Contacts of the strand formed by residues 467 - 477 (chain D) in PDB entry 3CB4


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 SER 467 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109D  GLU*     4.5     6.5    -      -       -      +
    110D  ALA*     3.0    35.4    +      -       -      +
    111D  GLN*     4.4    13.5    -      -       -      -
    408D  MET*     3.3    23.4    -      -       -      -
    409D  LEU*     3.1    16.1    +      -       -      +
    455D  PHE*     6.0     0.2    -      -       -      -
    459D  LYS*     4.3    11.8    -      -       -      +
    465D  TYR      3.4     4.7    +      -       -      -
    466D  ALA*     1.3    70.4    -      -       -      +
    468D  LEU*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 468 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81D  HIS*     4.8    12.5    -      -       -      -
    110D  ALA*     4.9     2.2    -      -       -      +
    111D  GLN*     5.5     4.3    +      -       -      +
    406D  CYS*     4.1    16.8    -      -       +      -
    407D  HIS      4.0     2.9    -      -       -      +
    408D  MET*     4.8     5.6    -      -       -      -
    450D  VAL*     4.6     2.7    -      -       +      -
    454D  PHE*     3.7    32.3    -      -       +      -
    455D  PHE*     3.7    45.5    -      -       +      -
    458D  LEU*     4.5     8.7    -      -       +      -
    466D  ALA      3.2     6.7    +      -       -      +
    467D  SER*     1.3    72.0    -      -       -      +
    469D  ASP*     1.3    93.5    +      -       -      +
    470D  TYR*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 469 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81D  HIS*     5.6     1.6    -      -       -      -
     82D  VAL*     3.3    27.6    +      -       -      +
    110D  ALA*     4.4    18.1    -      -       +      +
    111D  GLN*     4.8     5.8    -      -       -      +
    114D  ALA*     3.3    33.7    -      -       -      +
    405D  GLU      3.8     0.2    -      -       -      +
    406D  CYS*     3.4     1.9    -      -       -      -
    407D  HIS*     2.8    59.6    +      -       +      +
    468D  LEU*     1.3    79.2    -      -       -      +
    470D  TYR*     1.3    65.5    +      -       -      +
    471D  ASN*     5.2     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 470 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81D  HIS*     5.0    12.3    -      -       -      -
     82D  VAL*     3.1    30.4    -      -       +      +
     83D  ASP*     3.9    10.6    +      -       -      -
    294D  GLN*     3.5    31.6    +      -       -      -
    345D  LEU*     3.7    29.0    +      -       +      +
    346D  LEU*     4.8     4.4    -      -       +      +
    404D  ALA*     4.3     4.3    -      -       +      -
    405D  GLU      3.1    12.3    -      -       -      +
    406D  CYS*     3.8    16.8    -      -       -      -
    447D  MET*     3.8    24.6    -      -       +      -
    450D  VAL*     3.9    20.9    -      -       +      -
    451D  VAL*     4.9     1.9    -      -       -      +
    455D  PHE*     6.5     0.2    -      -       +      -
    468D  LEU*     3.7    21.5    -      -       +      -
    469D  ASP*     1.3    80.3    -      -       -      +
    471D  ASN*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 471 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82D  VAL*     5.5     7.0    -      -       +      -
     85D  SER*     5.6     5.2    -      -       -      +
    404D  ALA*     3.3     9.2    -      -       -      +
    405D  GLU*     3.0    62.4    +      -       -      +
    407D  HIS*     3.4    15.9    -      -       -      -
    469D  ASP*     5.2     1.4    -      -       -      +
    470D  TYR*     1.3    79.1    -      -       -      +
    472D  PHE*     1.3    76.0    +      -       -      +
    473D  LYS*     4.2     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 472 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294D  GLN*     5.3     5.4    +      -       -      +
    402D  PRO*     4.2    11.4    -      -       +      -
    403D  ILE      4.0     7.6    -      -       -      -
    447D  MET*     4.3    17.0    -      -       +      +
    471D  ASN*     1.3    85.8    +      -       -      +
    473D  LYS*     1.3    67.5    +      -       -      +
    474D  ARG*     3.8    28.9    -      -       -      -
    475D  PHE*     3.5    46.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with LYS 473 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    403D  ILE*     3.0    19.1    +      -       +      +
    404D  ALA      4.5     0.2    -      -       -      -
    405D  GLU*     2.8    53.6    +      -       +      +
    444D  GLU*     3.6    28.3    -      -       -      +
    471D  ASN*     4.4     2.7    -      -       -      +
    472D  PHE*     1.3    84.4    -      -       -      +
    474D  ARG*     1.3    74.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 474 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402D  PRO*     3.8     0.5    -      -       -      +
    403D  ILE*     2.8    56.1    +      -       -      +
    444D  GLU*     2.7    37.6    +      -       -      -
    472D  PHE*     3.8    12.4    -      -       -      -
    473D  LYS*     1.3    89.2    -      -       +      +
    475D  PHE*     1.3    72.6    +      -       -      +
    476D  GLN*     2.7    42.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 475 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371D  VAL*     3.3    29.4    -      -       +      -
    373D  GLU*     3.6    46.9    -      -       +      +
    383D  TYR*     4.2    22.0    -      +       -      -
    400D  ARG*     3.8    16.4    -      -       +      -
    401D  GLU      3.4     1.1    -      -       -      -
    402D  PRO*     3.7    25.1    -      -       +      -
    472D  PHE*     3.5    25.1    -      +       -      -
    474D  ARG*     1.3    90.1    -      -       -      +
    476D  GLN*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 476 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400D  ARG*     3.6     7.2    -      -       -      +
    401D  GLU*     2.8    33.6    +      -       -      +
    403D  ILE*     4.0    14.1    -      -       +      +
    474D  ARG*     2.7    42.5    +      -       -      +
    475D  PHE*     1.3    76.6    -      -       -      +
    477D  ALA*     1.3    73.9    +      -       +      +
    478D  SER*     3.4     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 477 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398D  GLU*     3.5    37.7    -      -       +      +
    399D  LEU      3.6     7.9    -      -       -      -
    400D  ARG*     3.4     7.3    -      -       -      +
    476D  GLN*     1.3    82.2    -      -       +      +
    478D  SER*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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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