Contacts of the strand formed by residues 778 - 785 (chain B) in PDB entry 1IU1


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 778 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    735B  ILE*     3.5     4.5    -      -       +      +
    736B  GLN*     3.4     5.9    -      -       -      -
    737B  ALA*     2.9    38.5    +      -       +      +
    748B  PHE*     3.7    23.6    -      -       +      -
    765B  PRO*     4.2    10.3    -      -       +      -
    766B  SER*     3.4     7.0    -      -       -      +
    767B  SER*     3.4    33.7    -      -       -      +
    768B  SER      3.7     2.5    -      -       -      -
    769B  ILE      3.3    40.8    -      -       -      +
    770B  VAL*     3.7    17.7    -      -       +      -
    777B  THR*     1.3    73.9    -      -       -      +
    779B  THR*     1.3    70.0    +      -       -      +
    780B  GLN*     4.2     3.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 779 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    734B  THR*     3.6    27.4    -      -       +      -
    735B  ILE      3.4     2.9    -      -       -      -
    736B  GLN*     2.5    23.6    +      -       -      +
    764B  SER      4.4     0.5    -      -       -      +
    765B  PRO*     3.5     0.9    -      -       -      +
    766B  SER*     2.7    42.1    +      -       -      -
    777B  THR*     3.9     5.9    +      -       -      -
    778B  ILE*     1.3    74.1    -      -       -      +
    780B  GLN*     1.3    66.7    +      -       -      +
    781B  VAL*     5.2     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 780 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    734B  THR*     3.6     0.6    -      -       -      -
    735B  ILE*     2.8    49.4    +      -       +      +
    748B  PHE*     5.5     0.7    -      -       -      -
    750B  PHE*     3.5    33.3    +      -       -      +
    762B  LEU*     3.5    31.6    -      -       +      +
    763B  LEU      3.0    28.5    +      -       -      +
    764B  SER      4.5     1.8    -      -       -      -
    765B  PRO*     3.6    33.2    -      -       +      +
    778B  ILE*     5.1     2.5    -      -       +      +
    779B  THR*     1.3    77.5    -      -       -      +
    781B  VAL*     1.3    64.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 781 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732B  VAL*     3.6    27.6    -      -       +      -
    733B  ILE      3.4     3.1    -      -       -      +
    734B  THR*     3.9    22.2    -      -       +      +
    762B  LEU*     3.4     4.9    -      -       -      +
    763B  LEU*     2.9    58.1    +      -       +      +
    764B  SER      4.9     1.0    +      -       -      -
    779B  THR*     5.2     4.3    -      -       +      -
    780B  GLN*     1.3    78.3    -      -       -      +
    782B  ILE*     1.3    67.1    +      -       -      +
    783B  LYS*     4.4     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 782 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    719B  PHE*     4.8     0.9    -      -       +      -
    732B  VAL*     3.6     2.3    -      -       -      -
    733B  ILE*     2.7    53.2    +      -       +      +
    735B  ILE*     3.9    17.9    -      -       +      -
    750B  PHE*     3.4    33.7    -      -       +      -
    752B  ALA*     4.3     2.9    -      -       +      -
    760B  LEU*     3.3    38.8    -      -       +      -
    761B  GLN      3.3     3.6    -      -       -      +
    762B  LEU*     3.5    16.8    -      -       +      -
    780B  GLN      4.7     0.7    -      -       -      +
    781B  VAL*     1.3    73.8    -      -       -      +
    783B  LYS*     1.3    63.3    +      -       -      +
    784B  VAL*     4.2    10.3    -      -       +      -
    794B  MET*     4.2    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 783 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    730B  VAL*     4.6    14.1    -      -       +      -
    731B  THR      3.8     3.4    -      -       -      -
    732B  VAL*     4.5    17.7    -      -       +      -
    759B  GLN      3.8     0.2    -      -       -      +
    760B  LEU*     3.3     5.7    -      -       -      +
    761B  GLN*     2.7    77.2    +      -       +      +
    763B  LEU*     4.0    24.3    -      -       +      +
    781B  VAL*     4.4    11.2    -      -       +      -
    782B  ILE*     1.3    76.0    -      -       -      +
    784B  VAL*     1.3    63.6    +      -       -      +
    785B  LEU      4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 784 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    729B  SER      3.5     2.3    -      -       -      +
    730B  VAL*     3.3     6.9    -      -       -      -
    731B  THR*     3.0    40.6    +      -       -      +
    733B  ILE*     4.0    25.8    -      -       +      -
    754B  VAL*     4.7     3.8    -      -       +      -
    758B  PHE*     4.2     9.0    -      -       +      -
    759B  GLN      3.4     7.9    -      -       -      +
    760B  LEU*     4.5     7.2    -      -       +      -
    782B  ILE*     4.2     6.1    -      -       +      -
    783B  LYS*     1.3    78.3    -      -       -      +
    785B  LEU*     1.3    70.5    +      -       -      +
    786B  ASN*     3.9     5.0    +      -       +      +
    792B  LEU*     3.8    26.5    -      -       +      -
    794B  MET*     4.2    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 785 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    727B  ASN*     4.2     9.9    -      -       -      +
    729B  SER*     3.5    30.7    -      -       -      +
    730B  VAL*     3.9    17.7    -      -       +      -
    758B  PHE*     3.4    10.7    -      -       -      +
    759B  GLN*     2.9    63.2    +      -       +      +
    783B  LYS      4.3     0.2    +      -       -      -
    784B  VAL*     1.3    73.4    -      -       -      +
    786B  ASN*     1.3    57.2    +      -       -      +
    787B  PRO*     3.5    18.6    -      -       +      +
----------------------------------------------------------
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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