Contacts of the strand formed by residues 117 - 120 (chain H) in PDB entry 1N33


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 GLY 117 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642A    A      3.9    13.2    +      -       -      -
    114H  THR*     2.6    42.6    +      -       -      -
    115H  SER      3.4     0.2    -      -       -      -
    116H  LYS*     1.3    80.4    -      -       -      +
    118H  VAL*     1.3    63.9    +      -       -      -
    119H  LEU*     2.8    13.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 118 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642A    A      3.7    15.6    +      -       -      +
     31H  PHE*     3.4    34.3    -      -       +      -
     34H  GLU*     4.1    32.3    +      -       +      +
     35H  ILE*     4.6     2.7    -      -       -      -
     38H  ILE*     4.1    23.6    -      -       +      +
     41H  ARG*     5.7     0.3    +      -       -      -
    111H  ILE*     3.7    25.4    -      -       +      -
    112H  LEU      3.1     5.4    -      -       -      +
    113H  SER*     3.8     9.0    -      -       -      +
    117H  GLY*     1.3    72.6    -      -       -      -
    119H  LEU*     1.3    70.3    +      -       -      +
    123H  GLU*     4.7     0.2    -      -       -      +
    134H  ILE*     4.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 119 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ILE*     4.5     7.0    -      -       -      -
    110H  ALA      4.4     0.2    -      -       -      -
    111H  ILE*     4.6     2.9    -      -       -      -
    112H  LEU*     2.6    38.4    +      -       -      +
    114H  THR*     3.7    12.8    -      -       +      +
    116H  LYS*     4.3     8.3    -      -       +      +
    117H  GLY*     2.8    39.7    -      -       -      +
    118H  VAL*     1.3    77.8    -      -       -      +
    120H  THR*     1.3    64.1    +      -       -      +
    123H  GLU*     3.0    23.3    -      -       +      +
    124H  ALA*     3.1    45.5    -      -       +      +
    127H  LEU*     3.8    15.5    -      -       +      -
    129H  VAL*     5.2     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 120 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ILE*     4.1    17.8    -      -       +      +
     41H  ARG*     4.6     0.7    -      -       -      +
     42H  GLU*     3.5    29.2    -      -       +      +
    109H  ILE*     5.1     7.0    -      -       +      -
    110H  ALA      3.4     8.7    -      -       -      -
    111H  ILE*     4.8     0.9    -      -       -      +
    119H  LEU*     1.3    77.2    -      -       -      +
    121H  ASP*     1.3    63.5    +      -       -      +
    122H  ARG*     3.6     4.8    +      -       -      +
    123H  GLU*     2.8    48.0    +      -       -      +
    124H  ALA*     2.8    26.2    +      -       -      +
----------------------------------------------------------
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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