Contacts of the strand formed by residues 339 - 348 (chain C) in PDB entry 3IW4


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 PHE 339 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334C  VAL*     3.5    37.9    -      -       +      -
    335C  LYS      3.2    25.6    -      -       -      -
    336C  LEU*     3.3    18.2    +      -       +      +
    337C  THR*     4.4     4.2    -      -       -      +
    338C  ASP*     1.3    79.3    -      -       +      +
    340C  ASN*     1.3    68.1    +      -       -      +
    341C  PHE*     4.0     8.8    +      -       +      -
    356C  ALA*     3.9    14.6    -      -       +      -
    357C  ASP      3.2    14.4    -      -       -      +
    358C  ARG*     4.2    13.9    -      -       +      -
    359C  LYS*     4.4     2.9    +      -       -      -
    365C  TYR*     3.9    27.8    -      +       -      -
    367C  ILE*     3.8    20.2    -      -       +      -
    404C  HIS*     5.6     0.9    -      +       -      -
    407C  PHE*     5.1     2.7    -      +       -      -
    416C  VAL*     4.0    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 340 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339C  PHE*     1.3    77.4    -      -       -      +
    341C  PHE*     1.3    68.2    +      -       -      +
    342C  LEU*     3.2     9.9    +      -       +      +
    356C  ALA*     3.3     0.8    -      -       -      -
    357C  ASP*     2.8    55.4    +      -       +      +
    359C  LYS*     3.5    28.1    +      -       -      +
    634C  GLN*     5.3     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 341 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336C  LEU*     3.6    31.2    -      -       +      -
    339C  PHE*     4.0     6.4    +      -       +      -
    340C  ASN*     1.3    71.1    -      -       -      +
    342C  LEU*     1.3    64.6    +      -       -      +
    354C  MET*     3.1    39.9    -      -       +      -
    355C  LEU      3.9     2.5    -      -       -      -
    356C  ALA*     4.0    17.0    -      -       +      -
    367C  ILE*     4.7    12.3    -      -       +      -
    369C  ILE*     3.8    21.5    -      -       +      -
    414C  TYR*     4.6     0.4    -      +       -      -
    634C  GLN*     3.2    26.8    +      -       -      +
    635C  PRO*     3.7    23.4    -      -       +      +
    636C  VAL*     5.1     0.9    -      -       -      -
    637C  LEU*     3.6    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 342 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340C  ASN*     3.8    17.5    -      -       +      +
    341C  PHE*     1.3    73.3    -      -       -      +
    343C  MET*     1.3    70.5    +      -       +      +
    355C  LEU*     2.7    40.0    +      -       +      +
    356C  ALA      4.3     0.4    -      -       -      -
    357C  ASP*     3.7    29.4    -      -       +      +
    364C  LEU*     4.4    12.1    -      -       +      -
    633C  GLY      5.4     0.2    -      -       -      +
    634C  GLN*     4.9     1.3    -      -       -      +
    635C  PRO*     3.5    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 343 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341C  PHE      3.9     0.4    -      -       -      -
    342C  LEU*     1.3    83.1    -      -       +      +
    344C  VAL*     1.3    82.3    +      -       +      +
    345C  LEU*     4.9     6.3    -      -       -      -
    354C  MET*     3.4     7.7    -      -       -      +
    355C  LEU*     2.5    58.5    +      -       +      -
    632C  ARG*     6.3     4.7    -      -       -      +
    635C  PRO*     4.0     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 344 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343C  MET*     1.3    92.2    -      -       +      +
    345C  LEU*     1.3    62.6    +      -       -      +
    346C  GLY*     3.3    34.1    -      -       -      +
    347C  LYS*     4.2    23.8    -      -       +      -
    352C  LYS*     4.7     7.0    -      -       +      -
    353C  VAL      3.7     5.6    -      -       -      +
    354C  MET*     4.0    16.2    -      -       -      +
    635C  PRO*     5.0     6.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 345 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343C  MET*     3.4     8.4    +      -       +      -
    344C  VAL*     1.3    75.2    -      -       -      +
    346C  GLY*     1.3    57.4    +      -       -      +
    353C  VAL*     2.6    22.6    +      -       +      +
    355C  LEU*     3.3    35.9    -      -       +      +
    366C  ALA*     3.5    33.0    -      -       +      -
    419C  TYR*     3.8    34.5    -      -       +      +
    901C  LW4      3.6    35.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 346 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344C  VAL*     3.2    16.5    -      -       -      +
    345C  LEU*     1.3    82.1    -      -       -      +
    347C  LYS*     1.3    60.2    +      -       -      +
    350C  PHE*     3.7     6.9    -      -       -      -
    353C  VAL*     2.8    31.2    +      -       -      -
    901C  LW4      3.7    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 347 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344C  VAL*     4.2    17.9    -      -       +      -
    346C  GLY*     1.3    78.1    -      -       -      +
    348C  GLY*     1.3    59.1    +      -       -      +
    350C  PHE*     3.3    17.5    -      -       -      -
    351C  GLY      3.4     3.1    -      -       -      +
    352C  LYS*     4.0    38.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 348 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347C  LYS*     1.3    77.7    -      -       -      +
    349C  SER*     1.3    68.8    +      -       -      -
    350C  PHE*     2.9    10.7    -      -       -      -
    351C  GLY*     2.8    18.1    +      -       -      +
----------------------------------------------------------
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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