Contacts of the strand formed by residues 113 - 118 (chain H) in PDB entry 5IYB


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 113 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99H  ILE*     2.6    27.2    +      -       -      +
    100H  GLU*     3.3    18.4    -      -       -      +
    101H  GLY*     4.9     0.6    -      -       -      +
    112H  LEU*     1.3    73.1    -      -       -      +
    114H  ALA*     1.3    57.9    +      -       -      +
    115H  TYR*     4.1     9.7    -      -       -      -
    124H  ARG*     4.4    13.0    -      -       -      -
    125H  LEU      3.3    10.3    -      -       -      -
    126H  GLN*     3.0    37.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96H  VAL*     4.7     7.2    -      -       +      -
     98H  ARG      4.0     7.0    -      -       -      +
     99H  ILE*     4.0    11.0    -      -       +      +
    112H  LEU*     3.3    16.7    -      -       +      +
    113H  SER*     1.3    73.6    -      -       -      +
    115H  TYR*     1.3    61.0    +      -       -      +
    116H  VAL*     4.5     6.4    +      -       +      +
    124H  ARG*     3.7     3.3    -      -       -      +
    125H  LEU*     3.1    40.3    +      -       +      +
    130H  ASN*     4.6    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 115 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    620A  HIS      5.2     0.7    +      -       -      -
    621A  ILE*     4.5    26.0    +      -       +      +
    623A  PRO*     4.8    11.0    -      -       +      -
     96H  VAL*     3.1    20.8    -      -       -      +
     97H  TYR*     3.2    31.1    +      +       +      -
     98H  ARG*     3.1    54.4    +      -       +      +
     99H  ILE      4.6     0.4    -      -       -      -
    100H  GLU*     4.4    14.0    +      -       +      +
    113H  SER*     4.1    19.0    -      -       -      -
    114H  ALA*     1.3    71.6    -      -       -      +
    116H  VAL*     1.3    62.6    +      -       -      +
    123H  MET      3.5     5.8    -      -       -      +
    124H  ARG*     3.3    48.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 116 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60H  ILE*     6.3     1.8    -      -       +      -
     95H  LYS      3.3    23.6    -      -       -      +
     96H  VAL*     4.0    16.2    -      -       +      -
     97H  TYR*     3.8     5.8    -      -       -      -
    114H  ALA*     4.9     7.2    -      -       +      +
    115H  TYR*     1.3    81.1    -      -       -      +
    117H  SER*     1.3    63.4    +      -       -      +
    118H  TYR*     3.3    34.8    -      -       +      +
    121H  LEU      3.9     0.2    -      -       -      +
    122H  LEU*     3.5     3.3    -      -       -      -
    123H  MET*     2.9    52.8    +      -       +      +
    125H  LEU*     6.0     3.4    -      -       +      +
    141H  VAL*     4.3     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 117 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    636A  ILE*     3.1    30.1    +      -       -      -
     94H  GLY*     3.2     2.6    -      -       -      -
     95H  LYS*     2.9    37.6    +      -       -      +
     97H  TYR*     3.6    24.0    -      -       -      -
    116H  VAL*     1.3    73.6    -      -       -      +
    118H  TYR*     1.3    62.5    +      -       -      +
    119H  GLY      3.6     4.0    +      -       -      -
    120H  GLY      3.5    10.2    +      -       -      -
    121H  LEU      3.6     3.6    -      -       -      -
    122H  LEU*     3.7     8.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 118 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578A  ALA*     4.1     9.7    -      -       -      +
     41H  LEU*     4.3     2.2    -      -       +      -
     60H  ILE*     5.1     2.6    -      -       -      +
     92H  MET*     4.0    34.9    -      -       +      +
     93H  TYR      3.4    29.4    -      -       -      +
     94H  GLY*     3.4    10.1    -      -       -      -
    116H  VAL*     3.3    27.6    -      -       +      +
    117H  SER*     1.3    70.4    +      -       -      +
    119H  GLY*     1.3    56.9    +      -       -      +
    120H  GLY      3.1     2.9    -      -       -      -
    121H  LEU*     2.8    50.8    +      -       +      +
    123H  MET*     3.2    35.6    -      -       +      +
    141H  VAL*     3.6    17.5    -      -       +      +
    143H  LEU*     3.4    35.3    -      -       +      +
----------------------------------------------------------
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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