Contacts of the strand formed by residues 375 - 381 (chain B) in PDB entry 1DY7


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 LYS 375 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329A  ASP*     3.7    11.2    -      -       -      +
    332A  ASN*     3.5    27.1    -      -       +      +
    338B  ILE*     4.1     7.5    -      -       -      +
    369B  ILE*     3.5     0.8    -      -       -      -
    370B  ASP*     2.9    32.3    +      -       +      +
    373B  GLU*     3.5    22.0    -      -       +      +
    374B  GLY*     1.3    83.3    -      -       -      +
    376B  LEU*     1.3    70.3    +      -       -      +
    377B  VAL*     3.5     5.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 376 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331A  ASP*     6.4     1.6    -      -       +      -
    332A  ASN*     2.9    20.3    +      -       -      +
    338B  ILE*     3.9    11.2    -      -       +      +
    339B  SER      3.8    17.9    -      -       -      +
    367B  VAL*     3.5    26.2    -      -       +      -
    368B  VAL      3.5    17.9    -      -       -      +
    369B  ILE*     4.1     6.3    -      -       +      -
    375B  LYS*     1.3    79.4    -      -       -      +
    377B  VAL*     1.3    63.5    +      -       -      +
    378B  ALA*     3.6    14.6    -      -       -      +
    379B  ILE*     4.0    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 377 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355B  TYR*     4.4     6.7    -      -       +      -
    368B  VAL*     2.8    41.9    +      -       +      +
    370B  ASP*     3.9    30.3    -      -       +      +
    375B  LYS*     3.5     6.5    +      -       +      +
    376B  LEU*     1.3    80.0    -      -       -      +
    378B  ALA*     1.3    63.4    +      -       -      +
    429B  TRP*     4.1    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 378 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366B  LEU      4.4     0.4    -      -       -      -
    367B  VAL*     3.6     0.2    -      -       -      -
    368B  VAL*     2.9    37.2    +      -       +      -
    376B  LEU*     3.6     6.3    -      -       -      +
    377B  VAL*     1.3    82.8    -      -       -      +
    379B  ILE*     1.3    69.9    +      -       -      +
    380B  GLU*     4.3     7.2    -      -       +      +
    429B  TRP*     3.6    37.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 379 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289B  TYR*     5.7     0.7    -      -       +      +
    340B  ALA      3.4    30.3    -      -       -      +
    341B  GLU*     4.7     7.9    -      -       +      +
    365B  LYS*     3.9    31.1    -      -       +      +
    366B  LEU      3.3     8.3    -      -       -      +
    367B  VAL*     4.2     9.6    -      -       +      -
    376B  LEU*     4.0    26.2    -      -       +      -
    378B  ALA*     1.3    80.9    -      -       -      +
    380B  GLU*     1.3    75.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 380 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365B  LYS*     3.9     4.7    -      -       -      -
    366B  LEU*     2.8    41.1    +      -       +      +
    368B  VAL*     6.3     0.2    -      -       +      -
    378B  ALA*     4.6     7.1    -      -       +      +
    379B  ILE*     1.3    88.2    +      -       -      +
    381B  ASP*     1.3    69.7    +      -       -      +
    382B  THR*     3.6     0.7    +      -       -      +
    417B  ILE*     4.7     7.6    -      -       +      -
    429B  TRP      3.0    28.7    -      -       -      +
    430B  LYS*     4.9    17.8    +      -       -      +
    431B  ILE*     4.5    17.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 381 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364B  ASN*     3.3    26.7    +      -       -      +
    365B  LYS*     2.9    34.1    +      -       +      +
    380B  GLU*     1.3    75.6    +      -       -      +
    382B  THR*     1.3    62.1    +      -       -      +
    383B  GLY*     2.8    31.7    +      -       -      -
    431B  ILE*     3.3    16.2    -      -       -      +
----------------------------------------------------------
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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