Contacts of the strand formed by residues 75 - 79 (chain D) 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 SER 75 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  ILE      3.7     0.7    -      -       -      +
     20D  GLU*     3.4     7.2    +      -       -      -
     21D  CYS*     3.0    31.2    +      -       -      +
     31D  MET*     3.4    38.4    -      -       -      +
     33D  TRP*     3.6    25.1    +      -       -      -
     67D  ILE*     4.5     1.4    -      -       -      +
     69D  HIS*     4.0    17.9    -      -       -      +
     73D  THR      3.1     1.8    +      -       -      -
     74D  LEU*     1.3    74.5    -      -       -      +
     76D  THR*     1.3    62.8    +      -       -      +
     77D  LEU      3.8     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 76 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  LYS*     4.7     8.5    -      -       +      -
     19D  ILE      3.8     6.1    -      -       -      +
     20D  GLU*     4.2    15.2    -      -       +      +
     33D  TRP*     4.5     1.3    -      -       -      -
     66D  LEU      3.0     7.7    -      -       -      +
     67D  ILE*     3.2     2.8    -      -       -      -
     68D  ASN*     2.7    54.6    +      -       +      +
     69D  HIS      4.3     1.2    -      -       -      +
     74D  LEU*     4.3     2.8    -      -       -      +
     75D  SER*     1.3    75.8    +      -       -      +
     77D  LEU*     1.3    60.3    +      -       -      +
     78D  THR*     3.0    28.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 77 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  VAL      3.7     1.2    -      -       -      +
     19D  ILE*     3.0    38.9    +      -       +      +
     33D  TRP*     3.2    54.6    -      -       +      +
     45D  MET*     3.8    21.5    -      -       +      -
     65D  PHE*     3.8    29.4    -      -       +      -
     66D  LEU      3.5     8.1    -      -       -      +
     67D  ILE*     4.1    13.9    -      -       +      -
     76D  THR*     1.3    69.9    -      -       -      +
     78D  THR*     1.3    64.0    +      -       -      +
     79D  VAL*     4.2     9.5    +      -       +      +
     90D  TYR*     4.2    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 78 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16D  SER*     4.7     6.7    -      -       -      -
     17D  VAL      3.2    15.3    -      -       -      +
     18D  LYS*     3.3    17.3    -      -       +      +
     64D  LYS      4.0     1.2    -      -       -      +
     65D  PHE*     3.8     0.7    -      -       -      -
     66D  LEU*     2.9    40.1    +      -       +      +
     76D  THR*     3.0    27.2    +      -       -      +
     77D  LEU*     1.3    73.3    -      -       -      +
     79D  VAL*     1.3    64.2    +      -       -      +
     80D  THR*     4.0    22.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 79 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  THR      3.2     4.2    -      -       -      +
     17D  VAL*     3.1    48.9    +      -       +      +
     19D  ILE*     5.5     5.6    -      -       +      -
     64D  LYS*     3.6     9.4    -      -       -      +
     65D  PHE*     3.2    39.9    -      -       +      -
     77D  LEU*     4.2    13.5    -      -       +      +
     78D  THR*     1.3    77.2    -      -       -      +
     80D  THR*     1.3    64.1    +      -       -      +
     82D  ALA*     5.1     4.5    +      -       +      -
     90D  TYR*     5.0    10.3    -      -       +      +
    111D  LEU*     5.4     4.9    -      -       +      -
----------------------------------------------------------
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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