Contacts of the strand formed by residues 213 - 218 (chain K) in PDB entry 3IT8


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 ILE 213 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98K  TYR*     4.3    16.2    -      -       +      +
    100K  THR*     3.9    19.5    -      -       +      +
    103K  LEU*     3.5    35.0    -      -       +      -
    211K  ASP*     6.2     0.2    -      -       +      -
    212K  VAL*     1.3    86.8    -      -       -      +
    214K  THR*     1.3    71.5    +      -       -      +
    215K  LYS*     4.9     4.7    -      -       +      -
    245K  PRO*     4.7    11.2    -      -       +      +
    246K  GLY*     4.4    19.1    -      -       -      +
    252K  TRP*     4.0    20.9    -      -       +      +
    283K  VAL*     3.8     1.2    -      -       -      -
    284K  PHE*     2.8    40.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 214 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202K  CYS*     4.2     2.9    -      -       -      +
    204K  VAL*     5.5     0.2    -      -       -      +
    212K  VAL*     5.4     0.4    -      -       -      -
    213K  ILE*     1.3    79.8    -      -       -      +
    215K  LYS*     1.3    64.7    +      -       -      +
    216K  TRP*     3.8    10.4    -      -       +      +
    239K  ARG*     5.5     3.8    -      -       -      +
    252K  TRP*     3.5    28.4    -      -       +      -
    265K  LEU*     5.1     8.7    -      -       -      +
    267K  ASP*     2.8    34.8    -      -       -      +
    281K  CYS*     3.3    26.2    -      -       -      -
    282K  VAL      3.4     4.1    +      -       -      -
    283K  VAL*     4.2     7.0    -      -       -      +
    284K  PHE*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 215 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103K  LEU*     4.2    23.3    -      -       -      +
    213K  ILE*     4.9     3.6    -      -       +      -
    214K  THR*     1.3    79.1    -      -       -      +
    216K  TRP*     1.3    62.0    +      -       -      +
    217K  ILE*     4.5     9.2    -      -       +      -
    228K  TYR*     3.9    21.0    +      -       +      +
    236K  GLU*     3.2    43.3    +      -       +      +
    280K  VAL      3.6     0.2    -      -       -      +
    281K  CYS*     3.8     0.9    -      -       -      -
    282K  VAL*     2.8    46.9    +      -       +      +
    284K  PHE*     3.4    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 216 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188K  VAL*     4.1     9.6    -      -       +      -
    200K  LEU*     3.8    33.2    -      -       +      -
    202K  CYS*     3.4    38.4    -      -       +      -
    214K  THR*     3.8     8.2    -      -       +      +
    215K  LYS*     1.3    74.4    -      -       -      +
    217K  ILE*     1.3    60.7    +      -       -      +
    236K  GLU      2.7    33.8    +      -       -      +
    237K  TRP*     3.4    20.2    +      -       +      +
    239K  ARG*     5.2     8.1    -      -       +      -
    267K  ASP*     2.7    34.7    +      -       -      -
    269K  VAL*     3.0    31.6    -      -       +      +
    279K  PRO*     3.7    30.7    -      -       +      -
    280K  VAL      3.5    12.6    -      -       -      -
    281K  CYS*     3.8    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 217 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215K  LYS*     4.5     9.9    -      -       +      +
    216K  TRP*     1.3    82.4    -      -       -      +
    218K  GLU*     1.3    73.7    +      -       -      +
    221K  HIS*     3.9    14.8    -      -       +      -
    222K  PHE*     3.7    19.3    -      -       +      -
    228K  TYR*     4.0    16.4    -      -       +      -
    234K  TYR*     3.8    25.1    -      -       +      -
    235K  PRO      3.5    21.3    -      -       -      +
    236K  GLU*     4.2     8.3    -      -       +      +
    279K  PRO*     3.8     4.3    -      -       -      -
    280K  VAL*     2.8    40.6    +      -       +      +
    282K  VAL*     3.9    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 218 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217K  ILE*     1.3    76.5    -      -       -      +
    219K  SER*     1.3    67.1    +      -       -      +
    220K  GLU*     3.0    22.2    +      -       +      +
    221K  HIS*     3.1    34.8    +      -       +      +
    222K  PHE*     4.0     0.9    -      -       -      -
    235K  PRO      5.1     0.4    +      -       -      -
    237K  TRP*     3.7    36.4    -      -       +      +
    275K  MET*     3.8    21.7    -      -       +      +
    276K  SER*     3.5    16.0    +      -       -      -
    277K  SER*     3.5    15.5    +      -       -      +
    278K  GLN      4.6     3.4    -      -       -      +
    279K  PRO*     3.9     9.1    -      -       -      +
----------------------------------------------------------
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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