Contacts of the strand formed by residues 355 - 360 (chain C) in PDB entry 2R2N


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 355 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200C  GLY      5.4     1.1    -      -       -      -
    201C  ASN      4.9     1.3    -      -       -      -
    202C  ASN*     3.5    37.7    -      -       +      -
    203C  PRO      3.7    17.3    -      -       -      +
    205C  GLY*     3.9    14.7    -      -       -      +
    233C  TYR*     3.6    19.3    -      +       -      -
    350C  PRO*     3.5    14.7    -      -       -      +
    352C  ALA      5.1     0.8    +      -       -      -
    353C  GLY      4.0     0.2    -      -       -      -
    354C  MET*     1.3    97.8    -      -       +      +
    356C  LEU*     1.3    59.9    +      -       -      +
    357C  TRP      4.3     0.2    +      -       -      -
    399C  ARG*     3.4    45.8    -      -       +      -
    400C  ALA      3.4     1.3    -      -       -      -
    401C  SER*     3.9    16.6    -      -       -      -
    402C  PHE*     3.3    12.9    -      -       -      -
    428C  KYN      4.9     0.9    -      -       -      -
     38D  GLY      3.7    16.2    -      -       -      -
     39D  GLY*     3.7    17.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 356 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203C  PRO      4.6     0.9    -      -       -      -
    333C  ILE*     4.2    33.7    -      -       +      -
    334C  LEU*     3.9    20.0    -      -       +      -
    337C  ALA*     4.3    19.7    -      -       +      -
    347C  TRP*     4.0    11.9    -      -       +      -
    348C  HIS      3.9    20.9    -      -       -      +
    350C  PRO*     4.1     7.4    -      -       +      -
    355C  PHE*     1.3    73.9    -      -       -      +
    357C  TRP*     1.3    63.3    +      -       -      +
    358C  ILE*     3.8    27.0    +      -       +      +
    398C  LEU      3.5     2.1    -      -       -      +
    399C  ARG*     3.5     2.4    -      -       -      +
    400C  ALA*     2.7    42.6    +      -       +      +
    402C  PHE*     3.9     6.3    -      -       +      -
    414C  PHE*     4.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 357 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140C  PRO*     3.6    26.5    -      -       +      +
    203C  PRO*     3.5    41.1    -      -       +      +
    204C  THR*     3.5    40.7    +      -       +      +
    206C  ASN*     5.6     1.8    -      -       -      -
    347C  TRP*     3.5    20.4    -      -       -      +
    348C  HIS*     4.5    11.0    +      +       -      +
    350C  PRO*     5.6     0.4    -      -       -      +
    355C  PHE      4.2     0.8    +      -       -      -
    356C  LEU*     1.3    76.0    -      -       -      +
    358C  ILE*     1.3    61.2    +      -       -      +
    359C  LYS      4.0     0.7    +      -       -      -
    384C  GLY*     3.6    30.3    -      -       -      -
    387C  PHE*     4.1     3.1    -      +       -      -
    388C  TYR*     3.6     8.1    -      -       -      -
    397C  TYR*     3.2    56.6    -      +       +      -
    398C  LEU      3.5    18.4    -      -       -      -
    399C  ARG*     4.1    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 358 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337C  ALA*     5.5     0.2    -      -       +      -
    341C  LEU*     4.4     9.6    -      -       +      -
    345C  ALA*     3.6    28.3    -      -       +      -
    346C  GLU      3.6     5.2    -      -       -      +
    347C  TRP*     4.5     8.1    -      -       +      -
    356C  LEU*     3.8    25.4    -      -       +      +
    357C  TRP*     1.3    77.1    -      -       -      +
    359C  LYS*     1.3    63.2    +      -       -      +
    360C  VAL*     3.6    10.0    +      -       +      +
    381C  MET*     3.6    29.6    -      -       +      -
    396C  PRO      3.7     0.2    -      -       -      +
    397C  TYR*     3.2     6.8    -      -       -      -
    398C  LEU*     2.8    43.7    +      -       +      +
    400C  ALA*     4.3     2.7    -      -       +      -
    414C  PHE*     3.7    25.8    -      -       +      -
    417C  LEU*     5.1     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 359 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345C  ALA*     3.1     4.0    -      -       -      -
    346C  GLU*     2.8    57.7    +      -       +      +
    357C  TRP      4.0     0.6    +      -       -      -
    358C  ILE*     1.3    69.7    -      -       -      +
    360C  VAL*     1.3    65.9    +      -       -      +
    361C  LYS*     3.6     2.6    +      -       +      +
    396C  PRO*     3.7    27.8    -      -       +      -
    397C  TYR*     3.3    41.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 360 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344C  LEU      3.8     3.6    -      -       -      +
    345C  ALA*     4.1     2.5    -      -       +      -
    358C  ILE*     4.5     8.5    -      -       +      +
    359C  LYS*     1.3    76.4    -      -       -      +
    361C  LYS*     1.3    67.3    +      -       -      +
    362C  GLY      3.8     0.7    +      -       -      -
    363C  ILE*     3.5    36.9    -      -       +      +
    366C  VAL*     4.1    10.3    -      -       +      -
    369C  LEU*     5.0     0.7    -      -       +      -
    396C  PRO*     2.9    36.4    +      -       -      +
    398C  LEU*     3.8    29.2    -      -       +      -
    421C  ILE*     3.9    34.5    -      -       +      -
----------------------------------------------------------
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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