Contacts of the strand formed by residues 353 - 361 (chain A) in PDB entry 4N7E


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 TYR 353 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281A  PHE*     3.6    15.2    -      -       -      -
    307A  ALA*     3.6    15.4    -      -       +      +
    308A  GLN*     3.1    44.7    +      -       -      +
    309A  LEU*     3.6    33.3    -      -       +      +
    328A  VAL*     3.6    22.9    -      -       +      +
    330A  MET*     4.1    11.8    -      -       +      +
    344A  PHE*     3.7    19.5    -      -       +      -
    345A  THR      3.5     1.3    -      -       -      -
    346A  SER*     3.5    25.8    -      -       -      -
    350A  GLY      2.6    32.3    +      -       -      -
    351A  ILE      3.4     6.7    -      -       -      -
    352A  VAL*     1.3    82.4    -      -       -      +
    354A  SER*     1.3    61.5    +      -       -      +
    355A  LYS      4.4     0.2    +      -       -      -
    641A  LEU*     5.9     0.4    -      -       -      +
    642A  CYS      5.6     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  PHE*     3.3     4.9    -      -       -      -
    345A  THR*     2.9    43.8    +      -       -      -
    353A  TYR*     1.3    77.3    -      -       -      +
    355A  LYS*     1.3    70.7    +      -       -      +
    356A  SER*     3.2     0.7    +      -       -      -
    641A  LEU*     5.2    20.6    -      -       -      +
    642A  CYS      6.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  THR*     3.8    22.2    -      -       +      -
    343A  ILE      4.0     0.2    -      -       -      -
    344A  PHE*     3.9    20.4    -      -       +      -
    353A  TYR      4.3     0.2    -      -       -      -
    354A  SER*     1.3    79.1    +      -       -      +
    356A  SER*     1.3    61.7    +      -       -      +
    357A  LEU      4.7     2.2    -      -       -      +
    358A  ASP*     2.8    43.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  ILE*     2.8    28.2    +      -       -      +
    345A  THR*     4.1    16.1    -      -       -      +
    354A  SER      3.2     2.8    +      -       -      -
    355A  LYS*     1.3    75.8    -      -       -      +
    357A  LEU*     1.3    58.2    +      -       -      +
    401A  GLY*     2.6    32.1    +      -       -      +
    404A  TRP*     2.7    35.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  GLY      4.2     0.2    -      -       -      +
    342A  THR*     3.3    10.5    -      -       -      +
    343A  ILE*     2.9    49.0    +      -       +      +
    355A  LYS*     3.9     1.9    -      -       -      +
    356A  SER*     1.3    80.7    -      -       -      +
    358A  ASP*     1.3    68.4    +      -       -      +
    360A  HIS*     4.6     3.5    -      -       +      +
    383A  THR*     3.1    36.1    -      -       +      -
    385A  VAL*     3.8    25.6    -      -       +      -
    395A  MET*     4.8     7.6    -      -       +      -
    404A  TRP*     3.7    42.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  GLY      4.5     0.4    -      -       -      -
    342A  THR*     3.8     9.5    +      -       -      -
    355A  LYS*     2.8    41.2    +      -       -      -
    357A  LEU*     1.3    75.4    -      -       -      +
    359A  ARG*     1.3    81.2    +      -       +      +
    360A  HIS      3.2     3.5    +      -       -      -
    385A  VAL*     3.5    16.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 359 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  PHE*     3.3    56.3    -      -       +      +
    341A  GLY      3.1    10.8    +      -       -      -
    342A  THR*     4.8     0.8    +      -       -      -
    358A  ASP*     1.3    83.7    +      -       +      +
    360A  HIS*     1.3    62.0    +      -       -      +
    361A  LEU      3.3     0.2    +      -       -      -
    385A  VAL*     3.2     5.0    -      -       +      -
    386A  LEU*     2.6    60.5    +      -       -      +
    387A  SER*     2.7    26.1    +      -       -      +
    388A  GLU*     3.5    40.2    +      -       -      +
    390A  ASN*     4.5     3.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321A  LEU*     3.6    18.6    -      -       +      -
    331A  HIS*     3.0    24.8    +      +       -      -
    340A  PHE*     3.2     0.6    -      -       -      -
    341A  GLY      2.6    37.7    +      -       -      +
    343A  ILE*     3.3    36.4    -      -       +      +
    357A  LEU*     4.6     6.1    -      -       +      +
    358A  ASP      3.2     2.7    -      -       -      +
    359A  ARG*     1.3    72.9    -      -       -      +
    361A  LEU*     1.3    68.1    +      -       -      +
    362A  TYR*     3.0     2.3    +      +       -      -
    369A  THR*     3.2    25.7    +      -       -      -
    371A  PHE*     3.9     4.3    -      -       +      +
    383A  THR*     2.4    35.2    +      -       +      -
    384A  SER      3.2    13.7    -      -       -      -
    385A  VAL*     4.2     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 361 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  GLY      3.6    11.9    -      -       -      +
    340A  PHE*     4.2     2.9    -      -       -      -
    359A  ARG      3.3     3.6    +      -       -      -
    360A  HIS*     1.3    73.8    +      -       -      +
    362A  TYR*     1.3    59.9    +      -       -      +
    363A  THR*     4.2     4.3    -      -       +      -
    368A  GLU      4.2     7.6    -      -       -      +
    369A  THR*     3.0    22.6    +      -       -      -
    370A  ASP      4.4     2.1    +      -       -      +
    384A  SER*     3.0    25.4    +      -       -      +
    386A  LEU*     4.6    16.4    -      -       +      +
    392A  ILE*     3.7    46.9    -      -       +      -
    433A  TYR*     3.4    45.5    -      -       +      -
----------------------------------------------------------
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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