Contacts of the strand formed by residues 421 - 426 (chain A) in PDB entry 3L73


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 ALA 421 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  LEU*     3.6    12.3    -      -       +      +
    156A  THR*     4.7     1.3    -      -       +      -
    157A  ALA*     3.6    37.9    -      -       +      +
    236A  PHE*     3.8    13.9    -      -       +      -
    237A  THR      3.9     4.9    -      -       -      +
    239A  SER      3.1     7.4    -      -       -      +
    255A  LEU*     3.4     5.6    -      -       -      +
    256A  ALA*     2.9    32.3    +      -       +      +
    420A  PRO*     1.3    73.9    -      -       -      +
    422A  LEU*     1.3    59.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 422 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  LEU*     4.7     1.3    -      -       -      -
    156A  THR*     4.3     2.1    -      -       -      +
    239A  SER      2.6     9.6    +      -       -      +
    240A  GLU*     3.0    32.1    -      -       +      +
    241A  ILE*     3.0    28.3    +      -       -      +
    242A  ARG*     4.0    10.5    -      -       +      +
    253A  VAL*     3.7    24.5    -      -       +      -
    254A  ALA      3.5    10.8    -      -       -      +
    255A  LEU*     3.6    20.4    -      -       +      -
    335A  MET*     4.2     4.9    -      -       +      -
    421A  ALA*     1.3    75.3    -      -       -      +
    423A  ALA*     1.3    69.9    +      -       -      +
    424A  ALA*     4.8     2.0    -      -       +      +
    431A  LEU*     4.2     8.3    -      -       +      -
    434A  TYR*     4.9     5.8    -      -       +      -
    437A  ILE*     3.4    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 423 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  THR*     3.7    30.1    -      -       +      +
    152A  TYR*     4.2     4.9    -      -       +      -
    153A  LEU*     3.7    24.2    -      -       +      +
    241A  ILE*     3.5    12.3    -      -       +      -
    252A  HIS      4.0     0.5    -      -       -      +
    253A  VAL*     3.4     4.3    -      -       -      +
    254A  ALA*     2.9    35.5    +      -       +      +
    422A  LEU*     1.3    75.6    -      -       -      +
    424A  ALA*     1.3    60.8    +      -       -      +
    425A  VAL*     5.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 424 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  TYR*     5.4     0.3    -      -       -      -
    241A  ILE      3.0    11.0    +      -       -      +
    242A  ARG*     3.4     6.8    -      -       +      -
    243A  ALA      2.7    32.1    +      -       -      +
    252A  HIS      3.5     5.4    -      -       -      +
    253A  VAL*     4.2     1.6    -      -       +      -
    422A  LEU*     5.0     3.1    -      -       +      -
    423A  ALA*     1.3    76.6    -      -       -      +
    425A  VAL*     1.3    61.0    +      -       -      +
    428A  ILE*     3.6    25.0    -      -       +      +
    431A  LEU*     3.9    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 425 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  MET*     4.3    24.5    -      -       +      -
    148A  VAL*     4.6    10.1    -      -       +      -
    149A  THR*     3.5    26.5    -      -       +      +
    152A  TYR*     3.7    30.3    -      -       +      -
    243A  ALA*     3.1    15.5    -      -       +      +
    245A  ASP*     6.1     1.1    -      -       +      -
    248A  LEU*     4.5     4.9    -      -       +      -
    250A  VAL      4.5     0.3    -      -       -      +
    251A  ALA*     3.4     4.0    -      -       -      +
    252A  HIS*     2.8    36.7    +      -       +      +
    423A  ALA      5.2     0.2    -      -       -      -
    424A  ALA*     1.3    83.6    -      -       -      +
    426A  GLY*     1.3    64.8    +      -       -      +
    428A  ILE*     3.8     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 426 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  ALA      3.1     7.3    +      -       -      -
    244A  ARG*     3.4     1.0    -      -       -      +
    245A  ASP*     3.1    28.6    +      -       -      +
    248A  LEU*     4.1    15.0    -      -       -      -
    250A  VAL      4.3     1.6    -      -       -      -
    425A  VAL*     1.3    79.5    -      -       -      +
    427A  PRO*     1.3    61.0    -      -       -      +
    428A  ILE*     2.8    25.9    +      -       -      +
----------------------------------------------------------
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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