Contacts of the strand formed by residues 241 - 244 (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 ILE 241 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231N  VAL*     3.3    28.8    -      -       +      +
    233N  LYS*     4.6     5.4    +      -       -      +
    236N  TYR*     3.8     7.3    -      -       -      -
    239N  GLY      4.7     1.3    -      -       -      +
    240N  GLU*     1.3    78.6    -      -       +      +
    242N  LEU*     1.3    60.7    +      -       -      +
    243N  ALA      4.8     4.0    -      -       -      +
    244N  GLU*     6.1     2.0    -      -       +      -
    310N  LEU*     3.7    32.1    -      -       +      -
    311N  LEU      3.5     8.7    -      -       -      +
    312N  ARG*     3.7    24.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 242 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223N  LEU*     3.8    19.1    -      -       +      -
    225N  LEU*     4.4     7.9    -      -       +      -
    230N  TRP*     3.5     6.6    -      -       -      -
    231N  VAL*     3.2    21.8    +      -       -      +
    236N  TYR*     3.3    45.5    +      -       +      +
    240N  GLU      3.3     3.9    +      -       -      +
    241N  ILE*     1.3    73.9    -      -       -      +
    243N  ALA*     1.3    62.9    +      -       +      +
    283N  PHE*     5.1     4.5    -      -       +      -
    285N  PRO*     3.7    33.4    -      -       +      -
    311N  LEU*     2.9    17.1    +      -       +      +
    312N  ARG*     4.5     6.1    -      -       -      +
    313N  MET*     4.7     7.4    -      -       +      +
    333N  LEU*     4.0    16.8    -      -       +      -
    335N  LEU*     5.4     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 243 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225N  LEU*     4.3    10.3    -      -       +      -
    229N  ALA*     3.2    22.9    -      -       +      +
    230N  TRP*     4.0     4.5    -      -       -      -
    231N  VAL*     4.3     7.4    -      -       -      +
    241N  ILE*     3.6     3.7    -      -       -      +
    242N  LEU*     1.3    82.2    -      -       -      +
    244N  GLU*     1.3    58.1    +      -       -      +
    245N  LEU*     4.3     4.3    -      -       +      -
    310N  LEU*     3.7     6.3    -      -       -      +
    311N  LEU*     2.8    53.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 244 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229N  ALA*     3.0    27.3    +      -       -      +
    231N  VAL*     4.7     6.1    -      -       +      +
    241N  ILE*     6.1     2.5    -      -       +      -
    243N  ALA*     1.3    74.8    -      -       -      +
    245N  LEU*     1.3    71.6    +      -       -      +
    246N  PRO*     3.1    16.0    -      -       -      +
    309N  GLY      4.1     2.6    -      -       -      +
    310N  LEU*     3.6    33.6    -      -       +      +
----------------------------------------------------------
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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