Contacts of the strand formed by residues 344 - 349 (chain B) in PDB entry 3LPK


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 ILE 344 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267B  VAL*     4.8     2.9    -      -       +      -
    268B  GLU      3.5     8.5    -      -       -      +
    269B  ILE*     3.9    18.6    -      -       +      -
    295B  LEU*     5.1    10.3    -      -       +      -
    305B  ALA*     6.3     0.4    -      -       +      -
    309B  ILE*     3.9    15.0    -      -       +      -
    342B  PRO      4.4     2.0    -      -       -      +
    343B  VAL*     1.3    78.4    -      -       -      +
    345B  SER*     1.3    62.4    +      -       -      +
    346B  LEU*     4.3    22.2    -      -       +      -
    359B  ILE      3.7     1.2    -      -       -      +
    360B  THR*     3.3     1.5    -      -       -      -
    361B  ILE*     2.7    51.9    +      -       +      +
    366B  TYR*     3.7    24.2    -      -       +      -
    385B  ILE*     3.6    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 345 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  ARG      3.9     0.3    -      -       -      +
    267B  VAL*     3.4     6.8    -      -       -      +
    268B  GLU*     3.0    53.4    +      -       -      +
    271B  GLY      5.7     1.0    +      -       -      -
    343B  VAL*     4.3     4.7    +      -       -      +
    344B  ILE*     1.3    72.6    -      -       -      +
    346B  LEU*     1.3    63.9    +      -       -      +
    347B  TYR*     4.0    14.9    -      -       -      -
    358B  ARG*     4.5     8.5    +      -       -      -
    359B  ILE      3.3     5.6    -      -       -      -
    360B  THR*     2.9    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 346 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264B  ILE*     4.7    20.9    -      -       +      -
    266B  ARG      3.8     2.0    -      -       -      -
    267B  VAL*     4.0    24.7    -      -       +      -
    295B  LEU*     4.8    17.7    -      -       +      -
    297B  LEU*     5.7     6.7    -      -       +      -
    344B  ILE*     4.3     9.6    -      -       +      -
    345B  SER*     1.3    79.7    -      -       -      +
    347B  TYR*     1.3    63.4    +      -       -      +
    348B  LEU*     3.7     5.7    +      -       +      +
    358B  ARG*     3.4     1.1    -      -       -      -
    359B  ILE*     2.9    40.9    +      -       +      +
    361B  ILE*     4.1    25.1    -      -       +      -
    394B  MET*     4.2    32.1    -      -       +      -
    398B  ILE*     5.0     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 347 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    264B  ILE*     3.4     8.1    -      -       -      +
    265B  VAL*     2.9    34.2    +      -       +      -
    266B  ARG*     2.8    52.3    +      -       +      +
    268B  GLU*     2.5    41.6    +      -       +      -
    345B  SER*     4.1     7.6    -      -       -      -
    346B  LEU*     1.3    75.2    -      -       -      +
    348B  LEU*     1.3    59.9    +      -       -      +
    356B  SER*     4.0    16.8    -      -       -      +
    357B  PHE      3.2     6.3    -      -       -      +
    358B  ARG*     2.9    45.0    +      -       +      -
    435B  PHE*     3.7    30.8    -      +       +      -
    437B  THR*     5.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 348 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  THR*     3.7    13.5    -      -       +      +
    262B  VAL*     4.3    15.5    -      -       +      -
    263B  ILE      3.6    13.5    -      -       -      +
    264B  ILE*     3.9    22.7    -      -       +      -
    265B  VAL*     4.4     1.6    -      -       -      -
    346B  LEU*     4.3     9.9    -      -       +      +
    347B  TYR*     1.3    74.6    -      -       -      +
    349B  MET*     1.3    64.9    +      -       -      +
    356B  SER*     3.2     7.2    -      -       -      -
    357B  PHE*     2.8    55.1    +      -       +      -
    359B  ILE*     4.5    11.9    -      -       +      -
    394B  MET*     4.8     7.6    -      -       +      -
    415B  PHE*     3.6    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 349 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252B  THR*     2.6    37.0    +      -       -      +
    253B  PRO*     3.2    17.5    -      -       +      +
    263B  ILE*     3.2    44.1    +      -       +      +
    265B  VAL*     4.2     3.8    -      -       +      +
    348B  LEU*     1.3    72.4    -      -       -      +
    350B  GLY*     1.3    70.8    +      -       -      +
    357B  PHE*     3.8     0.9    -      -       -      -
    440B  MET*     3.4    64.2    -      -       +      +
    441B  GLU*     3.8    13.9    -      -       +      +
----------------------------------------------------------
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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