*     1.3    72.5    -      -       -      +
     36L  TYR*     1.3    64.1    +      -       -      +
     46L  LEU*     3.9     1.0    -      -       -      +
     47L  LEU*     2.8    26.9    +      -       +      +
     48L  ILE*     3.0    41.3    +      -       +      +
     51L  ALA*     4.7     6.5    +      -       -      +
     64L  GLY*     4.8     4.3    -      -       -      -
     65L  SER      5.5     1.0    +      -       -      +
     71L  PHE*     4.1    11.7    -      -       +      +
     72L  THR      4.3     1.8    -      -       -      -
     73L  LEU*     3.5    58.1    -      -       +      +
     86L  TYR*     4.7     4.7    -      -       +      -
     87L  TYR      3.4    17.5    -      -       -      -
     88L  CYS*     3.8     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 36 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105H  PHE*     3.6     4.9    -      -       -      +
    106H  ASP*     3.1    39.1    +      -       -      +
    108H  TRP*     4.4     9.6    -      +       -      -
     34L  ALA*     3.7    18.6    -      -       +      +
     35L  TRP*     1.3    78.3    -      -       -      +
     37L  GLN*     1.3    59.3    +      -       -      +
     44L  PRO*     4.2    26.2    -      -       +      -
     45L  ARG      3.4     6.7    -      -       -      +
     46L  LEU*     3.8    28.5    -      -       +      -
     47L  LEU*     3.3     6.5    -      -       -      -
     86L  TYR*     3.3     8.3    -      -       -      +
     87L  TYR*     2.7    48.6    +      -       +      +
     89L  GLN*     2.5    44.3    +      -       +      -
     99L  PHE*     4.3    10.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 37 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36L  TYR*     1.3    72.4    -      -       -      +
     38L  GLN*     1.3    59.3    +      -       -      +
     39L  LYS*     3.6    35.1    +      -       -      +
     43L  ALA      4.4     0.3    -      -       -      +
     44L  PRO*     3.9     0.6    -      -       -      +
     45L  ARG*     2.8    65.7    +      -       -      +
     47L  LEU*     2.8    21.1    -      -       +      -
     62L  PHE*     4.3    13.7    -      -       -      -
     82L  ASP*     4.5     4.8    +      -       -      +
     84L  ALA*     3.5    19.9    -      -       +      +
     85L  VAL      3.7     3.1    -      -       -      -
     86L  TYR*     3.5    25.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 38 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39H  GLN*     3.7    20.3    +      -       -      +
     45H  LEU*     4.8     2.2    -      -       -      +
     95H  TYR*     4.4     6.9    +      -       -      -
     36L  TYR      4.2     0.4    -      -       -      -
     37L  GLN*     1.3    73.0    -      -       -      +
     39L  LYS*     1.3    65.7    +      -       -      +
     40L  PRO*     4.6     0.9    -      -       -      +
     42L  GLN      3.1    29.3    +      -       -      +
     43L  ALA      4.9     0.4    -      -       -      -
     44L  PRO*     3.4    28.8    -      -       +      +
     84L  ALA*     3.5     5.0    -      -       -      +
     85L  VAL*     2.9    41.9    +      -       +      +
     87L  TYR*     3.0    38.6    +      -       +      -
----------------------------------------------------------
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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