Contacts of the strand formed by residues 273 - 281 (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 SER 273 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233B  VAL      3.6     0.2    -      -       -      +
    234B  THR*     3.4     3.8    -      -       -      -
    235B  GLY      2.7    38.7    +      -       -      +
    236B  GLN      4.8     0.7    -      -       -      -
    237B  LEU*     3.5    20.4    -      -       -      +
    264B  VAL      3.3    15.7    -      -       -      -
    265B  GLU*     3.8     3.6    -      -       -      -
    266B  ASN*     3.0    20.5    +      -       -      -
    270B  LYS*     2.9    20.8    +      -       -      -
    272B  ARG*     1.3    74.6    -      -       -      +
    274B  THR*     1.3    65.7    +      -       -      +
    275B  LEU*     4.2     1.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 274 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232B  ASN*     3.9    14.8    -      -       -      +
    233B  VAL      3.1     9.9    -      -       -      +
    234B  THR*     4.3    12.1    -      -       +      +
    263B  SER*     3.5     2.3    -      -       -      -
    264B  VAL*     3.1    45.3    +      -       -      +
    272B  ARG      5.0     3.6    -      -       -      +
    273B  SER*     1.3    80.2    -      -       -      +
    275B  LEU*     1.3    64.6    +      -       -      +
    276B  ILE*     4.0     9.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 275 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ARG*     3.2    31.4    -      -       -      +
    231B  CYS      3.5     2.0    -      -       -      +
    233B  VAL*     2.9    54.6    +      -       +      +
    235B  GLY      5.2     1.1    -      -       -      +
    236B  GLN      3.8    13.2    -      -       -      +
    237B  LEU*     4.3     4.3    -      -       +      -
    239B  ASP*     3.1    38.8    -      -       +      +
    240B  ILE*     4.2     7.6    -      -       -      +
    241B  ALA*     4.1    12.1    -      -       +      +
    262B  TYR      3.7     4.3    -      -       -      +
    263B  SER*     3.4    10.3    -      -       -      +
    273B  SER*     5.0     2.9    -      -       -      +
    274B  THR*     1.3    77.9    -      -       -      +
    276B  ILE*     1.3    67.1    +      -       -      +
    277B  THR*     4.2     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 276 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230B  ILE*     3.9    21.8    -      -       +      -
    231B  CYS      3.5     1.6    -      -       -      +
    232B  ASN*     3.8    31.0    -      -       +      +
    260B  ASP      3.7     1.0    -      -       -      +
    261B  TYR*     3.7     1.6    -      -       -      +
    262B  TYR*     2.8    53.3    +      -       +      +
    264B  VAL*     5.3     7.0    -      -       +      -
    274B  THR*     4.3    14.6    -      -       -      +
    275B  LEU*     1.3    84.6    -      -       -      +
    277B  THR*     1.3    63.2    +      -       -      +
    278B  VAL*     4.0    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 277 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230B  ILE*     3.7     0.3    -      -       -      -
    231B  CYS*     3.0    34.1    +      -       -      -
    241B  ALA*     2.7    44.3    +      -       -      +
    243B  TRP*     3.2    17.9    +      -       +      -
    259B  GLU*     3.4    26.5    -      -       +      +
    260B  ASP      3.6     3.4    -      -       -      +
    261B  TYR*     3.4    22.6    -      -       +      +
    275B  LEU*     5.3     0.2    -      -       -      +
    276B  ILE*     1.3    73.8    +      -       -      +
    278B  VAL*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 278 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228B  GLN*     3.7    36.6    -      -       +      +
    229B  LEU      3.7     2.7    -      -       -      -
    230B  ILE*     4.1    20.9    -      -       +      +
    243B  TRP*     4.5     2.2    -      -       -      -
    258B  GLY      3.3     2.1    -      -       -      +
    259B  GLU*     3.1     7.9    -      -       -      -
    260B  ASP*     2.9    48.1    +      -       +      +
    262B  TYR*     4.5    11.7    -      -       +      -
    276B  ILE*     4.0    19.5    -      -       +      -
    277B  THR*     1.3    74.1    -      -       -      +
    279B  LEU*     1.3    61.0    +      -       -      +
    280B  ASN*     3.8    12.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 279 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227B  ILE      3.9     0.5    -      -       -      +
    228B  GLN*     3.3     5.4    -      -       -      +
    229B  LEU*     2.8    65.2    +      -       +      +
    243B  TRP*     3.7    28.5    -      -       +      +
    250B  ILE*     4.1    21.3    -      -       +      -
    257B  LEU*     4.4     6.3    -      -       +      -
    258B  GLY      3.5    21.8    -      -       -      +
    259B  GLU*     4.6     3.1    -      -       +      +
    277B  THR      3.8     0.4    +      -       -      -
    278B  VAL*     1.3    71.2    -      -       -      +
    280B  ASN*     1.3    67.5    -      -       -      +
    281B  ILE*     3.9    12.9    +      -       +      +
    293B  PHE*     3.7    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 280 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226B  GLN*     5.8     4.1    +      -       -      +
    227B  ILE      3.8     3.8    -      -       -      +
    228B  GLN*     3.0    36.5    +      -       -      +
    256B  VAL      3.0    13.3    -      -       -      +
    257B  LEU*     3.5     1.6    -      -       -      -
    258B  GLY*     2.9    35.6    +      -       -      +
    259B  GLU      4.9     0.2    -      -       -      -
    260B  ASP*     4.4    11.5    +      -       -      +
    278B  VAL*     3.8    16.8    +      -       -      +
    279B  LEU*     1.3    74.3    -      -       -      +
    281B  ILE*     1.3    61.3    +      -       -      +
    282B  SER*     3.8     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 281 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226B  GLN*     3.0     8.5    +      -       -      +
    227B  ILE*     3.0    63.3    +      -       +      +
    229B  LEU*     4.2     4.7    -      -       +      -
    256B  VAL      3.3     3.6    -      -       -      +
    257B  LEU*     3.6    14.4    -      -       +      -
    279B  LEU*     3.9    16.8    -      -       +      +
    280B  ASN*     1.3    73.7    -      -       -      +
    282B  SER*     1.3    61.4    +      -       -      +
    283B  GLU      3.4    13.2    -      -       -      +
    284B  ILE*     4.3     3.8    -      -       +      -
    288B  PHE*     3.6    31.6    -      -       +      -
    293B  PHE*     3.6    32.5    -      -       +      -
    310B  LEU*     4.4     3.8    -      -       +      -
----------------------------------------------------------
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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