Contacts of the strand formed by residues 15 - 22 (chain B) in PDB entry 3LZN


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 MET 15 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LYS      3.7     0.3    -      -       -      +
     11B  GLU*     3.3     4.2    -      -       -      -
     12B  LEU      2.9    31.8    +      -       -      +
     13B  ASN*     3.7    11.7    -      -       +      +
     14B  GLY*     1.3    83.9    -      -       -      +
     16B  GLU*     1.3    59.6    +      -       -      +
     17B  ILE*     4.0     6.8    +      -       +      +
     47B  ILE*     3.7    27.6    -      -       +      -
     48B  HIS      3.3     8.5    -      -       -      +
     50B  LEU*     3.5     8.0    -      -       -      +
     53B  ASN*     4.5     0.4    -      -       -      +
     63B  MET*     3.8    35.0    -      -       +      -
     66B  LEU*     4.3     7.6    -      -       -      -
    121B  ILE*     4.9     2.5    -      -       +      -
    143B  PHE*     3.4    35.7    -      -       +      -
    146B  PHE*     3.8    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  PRO*     4.2    24.0    -      -       +      +
     10B  LYS      3.4     8.3    -      -       -      +
     11B  GLU*     4.9     8.4    -      -       +      +
     15B  MET*     1.3    71.4    -      -       -      +
     17B  ILE*     1.3    62.9    +      -       -      +
     18B  ALA*     4.8     6.8    -      -       +      +
     46B  ASP      3.3     3.0    -      -       -      +
     47B  ILE*     3.2     6.8    -      -       -      +
     48B  HIS*     2.8    41.8    +      -       +      +
     49B  ALA      5.8     0.2    -      -       -      +
     50B  LEU*     3.5    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  PRO*     3.5     1.8    -      -       -      +
     10B  LYS*     2.8    33.4    +      -       +      +
     12B  LEU*     4.0    27.4    -      -       +      +
     15B  MET*     4.2     6.3    -      -       +      +
     16B  GLU*     1.3    77.6    -      -       -      +
     18B  ALA*     1.3    61.1    +      -       -      +
     46B  ASP      3.5     2.0    -      -       -      -
     47B  ILE*     4.1    25.8    -      -       +      -
    119B  PHE*     4.6     6.1    -      -       +      -
    121B  ILE*     4.1    19.3    -      -       +      -
    146B  PHE*     3.8    34.5    -      -       +      -
    148B  VAL*     4.3    10.5    -      -       +      -
    150B  TYR*     3.0    26.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  PRO*     3.8    22.9    -      -       +      -
     16B  GLU*     4.1     8.3    -      -       +      +
     17B  ILE*     1.3    75.2    -      -       -      +
     19B  ALA*     1.3    64.0    +      -       -      +
     20B  VAL*     5.3     3.8    -      -       +      -
     45B  ALA*     3.3     6.6    -      -       -      +
     46B  ASP*     2.8    49.3    +      -       +      +
    119B  PHE*     4.4     0.5    -      -       -      -
    150B  TYR*     4.1     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  PRO*     3.9     1.0    -      -       -      +
      6B  ILE*     2.9    42.8    +      -       +      +
      8B  ASP      6.1     0.2    -      -       -      -
     18B  ALA*     1.3    74.9    -      -       -      +
     20B  VAL*     1.3    68.1    +      -       -      +
     44B  GLU      3.4     5.6    -      -       -      +
    117B  LEU*     4.0    11.7    -      -       +      -
    119B  PHE*     3.8    22.4    -      -       +      -
    150B  TYR*     3.9    18.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  GLU*     4.0    31.4    -      -       +      +
      4B  VAL      3.2    15.5    -      -       -      +
      5B  PRO*     4.0    11.0    -      -       +      -
      6B  ILE*     3.6     6.5    -      -       -      -
     18B  ALA*     5.3     4.7    -      -       +      -
     19B  ALA*     1.3    81.0    -      -       -      +
     21B  TYR*     1.3    62.3    +      -       -      +
     22B  LEU*     4.2     2.5    -      -       +      -
     43B  LEU*     3.7     4.7    -      -       -      +
     44B  GLU*     2.9    59.6    +      -       +      +
     46B  ASP*     4.0    12.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  GLY      3.9     0.7    -      -       -      +
      3B  GLU*     3.6     2.8    -      -       -      -
      4B  VAL*     2.8    70.3    +      -       +      +
      6B  ILE*     3.8    21.3    -      -       +      -
     20B  VAL*     1.3    74.9    -      -       -      +
     22B  LEU*     1.3    63.3    +      -       -      +
     41B  ILE*     3.6    33.2    -      -       +      -
     42B  HIS      3.1    10.3    -      -       -      +
     43B  LEU*     4.5     1.3    -      -       +      -
    152B  PHE*     3.7    26.0    -      +       -      -
    153B  LYS      3.9     3.5    +      -       -      -
    154B  TYR*     3.8    12.9    -      +       -      -
    155B  THR*     3.6    31.0    +      -       -      -
    156B  GLY      3.8    16.9    +      -       -      -
    158B  PRO*     3.8    15.5    -      -       +      -
    159B  LYS*     5.3     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  HIS*     5.1     5.6    -      -       +      -
    137A  THR*     6.0     3.8    -      -       +      -
      2B  GLY      3.5    10.3    -      -       -      +
      3B  GLU*     3.7    25.8    -      -       +      +
     20B  VAL*     4.2     2.2    -      -       +      -
     21B  TYR*     1.3    77.2    -      -       -      +
     23B  GLN*     1.3    76.1    +      -       -      +
     25B  ILE*     4.3    20.6    -      -       +      -
     41B  ILE*     3.3     9.7    -      -       -      +
     42B  HIS*     2.8    61.7    +      -       +      +
     44B  GLU*     3.5    34.1    -      -       +      +
    158B  PRO*     3.7     9.2    -      -       -      +
----------------------------------------------------------
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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