Contacts of the strand formed by residues 56 - 61 (chain B) in PDB entry 3T0E


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 56 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  HIS*     3.5     1.9    -      -       -      -
     43B  GLU*     2.6    70.0    +      -       +      +
     45B  HIS*     4.0     9.4    -      -       +      +
     54B  ARG*     3.3    36.9    +      -       -      +
     55B  PHE*     1.3    85.5    -      -       -      +
     57B  ASP*     1.3    57.0    +      -       -      +
     58B  ARG*     3.9    13.9    -      -       +      +
     68B  ARG*     4.2    22.7    -      -       +      +
     69B  PHE      3.4    18.8    -      -       -      +
     70B  ASP*     3.9    17.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  LYS      4.0     1.8    -      -       -      -
     42B  HIS*     3.2    19.2    +      -       -      +
     55B  PHE*     3.5    16.6    -      -       +      -
     56B  LEU*     1.3    72.7    -      -       -      +
     58B  ARG*     1.3    64.1    +      -       -      +
     59B  TYR*     2.9    39.3    +      -       -      -
     68B  ARG*     3.4     3.6    -      -       -      -
     69B  PHE*     2.8    48.6    +      -       +      +
     76B  TYR*     4.1     2.2    -      -       +      +
    100B  LYS*     2.1    38.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  GLU      4.9     1.2    +      -       -      -
    143A  HIS*     3.2    30.8    +      -       -      -
     40B  VAL*     4.2     2.9    -      -       -      +
     41B  LYS*     2.9    27.9    +      -       -      +
     43B  GLU*     2.2    55.4    +      -       -      -
     56B  LEU*     4.4    20.9    -      -       +      +
     57B  ASP*     1.3    77.1    -      -       -      +
     59B  TYR*     1.3    81.5    +      -       -      +
     60B  PHE*     3.4    18.1    -      -       +      -
     65B  GLU*     3.2    39.8    +      -       -      +
     67B  VAL      4.1     4.0    -      -       -      -
     68B  ARG*     4.3     7.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ASN*     4.3     9.0    -      -       -      -
      7B  GLY      4.5     1.6    +      -       -      -
      8B  GLN*     3.3    44.1    -      -       +      +
      9B  ARG      4.5     1.0    +      -       -      -
     38B  GLU*     4.9     0.7    -      -       -      -
     39B  GLN      3.5     6.1    -      -       -      -
     40B  VAL*     3.6    17.7    -      -       +      -
     57B  ASP*     2.9    30.8    +      -       -      -
     58B  ARG*     1.3    88.7    -      -       -      +
     60B  PHE*     1.3    74.9    +      -       -      +
     65B  GLU*     3.5     2.9    -      -       -      +
     66B  TYR*     3.3    36.3    +      -       +      +
     67B  VAL*     3.3    35.1    +      -       +      +
     76B  TYR*     4.0    15.5    +      +       -      -
     90B  TRP*     3.9    27.6    -      +       -      -
    100B  LYS*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 60 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  HIS*     2.9    44.4    -      +       -      -
     38B  GLU*     2.6    28.8    -      -       -      +
     39B  GLN*     2.6    45.6    +      -       +      +
     41B  LYS*     3.7    30.5    -      -       +      -
     58B  ARG*     3.4    30.7    -      -       +      -
     59B  TYR*     1.3    78.3    -      -       -      +
     61B  TYR*     1.3    60.7    +      -       -      +
     62B  HIS      4.3     3.6    -      -       -      +
     63B  GLN      3.6    11.0    -      -       -      +
     64B  GLU      3.4     5.8    -      -       -      +
     65B  GLU*     3.5    33.4    -      -       +      -
     66B  TYR*     3.1    14.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 61 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  LEU*     4.5     7.9    -      -       +      -
     73A  MET*     3.2    49.4    -      -       +      -
     74A  THR*     3.7     7.9    -      -       -      -
     77A  SER*     3.1    22.5    +      -       -      -
     80A  THR*     3.0    20.9    +      -       +      -
     36B  PHE*     3.1    21.7    -      +       -      -
     37B  LEU      3.6     7.4    -      -       -      -
     38B  GLU*     5.4     0.9    -      -       -      -
     60B  PHE*     1.3    74.7    -      -       -      +
     62B  HIS*     1.3   108.0    +      +       -      +
     63B  GLN      2.9     3.5    +      -       -      -
     64B  GLU*     2.9    34.3    +      -       +      +
     66B  TYR*     4.5     8.7    -      -       +      -
----------------------------------------------------------
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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