Contacts of the strand formed by residues 381 - 386 (chain B) in PDB entry 3IFS


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 ASN 381 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ASP      4.7     2.1    -      -       -      +
      9B  TYR      5.0     0.2    -      -       -      +
     11B  LYS*     4.2     8.3    +      -       +      +
     12B  ALA*     3.6    24.9    +      -       -      +
     15B  PHE*     5.0     0.2    -      -       -      -
    327B  GLU*     3.3    37.4    +      -       -      +
    329B  VAL*     3.8    15.1    -      -       -      +
    371B  LEU*     3.7    40.1    -      -       +      +
    374B  HIS*     3.7    12.5    +      -       -      +
    375B  SER*     4.1    10.3    +      -       -      +
    379B  VAL      2.8    26.3    +      -       -      -
    380B  PRO*     1.3    75.1    +      -       -      +
    382B  LEU*     1.3    62.5    +      -       -      +
    383B  ILE*     5.0     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 382 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  PHE*     3.9    20.0    -      -       +      -
      8B  ASP      3.8     3.1    -      -       -      -
      9B  TYR*     3.9    17.9    -      -       +      -
     12B  ALA*     4.1    11.9    -      -       +      -
    254B  TYR*     4.2     9.4    -      -       +      -
    257B  VAL*     3.6    33.7    -      -       +      -
    258B  ARG      5.1     1.3    -      -       -      +
    261B  LEU*     4.3     5.6    -      -       +      -
    326B  PHE*     3.8    22.2    -      -       +      -
    327B  GLU      2.7    12.4    +      -       -      +
    328B  THR*     3.7    21.1    -      -       +      +
    329B  VAL*     2.7    28.6    +      -       -      +
    380B  PRO      5.2     0.2    -      -       -      +
    381B  ASN*     1.3    81.2    -      -       -      +
    383B  ILE*     1.3    65.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 383 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  THR      3.9     0.3    -      -       -      +
      7B  PHE*     3.5     6.9    -      -       -      -
      8B  ASP*     2.9    62.3    +      -       +      +
     11B  LYS*     4.0    18.8    -      -       +      +
    329B  VAL*     3.5     9.9    -      -       +      +
    331B  LYS*     4.2     4.5    -      -       +      -
    367B  TYR*     3.0    33.4    -      -       +      +
    371B  LEU*     3.7    23.1    -      -       +      -
    381B  ASN      5.0     0.9    -      -       -      +
    382B  LEU*     1.3    81.7    -      -       -      +
    384B  VAL*     1.3    66.5    +      -       -      +
    385B  ASN*     3.4    29.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 384 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  VAL*     3.7    25.8    -      -       +      -
      6B  THR      3.5     4.3    -      -       -      +
      7B  PHE*     4.1    11.4    -      -       +      -
    254B  TYR*     5.5     0.9    -      -       +      -
    328B  THR*     4.0    22.9    -      -       +      -
    329B  VAL      2.8     9.5    +      -       -      +
    330B  LEU*     3.5    16.9    -      -       +      -
    331B  LYS      3.0    24.1    +      -       -      -
    382B  LEU      4.4     0.2    -      -       -      -
    383B  ILE*     1.3    75.6    -      -       -      +
    385B  ASN*     1.3    59.9    +      -       -      +
    386B  ILE*     3.6     4.1    +      -       +      +
    397B  LEU*     3.9    18.4    -      -       +      -
    400B  PHE*     4.0    24.0    -      -       +      -
    401B  PHE*     4.2     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 385 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  HIS      4.2     0.4    -      -       -      +
      5B  VAL*     3.2    12.5    -      -       -      +
      6B  THR*     2.9    48.6    +      -       -      +
      8B  ASP*     4.2    17.8    +      -       -      +
    331B  LYS*     3.5    17.8    -      -       -      +
    367B  TYR*     4.9     0.3    +      -       -      -
    383B  ILE*     3.4    25.3    -      -       -      +
    384B  VAL*     1.3    70.2    -      -       -      +
    386B  ILE*     1.3    61.3    +      -       -      +
    387B  PRO*     3.6     3.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 386 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  VAL*     4.6     2.2    -      -       +      -
    278B  LEU*     4.6     7.9    -      -       +      -
    330B  LEU*     4.0    29.6    -      -       +      -
    331B  LYS      2.8    11.1    +      -       -      +
    332B  VAL*     3.1    16.7    -      -       +      +
    333B  GLY      2.8    24.9    +      -       -      -
    384B  VAL*     3.8     8.7    -      -       +      +
    385B  ASN*     1.3    77.1    -      -       -      +
    387B  PRO*     1.3    62.6    -      -       -      +
    388B  GLU      3.3    10.2    +      -       -      +
    389B  LEU*     4.2    15.9    -      -       +      -
    393B  THR*     3.5    27.6    -      -       +      -
    397B  LEU*     3.7    35.9    -      -       +      -
----------------------------------------------------------
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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