Contacts of the strand formed by residues 871 - 875 (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 LYS 871 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    867N  ARG*     3.3     6.7    -      -       -      +
    868N  TYR      2.9    31.9    +      -       -      +
    869N  MET*     3.0    24.3    -      -       -      +
    870N  GLY*     1.3    80.7    -      -       -      +
    872N  ARG*     1.3    62.6    +      -       -      +
    873N  LEU*     3.6    22.3    +      -       +      +
    897N  TRP*     3.2    34.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 872 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74L  ASP*     3.3    33.9    +      -       -      -
     76L  VAL*     3.8    25.8    -      -       -      +
     77L  GLU*     3.2    37.5    +      -       -      +
     80L  LEU*     4.9     5.5    -      -       +      +
    842N  VAL*     5.5     0.9    -      -       +      -
    865N  THR*     3.7    25.6    -      -       +      -
    866N  VAL      4.1     2.0    -      -       -      -
    867N  ARG*     4.4     8.3    -      -       +      +
    870N  GLY      4.1     1.2    +      -       -      -
    871N  LYS*     1.3    70.6    -      -       -      +
    873N  LEU*     1.3    63.8    +      -       -      +
    874N  GLU*     4.1     4.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 873 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    864N  VAL      3.7     0.3    -      -       -      +
    865N  THR*     3.3     8.8    -      -       -      +
    866N  VAL      2.8    39.2    +      -       -      +
    868N  TYR*     3.9    26.2    -      -       +      +
    871N  LYS*     4.3    24.9    -      -       +      +
    872N  ARG*     1.3    76.7    -      -       -      +
    874N  GLU*     1.3    62.7    +      -       -      +
    875N  THR*     3.8    11.7    -      -       +      -
    880N  ILE*     4.5     8.5    -      -       +      -
    897N  TRP*     3.8    30.1    -      -       +      -
    902N  LEU*     4.4    17.5    -      -       +      -
    903N  ASP*     5.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 874 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    832N  ARG*     5.4    10.5    +      -       -      -
    833N  GLU      5.2     3.6    -      -       -      +
    834N  THR*     3.9     9.5    +      -       -      -
    838N  ARG*     3.3    51.9    +      -       +      +
    839N  LEU*     5.8     1.4    -      -       -      +
    863N  VAL*     4.8     4.2    -      -       -      +
    864N  VAL      3.4     4.3    -      -       -      -
    865N  THR*     4.2     8.9    +      -       +      +
    872N  ARG*     4.1     4.4    +      -       +      +
    873N  LEU*     1.3    75.3    -      -       -      +
    875N  THR*     1.3    62.8    +      -       -      +
    903N  ASP*     4.2     9.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 875 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    795N  VAL*     5.9     0.4    -      -       -      -
    863N  VAL*     4.3     7.1    -      -       -      +
    864N  VAL*     2.9    39.9    +      -       -      +
    866N  VAL*     4.7     5.6    -      -       +      +
    873N  LEU*     3.8    16.1    -      -       +      -
    874N  GLU*     1.3    76.6    -      -       -      +
    876N  SER*     1.3    74.2    +      -       -      +
    879N  ARG*     3.5    25.0    +      -       -      +
    880N  ILE*     4.0    21.8    -      -       +      +
    902N  LEU*     4.1    12.9    -      -       +      +
    903N  ASP*     3.5    13.9    +      -       -      -
----------------------------------------------------------
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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