Contacts of the strand formed by residues 829 - 834 (chain A) in PDB entry 3LZI


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 829 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  ASN*     2.9    38.0    +      -       -      +
    285A  GLN      3.2    21.9    +      -       -      +
    286A  PRO*     3.6    10.1    -      -       +      +
    287A  SER*     5.4     0.7    -      -       -      -
    288A  TYR*     4.5    14.6    -      -       +      -
    735A  SER*     3.3    12.7    +      -       -      -
    782A  VAL*     3.9    12.6    -      -       +      -
    783A  SER      3.3     7.9    -      -       -      +
    784A  SER*     3.7    23.8    -      -       -      +
    827A  GLY      5.4     0.7    -      -       -      +
    828A  GLU*     1.3    83.8    +      -       -      +
    830A  VAL*     1.3    63.6    +      -       -      +
    849A  PRO*     3.9     3.6    -      -       -      +
    850A  SER*     3.1    32.6    +      -       -      +
    112P    T      4.3     7.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 830 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    782A  VAL*     3.2     6.4    -      -       -      +
    783A  SER*     2.9    46.6    +      -       -      +
    784A  SER      5.0     0.2    -      -       -      -
    785A  ALA*     4.5     5.4    -      -       +      -
    804A  HIS*     4.8     3.8    -      -       +      -
    808A  ILE*     4.1    24.9    -      -       +      -
    824A  VAL*     3.8    29.8    -      -       +      -
    828A  GLU      4.8     0.4    -      -       -      +
    829A  LYS*     1.3    79.6    -      -       -      +
    831A  TYR*     1.3    62.3    +      -       -      +
    832A  VAL*     4.2    15.0    -      -       +      -
    847A  ALA*     4.2     5.2    -      -       +      -
    848A  TRP      3.1    23.3    -      -       -      +
    849A  PRO*     4.2     1.8    -      -       +      -
    850A  SER*     3.8     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 831 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  PRO*     5.2     5.4    -      -       +      +
    287A  SER*     5.2     1.6    -      -       -      -
    292A  TYR*     5.1     9.9    -      -       -      -
    777A  ILE*     3.7    34.7    -      -       +      +
    780A  ALA*     3.9    15.3    -      -       +      -
    781A  SER      3.3     1.1    -      -       -      -
    782A  VAL*     3.7    26.9    -      -       +      -
    830A  VAL*     1.3    73.0    -      -       -      +
    832A  VAL*     1.3    58.7    +      -       -      +
    847A  ALA*     3.0    28.6    -      -       -      +
    848A  TRP*     2.7    58.1    +      +       +      -
    850A  SER*     3.5    16.3    -      -       -      +
    851A  GLY*     3.1    33.9    +      -       -      -
    852A  THR      3.7    10.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 832 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    781A  SER*     2.6    49.5    +      -       -      +
    782A  VAL      4.9     0.2    -      -       -      -
    783A  SER*     4.6     7.6    -      -       -      +
    803A  PHE*     3.7    35.4    -      -       +      -
    804A  HIS*     3.9    27.8    -      -       +      -
    830A  VAL*     4.1    10.3    -      -       +      +
    831A  TYR*     1.3    80.8    -      -       -      +
    833A  LEU*     1.3    71.4    +      -       -      +
    834A  PRO*     4.4     2.4    -      -       +      +
    845A  CYS*     4.9     3.1    -      -       +      -
    846A  ILE      3.6     7.9    -      -       -      +
    847A  ALA*     4.0    10.1    -      -       +      -
    871A  LEU*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 833 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    776A  TYR*     4.2    13.2    -      -       +      +
    779A  ILE      4.4     0.2    -      -       -      -
    780A  ALA*     3.7    26.7    -      -       +      +
    803A  PHE*     5.1     0.2    -      -       -      -
    832A  VAL*     1.3    77.0    -      -       -      +
    834A  PRO*     1.3    71.7    -      -       +      +
    835A  LEU*     4.1     2.4    -      -       +      +
    845A  CYS*     3.2     5.7    -      -       -      +
    846A  ILE*     2.9    42.2    +      -       +      +
    848A  TRP*     3.8    26.2    -      -       +      -
    862A  VAL*     3.9    20.0    -      -       +      -
    866A  MET*     4.0    23.1    -      -       +      -
    871A  LEU*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 834 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    781A  SER*     6.0     0.2    -      -       -      +
    803A  PHE*     4.6    14.3    -      -       +      -
    832A  VAL      4.4     1.1    -      -       -      +
    833A  LEU*     1.3    89.8    -      -       +      +
    835A  LEU*     1.3    65.6    +      -       -      +
    844A  LYS      3.5    10.1    -      -       -      +
    845A  CYS*     4.1     3.8    -      -       +      -
    866A  MET*     3.6     2.9    -      -       -      -
    867A  ASP*     3.0    45.3    +      -       +      +
    870A  VAL*     4.1    24.2    -      -       +      -
    871A  LEU*     3.8    27.8    -      -       +      +
    874A  LYS*     4.6     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