Contacts of the strand formed by residues 114 - 118 (chain N) in PDB entry 3INU


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 SER 114 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132M  SER*     4.7    14.3    +      -       -      -
    112N  ALA      4.7     2.1    +      -       -      -
    113N  PRO*     1.3    72.3    -      -       -      +
    115N  VAL*     1.3    60.3    +      -       -      +
    116N  PHE*     3.8    25.0    -      -       -      -
    135N  LEU      3.3     4.2    -      -       -      +
    136N  LEU*     3.5     0.5    -      -       -      -
    137N  ASN*     2.9    41.9    +      -       -      +
    138N  ASN*     5.7     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 115 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113N  PRO*     3.9    20.4    +      -       +      +
    114N  SER*     1.3    75.1    -      -       -      +
    116N  PHE*     1.3    74.2    +      -       -      +
    134N  CYS*     3.9    25.4    -      -       -      -
    135N  LEU      3.4     3.4    -      -       -      +
    136N  LEU*     4.6     2.2    -      -       +      -
    194N  CYS*     4.4     0.9    -      -       +      -
    196N  VAL*     4.0    25.4    -      -       +      -
    201N  LEU*     5.5     0.2    -      -       +      -
    205N  VAL*     4.1    23.1    -      -       +      -
    207N  LYS*     3.3    47.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 116 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129M  LYS      4.4     3.4    -      -       -      -
    130M  SER*     3.3    47.1    -      -       -      +
    131M  THR      4.1     1.6    -      -       -      -
    132M  SER*     4.2    18.6    -      -       -      -
    137M  THR*     5.0     4.0    -      -       -      -
    138M  ALA      5.2     1.1    -      -       -      -
    139M  ALA*     3.8    15.9    -      -       +      -
    192M  THR*     5.1     3.6    -      -       +      -
    114N  SER*     3.8    34.8    -      -       -      -
    115N  VAL*     1.3    84.1    -      -       -      +
    117N  ILE*     1.3    60.6    +      -       -      +
    118N  PHE*     4.1    17.9    -      -       +      -
    133N  VAL      3.9     0.3    -      -       -      +
    134N  CYS*     3.3     5.9    -      -       -      -
    135N  LEU*     2.8    56.2    +      -       +      +
    137N  ASN*     4.2    14.4    -      -       +      -
    207N  LYS*     4.9     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 117 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127M  SER*     4.7     3.8    +      -       -      -
    129M  LYS*     4.0    31.8    +      -       +      +
    130M  SER*     3.9     9.4    +      -       -      -
    116N  PHE*     1.3    74.5    -      -       -      +
    118N  PHE*     1.3    76.5    +      -       -      +
    119N  PRO*     4.2     4.9    -      -       +      +
    132N  VAL*     3.7    25.6    -      -       +      -
    133N  VAL      3.5     2.9    -      -       -      +
    148N  TRP*     4.1    15.9    -      -       +      -
    192N  TYR      4.5     2.0    -      -       -      +
    194N  CYS*     3.6    14.1    -      -       +      -
    207N  LYS*     3.5    35.0    -      -       +      +
    208N  SER      4.2    10.1    -      -       -      +
    209N  PHE*     3.8    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 118 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124M  LEU*     3.6    55.0    -      -       +      -
    125M  ALA      3.2    29.2    -      -       -      -
    130M  SER*     4.0     9.0    -      -       -      -
    139M  ALA*     3.4    32.3    -      -       +      -
    140M  LEU*     4.4     3.6    -      -       -      -
    190M  VAL*     5.4     4.3    -      -       +      -
    116N  PHE*     4.1    18.4    -      -       +      -
    117N  ILE*     1.3    80.3    -      -       -      +
    119N  PRO*     1.3    72.2    -      -       +      +
    131N  SER      4.2     0.7    -      -       -      +
    132N  VAL*     3.4     8.0    -      -       -      +
    133N  VAL*     2.7    47.3    +      -       +      +
    135N  LEU*     4.3    15.0    -      -       +      -
----------------------------------------------------------
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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