Contacts of the strand formed by residues 74 - 80 (chain B) in PDB entry 4NZD


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 ILE 74 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  TRP*     3.4     4.1    -      -       -      -
     33B  GLN*     2.5    60.2    +      -       +      +
     34B  ASP      4.0    14.8    -      -       -      +
     35B  GLN*     4.6     7.9    -      -       -      +
     37B  GLU*     5.2    10.1    -      -       +      -
     72B  ASP      3.7    10.1    -      -       -      +
     73B  ASP*     1.3    81.4    -      -       -      +
     75B  PHE*     1.3    61.2    +      -       -      +
     92B  SER*     3.9    25.8    -      -       -      +
     93B  PHE      3.5    12.1    -      -       -      +
     94B  LEU*     3.8    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 75 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  CYS*     3.6    37.7    -      -       +      -
      7B  TYR      4.6     2.7    -      -       -      -
      8B  THR*     4.9     9.4    -      -       +      -
     14B  VAL*     4.3    10.8    -      -       +      -
     30B  LEU*     3.5    35.4    -      -       +      -
     31B  THR      3.5     3.1    -      -       -      +
     32B  TRP*     3.5    46.2    -      +       +      -
     74B  ILE*     1.3    73.7    -      -       -      +
     76B  SER*     1.3    59.9    +      -       -      +
     77B  VAL*     4.5     2.2    -      -       +      -
     93B  PHE*     2.9    69.8    +      +       +      -
     95B  LEU*     5.0     4.3    -      -       -      -
     98B  SER*     4.4    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 76 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  LEU*     3.3     5.4    -      -       -      +
     31B  THR      3.0    30.3    +      -       -      -
     33B  GLN*     2.8    27.9    +      -       -      -
     74B  ILE*     4.2     0.3    -      -       -      +
     75B  PHE*     1.3    73.4    -      -       -      +
     77B  VAL*     1.3    65.8    +      -       -      +
     78B  GLN*     3.5    17.4    +      -       -      -
     89B  GLU*     4.0    11.2    +      -       -      -
     91B  GLY      3.4    10.8    -      -       -      -
     92B  SER*     3.1    21.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 77 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     3.7    22.9    -      -       +      -
      6B  CYS*     4.0    15.5    -      -       -      -
     16B  CYS*     4.3     5.4    -      -       -      -
     28B  LEU*     3.6    33.0    -      -       +      -
     29B  THR      3.4    10.3    -      -       -      +
     30B  LEU*     4.5    13.7    -      -       +      -
     48B  LEU*     5.0     2.5    -      -       +      -
     75B  PHE*     4.5     0.7    -      -       +      -
     76B  SER*     1.3    79.9    -      -       -      +
     78B  GLN*     1.3    64.6    +      -       -      +
     89B  GLU*     2.7    21.8    -      -       -      +
     90B  CYS*     3.1    15.7    +      -       +      +
     91B  GLY      3.2     6.0    +      -       -      +
     93B  PHE*     4.0    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  THR      3.3     3.8    -      -       -      +
     28B  LEU*     3.5     5.7    -      -       -      +
     29B  THR*     2.9    63.5    +      -       -      +
     31B  THR*     3.2    34.0    +      -       -      +
     33B  GLN*     4.9     0.4    -      -       -      +
     76B  SER*     3.5    24.3    +      -       -      +
     77B  VAL*     1.3    77.4    -      -       -      +
     79B  ILE*     1.3    64.4    +      -       -      +
     80B  THR*     4.2     2.7    -      -       -      +
     87B  SER*     4.6    10.8    -      -       -      +
     88B  GLN      3.3    13.5    -      -       -      +
     89B  GLU*     4.0    13.9    +      -       -      +
     90B  CYS*     4.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  CYS*     4.0     6.3    -      -       -      -
      2B  PRO*     4.1    10.5    -      -       +      -
     18B  LEU*     4.7     7.2    -      -       +      -
     23B  LEU*     4.1    13.7    -      -       +      -
     26B  SER*     4.2    18.2    -      -       -      -
     27B  THR      3.3     5.8    -      -       -      +
     28B  LEU*     3.7    19.1    -      -       +      -
     78B  GLN*     1.3    74.3    -      -       -      +
     80B  THR*     1.3    67.4    +      -       -      +
     86B  TYR      3.9     0.5    -      -       -      +
     87B  SER*     3.4     4.2    +      -       -      -
     88B  GLN*     2.8    48.9    +      -       +      +
     90B  CYS*     3.4    24.8    -      -       -      -
    159C  VAL*     3.7    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  ARG*     4.8     4.7    -      -       -      +
     26B  SER*     3.2     5.4    -      -       -      -
     27B  THR*     2.6    48.4    +      -       -      -
     29B  THR*     5.0     9.0    +      -       -      +
     78B  GLN*     5.2     1.9    -      -       -      +
     79B  ILE*     1.3    77.5    +      -       -      +
     81B  ASP*     1.3    72.8    +      -       -      +
     84B  GLY*     3.5    22.2    -      -       -      +
     86B  TYR      3.3    15.8    +      -       -      +
     87B  SER*     4.1    10.7    +      -       -      -
----------------------------------------------------------
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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