Contacts of the strand formed by residues 422 - 428 (chain B) in PDB entry 1L0N


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 LYS 422 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239B  TYR*     3.5     0.2    -      -       -      -
    241B  GLY*     3.6     2.8    -      -       -      -
    242B  GLY      3.4    16.5    +      -       -      +
    257B  LEU*     3.5    22.9    -      -       +      -
    258B  VAL      3.4    15.7    -      -       -      +
    259B  ALA*     4.6     0.7    -      -       +      -
    341B  TYR*     3.1    26.0    +      -       +      +
    417B  PHE*     2.9    31.1    +      -       +      -
    418B  VAL      2.5    33.3    +      -       -      -
    419B  SER*     3.6     1.0    -      -       -      +
    420B  GLY      3.1    20.5    +      -       -      +
    421B  ARG*     1.3    78.1    -      -       -      +
    423B  SER*     1.3    65.3    +      -       -      +
    436B  ILE*     4.5    25.5    -      -       +      +
    439B  LEU*     6.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 423 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  LEU*     3.7     9.8    -      -       -      +
    166B  ALA      4.8     0.2    -      -       -      -
    167B  ALA*     3.3    27.1    -      -       -      +
    239B  TYR*     2.6    30.3    +      -       -      -
    241B  GLY*     3.3     7.6    -      -       -      -
    242B  GLY      3.3     9.2    -      -       -      -
    257B  LEU*     3.8     0.5    -      -       -      +
    258B  VAL*     2.8    39.7    +      -       -      -
    422B  LYS*     1.3    74.6    +      -       -      +
    424B  MET*     1.3    62.5    +      -       -      +
    436B  ILE*     4.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 424 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  LEU*     3.9     4.4    -      -       -      +
    166B  ALA*     4.2     4.0    -      -       -      +
    242B  GLY      3.1     8.7    +      -       -      -
    243B  GLU*     3.1    23.8    -      -       +      +
    244B  ILE      2.8    31.2    +      -       -      +
    245B  ARG*     5.3     5.2    -      -       +      +
    255B  ALA*     5.0     7.0    -      -       +      -
    256B  ALA      3.3    12.6    -      -       -      +
    257B  LEU*     4.4    11.9    -      -       +      -
    337B  ILE*     4.6    20.0    -      -       +      -
    423B  SER*     1.3    77.7    -      -       -      +
    425B  ALA*     1.3    59.0    +      -       -      +
    426B  ALA*     5.2     4.3    -      -       +      +
    433B  THR*     4.9     5.8    -      -       +      -
    434B  PRO*     3.7    25.6    -      -       +      +
    436B  ILE*     3.5    30.5    -      -       +      +
    439B  LEU*     4.7    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 425 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159B  VAL*     3.4    36.0    -      -       +      +
    162B  ASN*     3.9    13.0    -      -       +      -
    163B  LEU*     3.6    20.1    -      -       +      +
    244B  ILE*     3.2     6.7    -      -       +      -
    255B  ALA*     3.4     0.9    -      -       -      +
    256B  ALA      2.8    30.1    +      -       -      +
    424B  MET*     1.3    75.3    -      -       -      +
    426B  ALA*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 426 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159B  VAL*     4.6     3.3    -      -       -      +
    162B  ASN*     5.7     0.7    -      -       -      +
    244B  ILE      3.2     7.9    +      -       -      +
    245B  ARG*     3.6     6.8    -      -       +      +
    246B  GLU*     2.9    25.6    +      -       -      +
    254B  HIS      3.1    12.6    -      -       -      +
    255B  ALA*     4.0    11.9    -      -       +      -
    424B  MET*     5.2     6.5    -      -       +      -
    425B  ALA*     1.3    76.9    -      -       -      +
    427B  SER*     1.3    60.1    +      -       -      +
    430B  LEU*     3.8    11.1    -      -       +      +
    433B  THR*     4.2    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 427 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  PRO*     4.9     6.6    +      -       -      +
    158B  HIS*     5.4     7.6    -      -       -      +
    159B  VAL*     4.2    12.3    -      -       -      +
    246B  GLU*     3.2    22.4    -      -       -      -
    248B  ASN*     4.4    10.7    +      -       -      -
    250B  ASP*     5.1     1.9    +      -       -      -
    252B  LEU      4.0     1.3    +      -       -      +
    253B  VAL*     3.4     3.1    -      -       -      +
    254B  HIS*     2.8    44.4    +      -       -      +
    426B  ALA*     1.3    75.7    -      -       -      +
    428B  GLY*     1.3    59.4    +      -       -      +
    430B  LEU*     3.8     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 428 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  GLU      3.2     5.5    +      -       -      -
    247B  GLN*     3.3     6.1    -      -       -      -
    248B  ASN*     2.7    38.6    +      -       -      +
    249B  GLY      3.7     2.7    -      -       -      -
    250B  ASP*     4.7     4.5    -      -       -      -
    252B  LEU      4.0    13.5    -      -       -      -
    253B  VAL*     4.2     1.8    -      -       -      -
    427B  SER*     1.3    75.9    -      -       -      +
    429B  ASN*     1.3    60.8    +      -       -      -
    430B  LEU*     3.1     9.9    +      -       -      +
----------------------------------------------------------
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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