Contacts of the strand formed by residues 293 - 299 (chain B) in PDB entry 1ITB


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 PHE 293 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229B  LEU*     3.9    18.6    -      -       +      -
    243B  TRP*     3.3    21.5    -      +       +      -
    244B  LYS      3.9     4.0    -      -       -      -
    245B  TRP*     3.3    40.6    -      +       +      -
    250B  ILE*     5.4     2.0    -      -       +      -
    257B  LEU*     4.1    14.8    -      -       +      -
    279B  LEU*     3.7    21.1    -      -       +      -
    281B  ILE*     3.6    23.8    -      -       +      -
    288B  PHE*     3.7    28.3    -      +       +      -
    291B  HIS      4.7     1.8    -      -       -      -
    292B  PRO*     1.3    70.5    -      -       -      +
    294B  THR*     1.3    59.1    +      -       -      +
    307B  TYR*     3.3     0.8    -      -       -      -
    308B  ILE      2.9    33.4    +      -       -      +
    310B  LEU*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 294 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242B  TYR      4.0     0.2    -      -       -      +
    243B  TRP*     3.1     8.8    -      -       -      -
    244B  LYS      2.9    34.7    +      -       -      +
    246B  ASN      5.5     1.2    +      -       -      -
    292B  PRO*     3.8    12.1    +      -       -      +
    293B  PHE*     1.3    74.1    -      -       -      +
    295B  CYS*     1.3    62.0    +      -       -      +
    296B  PHE*     4.0    20.8    -      -       +      -
    305B  ALA*     4.1    13.7    -      -       +      -
    306B  ALA      3.5    26.2    -      -       -      +
    307B  TYR*     3.8    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 295 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211B  ILE*     3.2    19.7    -      -       +      +
    214B  PRO*     4.0     4.7    -      -       +      -
    231B  CYS*     2.0    50.0    -      -       +      -
    233B  VAL*     5.0     0.2    -      -       -      -
    241B  ALA*     4.7     1.8    -      -       -      -
    242B  TYR      3.5    15.7    -      -       -      -
    243B  TRP*     3.8    16.2    -      -       +      -
    294B  THR*     1.3    74.5    -      -       -      +
    296B  PHE*     1.3    72.8    +      -       -      +
    305B  ALA*     3.5     2.8    -      -       -      -
    306B  ALA      2.8    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 296 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  ILE      3.5     1.4    -      -       -      +
    241B  ALA*     3.2     7.3    -      -       -      -
    242B  TYR*     2.8    65.1    +      +       +      +
    244B  LYS*     3.4    53.4    -      -       +      -
    294B  THR*     4.0    24.5    -      -       +      -
    295B  CYS*     1.3    77.0    -      -       -      +
    297B  ALA*     1.3    59.5    +      -       -      +
    298B  LYS      3.9     0.2    -      -       -      -
    303B  ILE*     3.9    19.7    -      -       +      -
    304B  ASP      3.2    12.8    -      -       -      +
    305B  ALA*     3.7    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 297 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209B  PRO*     3.3    30.6    -      -       +      +
    211B  ILE*     3.6    25.7    -      -       +      +
    233B  VAL*     4.1    13.5    -      -       +      -
    240B  ILE      3.4     6.7    -      -       -      -
    296B  PHE*     1.3    72.0    -      -       -      +
    298B  LYS*     1.3    58.2    +      -       -      +
    303B  ILE*     3.2     5.3    -      -       -      -
    304B  ASP*     2.8    39.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 298 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  GLU*     3.1    38.2    +      -       -      +
     53A  ASN*     4.5    12.7    -      -       -      +
     55A  LYS      4.5     2.2    +      -       -      -
     56A  ILE*     4.1    23.8    -      -       +      +
    209B  PRO*     4.1     1.7    -      -       -      +
    238B  SER      4.6     0.5    -      -       -      +
    239B  ASP*     3.6     2.9    -      -       -      +
    240B  ILE*     3.0    55.9    +      -       +      +
    242B  TYR*     3.1    32.8    +      -       +      -
    296B  PHE      3.9     0.8    -      -       -      -
    297B  ALA*     1.3    76.1    -      -       -      +
    299B  ASN*     1.3    78.4    +      -       -      +
    302B  GLY      4.1     2.7    -      -       -      -
    303B  ILE*     3.9    34.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  ASN*     4.6     4.9    +      -       -      +
     56A  ILE*     4.3    11.3    -      -       -      +
    207B  THR      3.0    27.5    +      -       -      +
    208B  ARG*     4.0     0.9    -      -       -      +
    209B  PRO*     3.7     8.1    -      -       -      +
    236B  GLN*     6.1     0.8    -      -       -      +
    238B  SER      4.8     5.6    -      -       -      +
    239B  ASP*     3.0    31.5    +      -       -      +
    298B  LYS*     1.3    82.6    -      -       -      +
    300B  THR*     1.3    63.8    +      -       -      +
    301B  HIS*     2.9    28.2    +      -       -      +
    302B  GLY      3.2    21.9    +      -       -      +
----------------------------------------------------------
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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