Contacts of the strand formed by residues 351 - 361 (chain B) in PDB entry 1LPB


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 VAL 351 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349B  LYS*     3.4     7.8    +      -       -      +
    350B  LYS*     1.3    78.8    -      -       -      +
    352B  THR*     1.3    68.8    +      -       -      +
    375B  THR*     3.6     5.7    -      -       -      +
    376B  LEU*     2.7    54.2    +      -       +      -
    402B  TRP*     3.9    27.4    -      -       +      -
    404B  ASN*     6.0     0.2    -      -       -      +
    409B  ASN*     5.4     5.4    -      -       +      -
    413B  PRO*     4.3    20.4    -      -       +      -
    415B  VAL*     3.7    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 352 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351B  VAL*     1.3    90.0    +      -       -      +
    353B  GLY*     1.3    60.0    +      -       -      +
    374B  GLY*     3.5    17.5    -      -       -      +
    375B  THR*     4.5     9.2    +      -       -      +
    402B  TRP*     4.7     0.5    -      -       -      -
    404B  ASN*     2.8    40.6    +      -       -      +
    407B  VAL*     5.9     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 353 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352B  THR*     1.3    77.0    -      -       -      +
    354B  HIS*     1.3    65.2    +      -       -      -
    373B  LYS*     3.4     0.3    -      -       -      -
    374B  GLY      3.0    31.8    +      -       -      +
    376B  LEU*     3.3    23.6    -      -       -      +
    402B  TRP*     4.9     1.3    -      -       -      -
    403B  TYR      3.2    12.6    -      -       -      -
    404B  ASN*     3.9     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 354 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353B  GLY*     1.3    79.0    -      -       -      -
    355B  ILE*     1.3    62.1    +      -       -      +
    356B  LEU*     3.6     4.0    -      -       +      +
    370B  GLU*     2.8    26.9    +      -       -      +
    372B  PHE      3.4     5.4    -      -       -      -
    373B  LYS*     3.5    29.8    -      -       +      +
    402B  TRP*     3.1    24.8    -      -       -      +
    403B  TYR*     2.9    57.6    +      +       +      -
    404B  ASN*     4.5    10.1    +      -       -      -
    406B  ASN*     4.9     5.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 355 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344B  VAL*     4.4    21.8    -      -       +      -
    346B  LEU*     4.2    18.4    -      -       +      -
    354B  HIS*     1.3    74.8    -      -       -      +
    356B  LEU*     1.3    57.4    +      -       -      +
    357B  VAL*     6.3     0.4    -      -       +      -
    370B  GLU*     3.6     3.6    -      -       -      +
    371B  ILE*     2.7    41.4    +      -       +      -
    372B  PHE*     2.8    46.6    +      -       +      +
    376B  LEU*     3.4    31.0    -      -       +      -
    382B  HIS*     4.8     7.0    -      -       +      -
    400B  PHE*     3.8    28.3    -      -       +      -
    401B  ILE      3.5     2.2    -      -       -      -
    402B  TRP*     3.9     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 356 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  ARG*     4.5    12.8    -      -       -      +
    354B  HIS*     3.6     6.7    -      -       +      +
    355B  ILE*     1.3    79.4    -      -       -      +
    357B  VAL*     1.3    69.8    +      -       -      +
    368B  GLN*     4.1    29.8    -      -       +      +
    369B  TYR      3.3     8.3    -      -       -      +
    370B  GLU*     4.3    20.2    -      -       +      +
    371B  ILE*     4.5     0.4    -      -       -      +
    400B  PHE*     3.5     1.7    -      -       -      -
    401B  ILE*     2.7    61.4    +      -       +      +
    403B  TYR*     3.6    33.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 357 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342B  VAL*     4.2    15.0    -      -       +      -
    344B  VAL*     4.1    20.0    -      -       +      -
    355B  ILE*     5.8     0.7    -      -       +      -
    356B  LEU*     1.3    81.2    -      -       -      +
    358B  SER*     1.3    62.7    +      -       -      +
    359B  LEU*     3.7    18.3    -      -       +      +
    367B  LYS      3.7     0.9    -      -       -      +
    368B  GLN*     3.2     3.9    -      -       -      -
    369B  TYR*     2.8    32.7    +      -       -      +
    371B  ILE*     4.1    14.1    -      -       +      -
    386B  PHE*     5.2     2.2    -      -       +      -
    398B  VAL*     3.6    20.0    -      -       +      -
    399B  LYS      3.4     8.3    -      -       -      +
    400B  PHE*     4.4     5.8    -      -       +      -
    420B  ILE*     4.1    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 358 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  GLU*     5.3     0.9    +      -       -      -
    357B  VAL*     1.3    74.5    -      -       -      +
    359B  LEU*     1.3    65.2    +      -       -      +
    360B  PHE*     3.6    20.3    -      -       -      -
    366B  SER*     3.8    12.1    -      -       -      -
    367B  LYS      3.5    18.4    -      -       -      -
    368B  GLN*     4.0    17.0    +      -       -      +
    398B  VAL*     3.4     9.4    -      -       -      +
    399B  LYS*     3.2    37.4    +      -       -      +
    443B  LEU*     4.9     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 359 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340B  TYR*     3.7    47.1    -      -       +      -
    342B  VAL*     4.4     7.6    -      -       +      -
    357B  VAL*     3.7    20.6    -      -       +      -
    358B  SER*     1.3    80.2    -      -       -      +
    360B  PHE*     1.3    64.5    +      -       -      +
    365B  ASN*     3.0    26.2    -      -       -      +
    366B  SER*     3.0    20.2    +      -       -      +
    386B  PHE*     4.0    20.4    -      -       +      -
    388B  SER*     5.5     1.1    -      -       -      +
    392B  VAL*     4.0    11.7    -      -       +      +
    395B  LEU*     3.9    15.9    -      -       +      -
    397B  MET      3.9     3.1    -      -       -      -
    398B  VAL*     4.5     2.5    -      -       +      -
    422B  VAL*     4.3    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 360 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  GLU*     3.5    38.6    -      -       +      -
     46A  ASN*     4.0     7.4    -      -       -      -
    358B  SER*     3.6    31.4    -      -       -      -
    359B  LEU*     1.3    77.1    -      -       -      +
    361B  GLY*     1.3    58.2    +      -       -      +
    364B  GLY      3.8     2.7    -      -       -      -
    365B  ASN*     3.2    36.8    -      -       +      -
    366B  SER      5.3     0.2    -      -       -      -
    392B  VAL*     4.6     2.2    -      -       -      -
    395B  LEU*     3.5     5.0    -      -       -      +
    396B  GLN*     2.8    28.1    +      -       -      +
    397B  MET*     2.8    46.1    +      -       +      +
    399B  LYS*     3.7    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 361 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360B  PHE*     1.3    74.4    -      -       -      +
    362B  ASN*     1.3    67.5    +      -       -      +
    363B  LYS      3.2     0.2    -      -       -      -
    364B  GLY*     2.9    21.5    +      -       -      +
    392B  VAL*     3.2    16.5    -      -       -      +
    394B  ASP      3.0    17.5    -      -       -      -
    395B  LEU*     4.1     0.9    -      -       -      -
    396B  GLN*     3.8    11.9    -      -       -      +
----------------------------------------------------------
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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