Contacts of the strand formed by residues 406 - 414 (chain A) in PDB entry 3H4B


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 LEU 406 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305A  GLU*     5.0     0.4    -      -       -      -
    306A  ASP*     2.9    32.0    +      -       +      +
    308A  PHE*     3.9    24.2    -      -       +      -
    312A  SER*     4.5     8.1    -      -       -      +
    317A  ALA      3.8    21.5    -      -       -      +
    320A  LYS*     4.6     5.8    -      -       +      -
    321A  ILE*     4.0    26.5    -      -       +      -
    324A  LEU*     3.5    16.6    -      -       +      +
    345A  ILE      3.7     2.7    -      -       -      +
    346A  ILE*     3.4    27.8    -      -       +      -
    391A  PHE*     5.9     9.0    -      -       +      -
    404A  THR      6.2     0.4    -      -       -      +
    405A  LEU*     1.3    86.2    -      -       -      +
    407A  SER*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 407 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  SER*     5.6     2.2    -      -       -      -
    304A  GLU      2.9    21.1    -      -       -      -
    305A  GLU*     3.5    22.4    +      -       -      +
    324A  LEU*     3.6     2.7    -      -       -      +
    343A  ARG      3.9     0.2    -      -       -      +
    344A  LEU*     3.5     5.4    -      -       -      +
    345A  ILE*     3.1    55.1    +      -       -      +
    406A  LEU*     1.3    76.0    -      -       -      +
    408A  VAL*     1.3    65.3    +      -       -      +
    409A  CYS*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 408 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  SER*     3.2    19.4    -      -       -      -
    304A  GLU      3.3    13.2    +      -       -      +
    321A  ILE*     4.1     7.4    -      -       +      -
    324A  LEU*     3.7    16.0    -      -       +      +
    325A  LEU*     3.3    27.4    -      -       +      -
    328A  LEU*     3.4    24.4    -      -       +      +
    342A  VAL*     4.1     5.2    -      -       +      -
    343A  ARG      3.4    11.4    -      -       -      +
    344A  LEU*     4.8     4.0    -      -       +      -
    387A  LEU*     3.7    16.8    -      -       +      -
    407A  SER*     1.3    78.8    -      -       -      +
    409A  CYS*     1.3    65.5    +      -       -      +
    410A  PHE*     3.6    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 409 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  SER*     4.2    17.0    -      -       -      -
    302A  PHE      3.4    11.0    -      -       -      -
    303A  SER*     3.8    12.3    -      -       -      -
    342A  VAL*     3.4     5.7    -      -       -      -
    343A  ARG*     3.1    50.6    +      -       +      +
    345A  ILE*     5.3     8.3    -      -       +      -
    408A  VAL*     1.3    79.2    -      -       -      +
    410A  PHE*     1.3    73.0    +      -       -      +
    411A  CYS*     3.6    11.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  SER*     3.6     2.4    -      -       -      -
    302A  PHE*     2.8    34.4    +      -       +      +
    325A  LEU*     4.9     4.9    -      -       +      -
    328A  LEU*     3.7    30.1    -      -       +      -
    329A  LEU*     3.7    26.2    -      -       +      -
    332A  VAL*     3.6    26.9    -      -       +      -
    339A  PRO*     3.4    30.5    -      -       +      -
    341A  THR      3.6     3.8    -      -       -      -
    342A  VAL*     4.1    10.8    -      -       +      -
    364A  ILE*     4.2    17.0    -      -       +      -
    383A  MET*     4.6    13.9    -      -       +      -
    408A  VAL*     3.6    21.8    -      -       +      -
    409A  CYS*     1.3    76.1    -      -       -      +
    411A  CYS*     1.3    58.9    +      -       -      +
    413A  LEU*     3.8     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  GLN      4.3     2.7    -      -       -      +
    301A  SER*     4.3     9.2    -      -       -      -
    339A  PRO*     3.6     2.8    -      -       -      +
    340A  HIS      3.6     2.4    +      -       -      -
    341A  THR*     3.2    45.2    +      -       -      +
    343A  ARG*     3.9    27.1    -      -       -      +
    361A  GLN*     5.1     1.8    -      -       -      -
    409A  CYS*     4.2    16.8    -      -       -      -
    410A  PHE*     1.3    75.6    -      -       -      +
    412A  ASN*     1.3    77.8    +      -       -      +
    413A  LEU*     3.5     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  GLN      4.2     4.2    +      -       -      -
    340A  HIS*     2.8    30.7    +      -       -      +
    341A  THR*     3.4    24.4    +      -       -      +
    411A  CYS*     1.3    80.2    -      -       -      +
    413A  LEU*     1.3    62.0    +      -       -      +
    414A  LYS*     3.1    29.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  GLN*     3.5    27.3    +      -       -      +
    302A  PHE*     3.6    24.0    -      -       +      -
    332A  VAL*     5.0     2.2    -      -       +      -
    335A  ASP*     4.6     1.3    -      -       -      +
    337A  ARG*     3.2    42.6    -      -       +      +
    338A  LYS      3.8     5.4    -      -       -      +
    339A  PRO*     3.7    28.0    -      -       +      -
    410A  PHE      3.8     7.9    -      -       -      +
    411A  CYS*     3.5    20.4    -      -       -      -
    412A  ASN*     1.3    69.9    -      -       -      +
    414A  LYS*     1.3    72.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 414 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337A  ARG*     3.1    20.2    -      -       -      +
    338A  LYS*     3.0    31.6    +      -       -      +
    340A  HIS*     3.4    38.3    +      -       +      +
    412A  ASN*     3.1    29.3    +      -       -      +
    413A  LEU*     1.3    87.1    -      -       -      +
----------------------------------------------------------
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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