Contacts of the strand formed by residues 195 - 201 (chain A) in PDB entry 1NTZ


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 MET 195 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  GLY      4.0     1.9    -      -       -      +
     23A  LEU*     3.3    17.4    -      -       +      +
     24A  ARG*     3.5     9.2    +      -       -      -
     39A  VAL*     3.7    19.1    -      -       +      -
     40A  TRP      3.1     9.6    -      -       -      +
     41A  ILE*     3.9    19.5    -      -       +      -
    117A  VAL*     3.9    28.7    -      -       +      +
    190A  TYR*     4.2    21.5    -      -       -      +
    191A  LYS      3.8     9.9    -      -       -      +
    192A  ALA*     2.9    23.9    +      -       -      +
    193A  PRO      3.5     0.2    -      -       -      -
    194A  ARG*     1.3    82.2    -      -       -      +
    196A  VAL*     1.3    68.9    +      -       -      +
    216A  PHE*     4.1    11.9    -      -       +      -
    219A  LEU*     4.1    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     4.1     1.3    -      -       -      -
     24A  ARG*     3.4    38.4    -      -       +      +
     26A  ALA*     4.9     3.8    -      -       +      +
     39A  VAL*     3.4     3.9    -      -       -      -
     40A  TRP*     2.8    39.4    +      -       +      +
    195A  MET*     1.3    80.4    -      -       -      +
    197A  LEU*     1.3    72.4    +      -       -      +
    198A  ALA*     3.4     4.1    +      -       +      +
    380A  GLY*     4.2    24.0    -      -       -      +
    383A  LEU*     4.1    22.2    -      -       +      -
    384A  LEU*     3.9    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     4.0    16.4    -      -       +      +
     24A  ARG      2.9    11.0    +      -       -      +
     25A  VAL*     3.5     7.1    -      -       +      +
     26A  ALA      3.0    26.5    +      -       -      +
     37A  VAL*     4.2    16.8    -      -       +      -
     38A  GLY*     3.4    21.1    -      -       -      +
     39A  VAL*     4.2    13.5    -      -       +      +
    110A  VAL*     4.3     9.6    -      -       +      -
    113A  LEU*     4.8     4.3    -      -       +      -
    196A  VAL*     1.3    71.3    -      -       -      +
    198A  ALA*     1.3    58.6    +      -       -      +
    208A  LEU*     3.8    27.5    -      -       +      +
    212A  ALA*     4.0    24.2    -      -       +      -
    216A  PHE*     4.1    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ALA      3.4     3.4    -      -       -      -
     37A  VAL*     3.3     4.3    -      -       -      +
     38A  GLY      2.7    38.7    +      -       -      +
     40A  TRP*     4.1     5.2    -      -       +      -
    196A  VAL*     3.4     3.3    +      -       +      +
    197A  LEU*     1.3    75.2    -      -       -      +
    199A  ALA*     1.3    62.6    +      -       -      +
    208A  LEU*     4.8     0.7    -      -       -      -
    376A  CYS*     3.2    28.5    -      -       -      +
    379A  ILE*     4.1     9.0    -      -       +      -
    380A  GLY*     3.8    21.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ALA      3.1     7.5    +      -       -      -
     27A  SER*     3.4     3.3    -      -       -      -
     28A  GLU      3.4    18.4    +      -       -      -
     36A  THR      3.1    11.9    -      -       -      +
     37A  VAL*     4.0    13.2    -      -       +      -
    106A  LEU*     4.9     0.2    -      -       +      -
    198A  ALA*     1.3    77.1    -      -       -      +
    200A  ALA*     1.3    63.7    +      -       -      +
    203A  LEU*     3.7    21.8    -      -       +      -
    208A  LEU*     3.6    24.5    -      -       +      -
    376A  CYS*     3.7     3.1    -      -       -      -
    379A  ILE*     3.4     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  GLU*     3.6    12.6    -      -       -      +
     35A  CYS*     3.2     5.6    -      -       -      +
     36A  THR      3.0    28.8    +      -       -      +
    199A  ALA*     1.3    79.1    -      -       -      +
    201A  GLY*     1.3    59.5    +      -       -      +
    203A  LEU*     3.8     5.6    -      -       -      +
    372A  THR*     3.3    31.6    -      -       -      +
    375A  VAL*     4.1    15.7    -      -       +      -
    376A  CYS*     3.9    11.4    -      -       -      +
    379A  ILE*     4.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  GLU      3.3     8.5    +      -       -      -
     29A  GLN*     3.4     5.5    -      -       -      -
     30A  SER*     2.8    43.4    +      -       -      +
     34A  THR      3.8    10.8    -      -       -      -
     35A  CYS*     4.3     0.9    -      -       -      -
    200A  ALA*     1.3    73.3    -      -       -      +
    202A  GLY*     1.3    60.6    +      -       -      -
    203A  LEU*     2.9    12.1    +      -       -      +
    372A  THR*     4.0     4.9    -      -       -      -
----------------------------------------------------------
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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