Contacts of the strand formed by residues 296 - 304 (chain A) in PDB entry 3I5D


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 296 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  PHE*     5.3     0.4    -      -       -      -
    292A  ALA*     6.0     5.3    -      -       -      +
    293A  PRO      5.3     4.2    +      -       -      -
    295A  TYR*     1.3    87.6    -      -       -      +
    297A  PHE*     1.3    71.0    +      -       -      +
    298A  ARG*     5.5     1.0    +      -       -      +
    316A  LYS*     3.2    37.7    -      -       -      +
    317A  GLY      3.0    16.6    -      -       -      +
    318A  TYR*     3.6    24.2    -      -       +      +
     70B  LYS*     5.8     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  PRO*     3.6    22.9    -      -       +      -
     96A  PRO*     5.5     0.2    -      -       +      -
    103A  PHE*     3.4    44.6    -      +       +      -
    295A  TYR*     4.3    18.4    -      +       -      -
    296A  ASN*     1.3    82.1    -      -       -      +
    298A  ARG*     1.3    77.0    +      -       -      +
    299A  PHE*     3.1    28.7    -      +       +      -
    315A  ILE      3.6     0.3    -      -       -      +
    316A  LYS*     3.7     0.9    -      -       -      -
    317A  GLY*     3.0    29.3    +      -       -      +
     97B  GLN*     4.4    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ASP*     5.9     5.7    -      -       -      +
    171A  GLU*     2.7    43.5    +      -       -      +
    296A  ASN*     5.5     0.4    -      -       -      +
    297A  PHE*     1.3    87.5    -      -       -      +
    299A  PHE*     1.3    65.7    +      -       -      +
    314A  LEU*     3.9    27.5    -      -       +      +
    315A  ILE      3.3     5.6    -      -       -      +
    316A  LYS*     3.7    33.3    -      -       +      +
     88B  ASP*     6.1     0.4    -      -       -      -
     90B  ALA*     4.3    35.0    -      -       +      +
     91B  ASP*     4.5     4.4    -      -       +      -
     97B  GLN*     4.2    12.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  TRP*     6.5     0.2    -      +       -      -
     92A  TYR*     6.0     3.8    -      +       -      -
     95A  PRO*     3.8    27.1    -      -       +      -
    105A  LEU*     4.5    13.9    -      -       +      -
    297A  PHE*     3.1    33.4    -      +       +      -
    298A  ARG*     1.3    75.6    -      -       -      +
    300A  ALA*     1.3    69.4    -      -       -      +
    301A  LYS*     4.8     8.3    -      -       +      -
    314A  LEU*     3.5     4.3    -      -       -      +
    315A  ILE*     2.9    76.5    +      -       +      +
    317A  GLY*     4.8     9.2    -      -       -      -
     91B  ASP*     4.4     9.2    -      -       -      +
     97B  GLN*     4.6    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  PHE*     1.3    82.3    -      -       -      +
    301A  LYS*     1.3    71.3    +      -       -      +
    302A  TYR*     3.7    37.7    -      -       +      +
    312A  ARG*     3.9    22.4    -      -       -      +
    313A  THR      3.3    12.1    -      -       -      +
    314A  LEU*     4.6     0.9    -      -       -      -
     91B  ASP*     4.5     5.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  TYR*     2.7    39.0    +      -       -      -
    299A  PHE*     4.8     7.9    -      -       +      -
    300A  ALA*     1.3    83.2    -      -       -      +
    302A  TYR*     1.3    62.8    +      -       -      +
    303A  TYR*     3.3    26.7    +      -       +      +
    312A  ARG*     3.1     5.5    -      -       -      -
    313A  THR*     2.9    41.1    +      -       +      +
    315A  ILE*     4.5    16.2    -      -       +      +
    302C  TYR*     3.2    39.4    -      -       +      -
    310C  GLU*     3.7    10.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 302 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  TRP*     4.3     0.7    -      +       -      -
    300A  ALA*     3.7    30.5    -      -       +      +
    301A  LYS*     1.3    74.8    -      -       -      +
    303A  TYR*     1.3    70.9    +      -       -      +
    310A  GLU*     4.0    24.7    -      -       -      +
    311A  THR      3.7     2.5    -      -       -      +
    312A  ARG*     3.6    33.5    +      -       +      -
     91B  ASP      3.7     7.3    +      -       -      -
     92B  TYR*     3.5    51.7    -      +       -      +
    301B  LYS*     3.2    31.4    -      -       +      -
    302B  TYR      4.4     2.3    -      -       -      +
    303B  TYR*     3.8    17.1    -      -       +      -
    302C  TYR      4.3     5.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 303 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  LYS*     3.3    33.9    +      -       +      +
    302A  TYR*     1.3    90.8    -      -       -      +
    304A  LYS*     1.3    62.0    +      -       -      +
    305A  ASN*     3.0     8.7    +      -       -      +
    310A  GLU*     4.0     3.2    -      -       -      +
    311A  THR*     2.8    46.9    +      -       -      +
    312A  ARG*     4.9     0.9    -      -       -      -
    313A  THR*     3.6    23.7    +      -       -      -
    303B  TYR*     4.1     3.1    -      -       -      -
    302C  TYR*     3.8    22.1    -      -       +      +
    303C  TYR*     4.1     1.3    -      -       -      -
    304C  LYS*     3.3    48.9    -      -       +      +
    310C  GLU*     2.9    27.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  TYR*     1.3    69.1    -      -       -      +
    305A  ASN*     1.3    69.4    +      -       -      +
    306A  SER*     3.7     1.0    +      -       -      -
    308A  GLY*     5.5     5.6    -      -       -      +
    309A  THR      4.2     4.5    -      -       -      -
    310A  GLU*     5.0     4.7    -      -       +      +
    303B  TYR*     3.3    48.9    -      -       +      +
    304B  LYS      5.4     3.5    -      -       -      +
    304C  LYS      5.3     4.9    -      -       -      +
----------------------------------------------------------
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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