Contacts of the strand formed by residues 413 - 421 (chain G) in PDB entry 1RZK


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 413 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332G  ASN*     4.5    13.2    -      -       +      +
    333G  LEU      3.2    14.1    +      -       -      +
    334G  SER*     4.5     7.1    -      -       -      +
    335G  LYS*     4.0     9.5    +      -       -      +
    411G  GLY*     4.5     2.6    -      -       -      -
    412G  ARG*     1.3   115.5    +      -       -      +
    414G  ILE*     1.3    66.5    +      -       -      +
    415G  THR*     3.7     7.0    +      -       -      +
    795G  NAG      3.7    23.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 414 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331G  CYS      3.4     1.0    -      -       -      +
    332G  ASN*     3.2     5.7    -      -       -      +
    333G  LEU*     2.6    44.0    +      -       +      +
    335G  LYS*     3.6    36.3    -      -       +      +
    338G  TRP*     3.6    35.2    -      -       +      -
    389G  GLN*     3.9    22.7    -      -       +      +
    390G  LEU*     3.7    18.2    -      -       +      -
    407G  LEU*     6.1     3.8    -      -       +      -
    413G  ASN*     1.3    72.0    -      -       -      +
    415G  THR*     1.3    61.3    +      -       -      +
    416G  LEU*     3.3    27.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 415 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330G  HIS*     3.5    41.1    -      -       +      +
    331G  CYS      3.2     1.6    -      -       -      -
    332G  ASN*     2.9    14.3    +      -       -      +
    389G  GLN*     3.1    23.1    +      -       -      +
    413G  ASN*     3.7     7.4    +      -       -      +
    414G  ILE*     1.3    75.8    -      -       -      +
    416G  LEU*     1.3    63.3    -      -       -      +
    417G  PRO*     3.5     4.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 416 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294G  ILE*     4.5    17.7    -      -       +      -
    330G  HIS*     3.1     4.4    -      -       -      +
    331G  CYS*     2.8    37.3    +      -       +      +
    333G  LEU*     5.1     3.6    -      -       +      -
    374G  HIS*     5.4     2.7    -      -       +      -
    385G  CYS*     4.2    17.3    -      -       +      -
    386G  ASN      3.1    22.7    -      -       -      +
    387G  SER*     4.7     4.7    -      -       -      -
    389G  GLN*     4.0    14.8    -      -       +      +
    390G  LEU*     3.5    37.0    -      -       +      -
    414G  ILE*     3.3    28.0    -      -       +      -
    415G  THR*     1.3    72.5    -      -       -      +
    417G  PRO*     1.4    61.5    -      -       -      +
    418G  CYS*     3.0     9.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 417 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329G  GLY      3.9     7.2    -      -       -      +
    330G  HIS*     4.4     2.2    -      -       +      -
    384G  TYR      4.1     1.2    -      -       -      +
    385G  CYS*     4.0     0.2    -      -       -      -
    386G  ASN*     3.3    40.4    +      -       +      +
    389G  GLN*     3.8     7.4    -      -       -      +
    415G  THR*     3.5     8.9    -      -       +      +
    416G  LEU*     1.4    79.1    -      -       -      +
    418G  CYS*     1.3    63.5    +      -       -      +
    419G  ARG*     5.5     0.2    -      -       -      +
    886G  NAG      3.9    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 418 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329G  GLY*     2.9    25.3    +      -       -      +
    330G  HIS*     3.6    21.8    -      -       -      +
    331G  CYS*     4.3     0.4    -      -       -      -
    383G  PHE*     3.7    20.2    -      -       +      -
    384G  TYR      3.2    14.6    -      -       -      -
    385G  CYS*     2.0    58.8    -      -       -      +
    416G  LEU      3.0     2.6    +      -       -      +
    417G  PRO*     1.3    75.0    -      -       -      +
    419G  ARG*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 419 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329G  GLY*     5.6     1.1    -      -       -      -
    383G  PHE*     3.5     1.1    -      -       -      -
    384G  TYR*     2.6    48.7    +      -       +      +
    417G  PRO      5.5     0.4    -      -       -      +
    418G  CYS*     1.3    77.9    -      -       -      +
    420G  ILE*     1.3    72.8    +      -       -      +
    421G  LYS*     4.6     9.8    -      -       +      +
     99H  GLU*     2.3    54.9    +      -       -      +
    100H  GLU*     3.0    52.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 420 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298G  GLY*     3.9    19.7    -      -       -      +
    329G  GLY*     6.5     0.4    -      -       -      -
    381G  GLU*     3.6    44.2    -      -       +      +
    382G  PHE      3.4     9.4    -      -       -      +
    383G  PHE*     3.7    33.7    -      -       +      -
    419G  ARG*     1.3    83.6    -      -       -      +
    421G  LYS*     1.3    71.0    +      -       -      +
    422G  GLN*     4.0    16.7    +      -       -      +
    438G  PRO*     4.2    14.8    -      -       +      -
    443G  ILE*     5.3     1.8    -      -       +      -
    100H  GLU*     4.9     7.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 421 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369G  PRO*     3.4    31.2    -      -       +      +
    370G  GLU*     5.2     0.9    -      -       -      +
    381G  GLU*     5.5     0.5    -      -       -      +
    382G  PHE*     3.1    18.7    +      -       -      +
    384G  TYR*     3.7    47.6    -      -       +      -
    419G  ARG*     4.6    14.4    -      -       +      +
    420G  ILE*     1.3    85.0    -      -       -      +
    422G  GLN*     1.3    65.4    +      -       -      +
    423G  ILE      4.0    11.0    -      -       -      +
    424G  ILE*     4.0     8.2    -      -       +      +
    435G  TYR*     5.5     0.7    -      -       -      +
    100H  GLY*     3.0    46.7    -      -       -      +
----------------------------------------------------------
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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