Contacts of the strand formed by residues 348 - 355 (chain B) in PDB entry 5J2M


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 ASN 348 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270B  ILE*     4.0    20.6    -      -       -      +
    314B  VAL*     4.5    19.8    -      -       +      +
    317B  VAL*     3.6    15.8    -      -       -      +
    340B  GLN*     3.9     7.4    -      -       -      +
    341B  ILE      3.5     5.8    -      -       -      +
    342B  TYR*     3.7    22.9    -      -       -      +
    346B  PHE*     3.6     5.9    +      -       -      -
    347B  LYS*     1.3    79.0    +      -       -      +
    349B  LEU*     1.3    60.6    +      -       -      +
    350B  LYS      4.3     1.3    -      -       -      +
    351B  THR*     3.6    28.8    -      -       +      +
    427B  TYR*     3.5    23.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 349 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317B  VAL*     3.6    27.4    -      -       +      +
    318B  TYR      4.6     0.2    -      -       -      -
    319B  TYR*     4.2    34.1    -      -       +      +
    325B  LEU*     3.7    30.1    -      -       +      -
    341B  ILE*     2.6    13.9    +      -       +      +
    342B  TYR*     4.6     6.7    -      -       -      -
    343B  GLN*     4.2    14.8    -      -       +      +
    347B  LYS      3.4     3.3    +      -       -      +
    348B  ASN*     1.3    72.8    -      -       -      +
    350B  LYS*     1.3    59.2    +      -       -      +
    383B  TRP*     3.6    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 350 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239B  TRP*     5.1    10.7    -      -       -      +
    240B  THR      3.3    25.1    +      -       -      +
    241B  VAL*     4.3    15.7    -      -       +      -
    339B  TYR*     3.1    28.7    +      -       +      -
    340B  GLN*     3.4     2.8    -      -       -      -
    341B  ILE*     2.8    45.2    +      -       +      +
    348B  ASN      3.5     1.6    -      -       -      -
    349B  LEU*     1.3    82.5    -      -       -      +
    351B  THR*     1.3    67.8    +      -       -      +
    352B  GLY*     4.4     4.4    -      -       -      +
    378B  GLU*     3.4    20.2    +      -       +      +
    382B  ILE*     4.0    25.1    -      -       +      -
    383B  TRP*     4.2    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 351 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  VAL*     3.2    15.0    -      -       -      +
    242B  GLN*     2.7    49.4    +      -       -      -
    243B  PRO*     4.8     2.1    -      -       -      +
    339B  TYR      3.5     6.5    -      -       -      -
    340B  GLN*     3.8    14.8    -      -       +      -
    348B  ASN*     3.6    32.5    -      -       +      +
    350B  LYS*     1.3    83.8    -      -       -      +
    352B  GLY*     1.3    53.5    +      -       -      +
    427B  TYR*     4.6     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 352 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  THR      4.6     4.0    -      -       -      -
    242B  GLN*     3.9    13.8    -      -       -      +
    338B  THR*     3.6     5.0    -      -       -      +
    339B  TYR*     3.0    54.7    +      -       -      +
    340B  GLN*     5.1     0.2    +      -       -      -
    350B  LYS*     4.4     4.3    -      -       -      -
    351B  THR*     1.3    74.3    -      -       -      +
    353B  LYS*     1.3    59.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 353 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242B  GLN*     3.9    28.3    -      -       +      +
    336B  GLN*     4.2    22.4    +      -       +      +
    337B  TRP      3.1    12.1    -      -       -      +
    338B  THR*     4.1    13.5    -      -       +      +
    339B  TYR*     3.6    10.0    +      -       -      -
    352B  GLY*     1.3    74.5    -      -       -      +
    354B  TYR*     1.3    65.0    +      -       -      +
    355B  ALA*     4.8     9.5    -      -       +      +
    429B  LEU*     4.2    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 354 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336B  GLN*     4.7     0.2    -      -       -      -
    337B  TRP*     2.5    57.9    +      +       +      +
    339B  TYR*     4.7    10.3    -      -       +      -
    353B  LYS*     1.3    77.7    -      -       -      +
    355B  ALA*     1.3    61.2    +      -       -      +
    356B  ARG*     3.2    45.8    +      -       +      -
    367B  GLN      3.9    18.6    -      -       -      -
    370B  GLU*     3.4    26.8    +      -       +      +
    371B  ALA*     3.7    22.0    -      -       +      -
    374B  LYS*     4.7    26.9    -      -       +      -
    375B  ILE*     6.2     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 355 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335B  GLY      3.4     4.7    -      -       -      -
    336B  GLN*     3.2    27.6    -      -       -      +
    353B  LYS*     4.2    13.5    -      -       -      +
    354B  TYR*     1.3    77.4    -      -       -      +
    356B  ARG*     1.3    75.5    +      -       -      +
----------------------------------------------------------
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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