Contacts of the strand formed by residues 744 - 748 (chain N) in PDB entry 5D4D


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 GLN 744 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1004M  LYS*     3.4    48.3    +      -       -      +
    628N  ARG*     3.6    41.4    +      -       -      +
    629N  SER      3.2    15.3    -      -       -      +
    630N  VAL*     3.8    11.0    -      -       +      +
    631N  ILE      4.5     0.7    -      -       -      +
    704N  ARG*     4.1    14.4    -      -       -      +
    705N  ALA      5.0     1.7    +      -       -      -
    742N  GLY      3.6     9.1    +      -       -      +
    743N  ASP*     1.3    78.9    -      -       -      +
    745N  MET*     1.3    69.4    +      -       -      +
   2005N    C      4.8     2.7    +      -       -      -
     17R    A      5.9     1.2    -      -       -      -
    101R    A      5.0     6.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 745 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    628N  ARG*     3.1     9.4    -      -       -      +
    629N  SER      2.9    31.5    +      -       -      +
    631N  ILE*     3.5    28.0    -      -       +      +
    702N  LEU*     4.3    19.5    -      -       +      -
    703N  ASN      3.4    15.3    -      -       -      +
    704N  ARG*     3.7    11.4    -      -       +      -
    726N  ILE*     3.9    10.9    -      -       +      +
    728N  LEU*     3.6    33.7    -      -       +      -
    736N  PHE*     3.5    38.6    -      -       +      -
    738N  ALA*     4.0     7.9    -      -       +      -
    744N  GLN*     1.3    78.1    -      -       -      +
    746N  ALA*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 746 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1030M  GLN*     4.2     8.1    -      -       +      +
    627N  GLY      3.2    12.1    -      -       -      +
    628N  ARG*     3.8    21.8    -      -       -      +
    701N  LEU      3.6     0.5    -      -       -      +
    702N  LEU*     3.4     5.7    -      -       -      +
    703N  ASN*     2.9    43.8    +      -       -      +
    745N  MET*     1.3    74.2    -      -       -      +
    747N  VAL*     1.3    62.9    +      -       -      +
    748N  HIS*     3.9    19.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 747 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    626N  SER*     3.2     6.1    -      -       -      -
    627N  GLY      2.8    32.4    +      -       -      +
    644N  LEU*     4.2     8.5    -      -       +      -
    648N  MET*     3.6    29.8    -      -       +      -
    652N  LEU*     4.1    19.6    -      -       +      +
    700N  VAL*     3.7    24.9    -      -       +      -
    701N  LEU      3.2     9.0    -      -       -      +
    702N  LEU*     3.8    11.9    -      -       +      -
    726N  ILE*     3.6    21.8    -      -       +      -
    746N  ALA*     1.3    75.8    -      -       -      +
    748N  HIS*     1.3    68.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 748 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1030M  GLN*     4.2     8.2    -      -       +      +
   1031M  ARG      5.3     1.6    +      -       -      -
   1032M  PHE*     3.6    31.8    -      +       +      -
   1052M  MET*     3.9    27.1    -      -       +      +
   1056M  LYS*     4.8     1.3    -      -       -      +
    623N  VAL*     3.6    22.9    -      -       +      +
    624N  ASP      5.3     0.4    +      -       -      -
    625N  TYR      3.7     5.6    +      -       -      +
    626N  SER*     3.7    17.2    -      -       -      -
    700N  VAL*     3.4     5.0    -      -       -      +
    701N  LEU*     2.9    45.9    +      -       +      -
    703N  ASN*     4.8    10.7    +      -       +      +
    746N  ALA*     3.9    20.8    -      -       +      +
    747N  VAL*     1.3    82.1    -      -       -      +
    749N  VAL*     1.3    64.6    +      -       -      +
    750N  PRO*     3.2     2.9    -      -       -      +
----------------------------------------------------------
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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