Contacts of the strand formed by residues 402 - 411 (chain A) in PDB entry 4I2C


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 GLN 402 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  GLU      3.3    21.0    -      -       -      +
    359A  GLN*     2.7    30.5    +      -       -      +
    362A  LEU*     3.7    27.2    -      -       +      +
    363A  HIS*     3.8     6.5    +      -       -      -
    380A  ILE*     4.3     5.1    -      -       +      +
    381A  LEU      3.4    18.2    -      -       -      +
    382A  GLU*     3.5    25.9    +      -       -      -
    383A  SER*     3.6    25.8    -      -       -      +
    401A  PHE*     1.3    73.0    -      -       -      +
    403A  LYS*     1.3    60.9    +      -       -      +
    436A  VAL*     3.6     1.9    -      -       -      +
    437A  MET*     3.0    37.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 403 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  LEU*     3.9     5.6    -      -       -      -
    380A  ILE*     3.5     2.6    -      -       -      +
    381A  LEU*     2.7    57.4    +      -       +      +
    399A  ASP*     2.7    50.4    +      -       -      -
    401A  PHE      2.8    18.7    +      -       -      +
    402A  GLN*     1.3    73.7    -      -       -      +
    404A  CYS*     1.3    60.1    +      -       -      +
    405A  PHE*     3.6    29.8    -      -       +      -
    434A  ASP*     6.6     0.4    -      -       +      -
    435A  LEU      3.2    13.5    -      -       -      +
    436A  VAL*     4.3     7.9    -      -       +      -
    450A  TRP*     3.7    21.5    -      -       +      -
    602A  APC      4.9     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 404 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  LEU*     4.1    13.9    -      -       +      -
    366A  THR*     4.5     5.8    -      -       -      -
    379A  ASP      3.1    12.3    -      -       -      +
    380A  ILE*     3.8    17.3    -      -       +      -
    403A  LYS*     1.3    76.9    -      -       -      +
    405A  PHE*     1.3    64.2    +      -       -      +
    406A  LEU*     3.8    22.0    -      -       +      -
    433A  VAL      3.9     0.5    -      -       -      +
    434A  ASP*     3.3     8.7    -      -       -      +
    435A  LEU*     2.9    64.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 405 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256A  PHE*     4.9     7.2    -      -       +      -
    288A  MET*     6.3     0.9    -      -       +      -
    377A  TYR*     3.7    10.6    -      -       +      -
    379A  ASP*     2.9    51.4    +      -       +      +
    381A  LEU*     3.5    28.7    -      -       +      -
    403A  LYS*     3.6    28.9    -      -       +      -
    404A  CYS*     1.3    72.2    -      -       -      +
    406A  LEU*     1.3    60.5    +      -       -      +
    432A  ARG*     3.9     4.3    -      -       -      +
    434A  ASP*     3.2    22.7    -      -       +      +
    450A  TRP*     5.3     0.9    -      +       -      -
    602A  APC      2.9    30.5    -      +       -      -
      4C    A      3.2    47.3    -      +       +      +
----------------------------------------------------------
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Residues in contact with LEU 406 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366A  THR*     3.8     7.0    -      -       +      -
    369A  TRP*     3.7    31.9    -      -       +      -
    375A  LEU*     4.2     2.0    -      -       +      -
    377A  TYR*     3.4     7.4    -      -       -      +
    378A  CYS*     3.4    36.6    -      -       +      -
    404A  CYS*     3.8    18.2    -      -       +      -
    405A  PHE*     1.3    79.1    -      -       -      +
    407A  ILE*     1.3    64.1    +      -       -      +
    408A  LEU*     4.3    12.1    -      -       +      -
    432A  ARG*     2.9    23.5    +      -       -      +
    433A  VAL*     2.8    36.9    +      -       +      +
    435A  LEU*     3.8    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 407 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256A  PHE*     3.7    31.4    -      -       +      -
    291A  ALA*     4.0    12.1    -      -       +      +
    295A  TYR*     4.2     9.0    -      -       +      -
    299A  LEU*     3.8    17.0    -      -       +      -
    376A  LEU*     2.9    38.8    +      -       +      -
    377A  TYR*     3.0    29.3    +      -       +      +
    406A  LEU*     1.3    77.2    -      -       -      +
    408A  LEU*     1.3    65.9    +      -       -      +
    430A  ALA*     3.8    28.9    -      -       +      -
    431A  ILE      3.3     8.5    -      -       -      +
    432A  ARG*     3.8    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 408 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311A  VAL*     4.9     9.4    -      -       +      -
    314A  LEU*     5.1    13.9    -      -       +      -
    315A  VAL*     5.3     0.9    -      -       +      -
    369A  TRP*     3.7    53.6    -      -       +      -
    374A  LEU*     3.3    13.0    -      -       +      +
    375A  LEU*     4.2    15.0    -      -       +      -
    376A  LEU*     4.0     3.6    -      -       -      -
    406A  LEU*     4.3     5.8    -      -       +      -
    407A  ILE*     1.3    80.5    -      -       -      +
    409A  LYS*     1.3    66.0    +      -       -      +
    410A  LEU*     3.5     2.5    +      -       +      -
    430A  ALA*     3.5     4.5    -      -       -      -
    431A  ILE*     2.9    37.3    +      -       +      +
    433A  VAL*     4.1    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 409 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314A  LEU*     4.7     5.7    -      -       -      +
    373A  GLY      3.8    17.3    +      -       -      +
    374A  LEU*     2.8    49.2    +      -       +      +
    376A  LEU*     3.9    23.0    -      -       +      +
    408A  LEU*     1.3    72.1    -      -       -      +
    410A  LEU*     1.3    60.5    +      -       -      +
    411A  ASP*     3.7    16.9    +      -       -      +
    428A  TRP*     3.6    51.2    -      -       +      +
    429A  LYS      4.1     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  GLU*     3.9    30.3    -      -       +      +
    310A  ALA*     3.8    23.6    -      -       +      -
    311A  VAL*     4.1     5.6    -      -       +      -
    314A  LEU*     4.0    23.8    -      -       +      -
    408A  LEU*     3.5     2.2    +      -       +      +
    409A  LYS*     1.3    70.1    -      -       -      +
    411A  ASP*     1.3    72.3    +      -       -      +
    412A  HIS*     3.6     2.4    +      -       -      -
    414A  ARG*     4.3     5.6    -      -       +      -
    415A  VAL*     3.7    23.8    -      -       +      -
    428A  TRP*     3.2     2.1    -      -       -      -
    429A  LYS*     2.9    46.2    +      -       +      +
    431A  ILE*     3.7    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  LEU*     4.7    13.6    -      -       -      +
    409A  LYS*     3.7    18.5    +      -       -      +
    410A  LEU*     1.3    74.8    -      -       -      +
    412A  HIS*     1.4    65.1    +      -       -      +
    413A  GLY*     3.2     4.5    -      -       -      +
    414A  ARG*     3.1    38.5    +      -       +      +
    415A  VAL*     3.9     6.2    -      -       -      +
    427A  GLY      3.8     7.3    -      -       -      +
    428A  TRP*     3.7    14.8    -      -       -      +
----------------------------------------------------------
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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