Contacts of the strand formed by residues 76 - 79 (chain B) in PDB entry 3U1J


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 76 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  THR      3.6     9.2    -      -       -      +
     49B  MET*     4.4     2.2    -      -       +      -
     50B  TRP*     3.7     3.3    -      -       -      +
     69B  TRP*     3.7    18.0    -      -       +      -
     71B  SER      3.0    29.8    +      -       -      +
     74B  LYS*     3.4    18.6    -      -       +      +
     75B  ASP*     1.3    83.3    -      -       -      +
     77B  ILE*     1.3    64.7    +      -       -      +
     83B  TRP*     3.7    22.4    -      -       +      -
    149B  LEU*     4.1    11.2    -      -       +      -
    166B  ALA*     4.0    19.1    -      -       +      +
    167B  GLN*     3.6    37.9    -      -       -      +
    168B  THR*     3.8    17.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 77 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  PHE      3.9     0.5    -      -       -      +
     48B  THR*     3.0    58.7    +      -       +      +
     49B  MET      3.8    12.1    -      -       -      +
     50B  TRP*     3.9    16.2    -      -       +      -
     53B  THR*     3.9     3.8    -      -       -      +
     55B  GLY*     3.4    36.8    -      -       -      +
     67B  PRO*     3.6    22.2    -      -       +      -
     69B  TRP*     3.4    16.2    -      -       -      +
     70B  ALA*     3.8     6.5    -      -       +      -
     76B  LEU*     1.3    78.7    -      -       -      +
     78B  SER*     1.3    62.6    +      -       -      +
     79B  TYR*     3.7    11.9    -      -       +      +
     83B  TRP*     3.5     7.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  VAL*     3.7    14.8    -      -       -      -
     46B  PHE      3.2     5.4    -      -       -      -
     47B  HIS*     4.3     1.8    -      -       -      -
     67B  PRO*     3.4     4.7    -      -       -      +
     68B  ASN      2.8    28.4    +      -       -      -
     69B  TRP*     2.9    28.4    +      -       -      +
     77B  ILE*     1.3    76.5    -      -       -      +
     79B  TYR*     1.3    58.3    +      -       -      +
     81B  GLY      2.8    23.9    +      -       -      -
     82B  GLY      3.7     6.3    -      -       -      -
     83B  TRP*     3.7    17.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ALA*     3.8     5.5    -      -       -      +
     45B  VAL*     3.5     3.3    -      -       -      -
     46B  PHE*     2.8    47.7    +      +       +      +
     48B  THR*     4.3     8.7    -      -       +      -
     53B  THR*     2.8    25.8    +      -       +      +
     55B  GLY      3.8     0.2    -      -       -      -
     56B  ALA      2.7    30.3    +      -       -      -
     58B  LEU*     3.5    37.5    -      -       +      -
     65B  LEU*     3.5    25.4    -      -       +      -
     66B  GLU      3.6     4.9    -      -       -      +
     67B  PRO*     3.5    30.5    -      -       +      -
     77B  ILE*     3.7    28.2    -      -       +      +
     78B  SER*     1.3    77.1    -      -       -      +
     80B  GLY*     1.3    56.9    +      -       -      +
     81B  GLY      3.3     7.0    +      -       -      -
----------------------------------------------------------
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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