Contacts of the strand formed by residues 49 - 57 (chain R) in PDB entry 1NVU


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 GLU 49 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2R  THR*     4.8     9.2    +      -       -      -
      4R  TYR*     4.2     5.9    +      -       -      -
     45R  VAL*     3.6     1.0    -      -       -      -
     46R  ILE      2.9    31.1    +      -       -      +
     47R  ASP      3.1     3.9    +      -       -      +
     48R  GLY*     1.3    78.6    -      -       -      +
     50R  THR*     1.3    67.6    +      -       -      +
     51R  CYS*     3.7     0.9    +      -       -      -
    164R  ARG*     3.2    47.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 50 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1R  MET*     3.9    32.5    -      -       +      +
      2R  THR*     4.8     3.1    +      -       -      -
     43R  GLN*     3.9    21.8    -      -       +      +
     44R  VAL      3.4    11.2    -      -       -      +
     45R  VAL*     3.4    20.1    -      -       +      +
     48R  GLY      3.9     3.2    +      -       -      -
     49R  GLU*     1.3    79.4    -      -       -      +
     51R  CYS*     1.3    65.1    +      -       -      +
    164R  ARG*     4.9     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 51 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1R  MET*     3.7     9.6    -      -       -      -
      2R  THR*     3.5    16.8    -      -       -      +
      4R  TYR*     3.6    25.6    -      -       +      -
     43R  GLN*     3.4     5.4    -      -       -      +
     44R  VAL*     2.8    46.5    +      -       -      +
     46R  ILE*     4.0     7.6    -      -       -      -
     49R  GLU      4.4     0.9    -      -       -      -
     50R  THR*     1.3    77.0    -      -       -      +
     52R  LEU*     1.3    59.7    +      -       -      +
     53R  LEU*     3.6    24.7    -      -       -      -
    164R  ARG*     3.9    14.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 52 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1R  MET*     3.9    14.1    -      -       +      +
      2R  THR      2.9    12.9    +      -       -      +
      3R  GLU*     3.2    31.3    -      -       +      +
      4R  TYR*     2.7    28.4    +      -       -      +
     41R  ARG*     4.3    21.8    -      -       +      +
     42R  LYS*     3.6    31.0    -      -       -      +
     43R  GLN*     3.9    11.2    -      -       +      +
     51R  CYS*     1.3    73.3    -      -       -      +
     53R  LEU*     1.3    66.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 53 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4R  TYR*     3.7     8.5    -      -       +      -
      6R  LEU*     4.0    19.7    -      -       +      -
     23R  LEU*     4.4    20.0    -      -       +      -
     40R  TYR      3.7     1.2    -      -       -      +
     41R  ARG*     3.2     7.8    -      -       -      +
     42R  LYS*     2.9    37.2    +      -       +      +
     44R  VAL*     3.8    25.6    -      -       +      -
     51R  CYS*     3.6    29.4    -      -       -      -
     52R  LEU*     1.3    76.7    -      -       -      +
     54R  ASP*     1.3    59.2    +      -       -      +
     55R  ILE*     3.9    12.8    -      -       +      +
    156R  PHE*     4.9     3.8    -      -       +      -
    157R  TYR*     4.6    10.8    -      -       +      -
    160R  VAL*     4.0    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 54 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3R  GLU*     3.8    24.0    -      -       +      +
      4R  TYR      2.8    14.8    +      -       -      +
      5R  LYS*     3.4    18.1    -      -       +      -
      6R  LEU*     2.8    27.0    +      -       -      +
     40R  TYR*     3.7     4.4    -      -       -      -
     41R  ARG*     3.0    37.6    +      -       -      +
     52R  LEU      3.8     0.6    +      -       -      -
     53R  LEU*     1.3    73.0    -      -       -      +
     55R  ILE*     1.3    61.4    +      -       -      +
     56R  LEU*     4.0     1.0    +      -       -      +
    911S  HIS*     2.9    29.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 55 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6R  LEU*     3.4    15.5    -      -       +      +
      8R  VAL*     3.9    18.2    -      -       +      -
     20R  THR*     3.8    31.9    -      -       +      +
     23R  LEU*     3.1    36.8    -      -       +      -
     24R  ILE*     3.4    22.9    -      -       +      -
     40R  TYR*     3.0    21.6    +      -       -      +
     53R  LEU*     4.6     6.3    -      -       +      -
     54R  ASP*     1.3    80.3    +      -       -      +
     56R  LEU*     1.3    64.2    +      -       -      +
     57R  ASP      3.8     2.1    +      -       -      -
    156R  PHE*     4.0    13.2    -      -       +      -
    911S  HIS*     3.2    17.8    -      -       -      -
    939S  LYS*     5.8     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 56 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6R  LEU      2.8    13.7    +      -       -      +
      7R  VAL*     3.5    15.8    -      -       +      +
      8R  VAL*     3.0    28.2    +      -       -      +
     54R  ASP*     4.0     1.3    +      -       -      +
     55R  ILE*     1.3    71.9    -      -       -      +
     57R  ASP*     1.3    64.1    +      -       -      +
     58R  THR*     4.2    17.2    +      -       +      +
     71R  TYR*     3.6    52.9    -      -       +      +
     74R  THR*     3.8    11.4    -      -       +      +
    911S  HIS*     3.9    25.8    -      -       +      +
    912S  TYR*     6.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 57 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8R  VAL*     4.6     7.0    -      -       +      +
     16R  LYS*     3.7    17.5    -      -       -      +
     17R  SER*     3.2    21.9    +      -       -      -
     20R  THR*     3.4    33.0    -      -       +      +
     55R  ILE      3.8     3.0    +      -       -      -
     56R  LEU*     1.3    78.3    -      -       -      +
     58R  THR*     1.3    62.4    +      -       -      +
     59R  GLY*     3.0    20.4    +      -       -      -
     61R  GLN*     5.2     0.2    +      -       -      -
    911S  HIS*     5.3     0.2    -      -       -      -
    935S  THR*     3.9     8.0    -      -       -      +
    939S  LYS*     2.8    40.7    +      -       -      +
----------------------------------------------------------
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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