Contacts of the helix formed by residues 14 - 22 (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 SER 14 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12N  LEU      4.1     0.8    +      -       -      -
     13N  ALA*     1.3    75.7    -      -       -      +
     15N  PRO*     1.3    70.5    -      -       -      +
     16N  GLU*     3.3    23.5    +      -       -      +
     17N  LYS*     2.9    32.6    +      -       -      +
     18N  ILE*     2.9    22.8    +      -       -      +
    511N  TRP*     3.3    37.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 15 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13N  ALA      4.4     1.8    -      -       -      +
     14N  SER*     1.3    83.5    -      -       -      +
     16N  GLU*     1.3    74.0    +      -       -      +
     18N  ILE*     3.5    13.8    +      -       +      +
     19N  ARG*     2.9    47.9    +      -       -      +
    462N  GLN*     5.5     2.2    -      -       -      +
    510N  GLU      5.7     0.7    -      -       -      +
    511N  TRP*     4.1    16.6    -      -       +      +
    513N  ILE      4.6     7.2    -      -       -      +
    514N  LEU*     5.3     0.9    -      -       +      -
    515N  GLU*     3.8    45.1    -      -       +      +
    516N  ALA*     4.3     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 16 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14N  SER*     3.0    20.8    +      -       -      +
     15N  PRO*     1.3    95.8    -      -       -      +
     17N  LYS*     1.3    56.8    +      -       -      +
     19N  ARG*     3.2    23.3    +      -       -      +
     20N  SER*     2.9    26.6    +      -       -      -
    511N  TRP*     4.2     7.6    +      -       -      -
    515N  GLU*     4.6     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 17 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1098M  ASP*     2.9    38.2    +      -       -      +
     11N  ALA*     6.0     2.2    -      -       -      +
     12N  LEU      4.3     5.6    +      -       -      -
     13N  ALA*     4.2    13.7    -      -       +      +
     14N  SER*     2.9    25.0    +      -       -      +
     16N  GLU*     1.3    71.9    -      -       -      +
     18N  ILE*     1.3    60.2    +      -       -      +
     20N  SER*     2.8    36.6    +      -       -      +
     21N  TRP*     2.9    33.1    +      -       +      +
    511N  TRP*     5.9     4.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 18 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1096M  ALA*     4.3     4.9    -      -       +      -
     13N  ALA*     3.9    22.9    -      -       +      +
     14N  SER      2.9    17.9    +      -       -      +
     15N  PRO*     3.5    13.0    -      -       +      +
     17N  LYS*     1.3    74.0    -      -       -      +
     19N  ARG*     1.3    63.7    +      -       -      +
     21N  TRP*     3.1    31.6    +      -       +      +
     22N  SER*     3.2    11.8    +      -       -      -
     90N  MET*     5.7     0.2    -      -       -      +
     91N  GLY      5.3     0.7    -      -       -      +
     92N  HIS*     4.4     5.8    -      -       +      -
    514N  LEU*     4.2    16.2    -      -       +      -
    516N  ALA*     3.1    39.0    -      -       +      +
    518N  PRO*     4.1    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 19 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1118M  LYS*     3.5    10.0    +      -       -      -
     15N  PRO*     2.9    39.7    +      -       -      +
     16N  GLU*     3.4    23.2    +      -       -      +
     18N  ILE*     1.3    76.9    -      -       -      +
     20N  SER*     1.3    60.2    +      -       -      +
     22N  SER*     3.3    19.6    +      -       -      +
     92N  HIS*     4.5    11.9    -      -       +      +
     94N  GLU*     2.8    43.9    +      -       -      +
    515N  GLU*     3.0    29.3    +      -       -      +
    516N  ALA*     4.2     8.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 20 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1118M  LYS*     3.2    26.9    +      -       -      +
     16N  GLU      2.9    12.3    +      -       -      -
     17N  LYS*     2.8    21.3    +      -       -      +
     19N  ARG*     1.3    74.7    -      -       -      +
     21N  TRP*     1.3    69.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 21 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1090M  LYS*     5.7     1.3    -      -       -      +
   1093M  GLN*     3.4    63.3    -      -       +      +
   1096M  ALA*     4.8     0.7    -      -       -      -
   1097M  LEU      3.9    10.5    -      -       -      -
   1098M  ASP*     3.8    28.2    +      -       +      -
   1116M  ALA      4.5     6.2    -      -       -      +
   1118M  LYS*     4.6     0.9    -      -       -      +
     13N  ALA*     3.7    18.8    -      -       +      -
     17N  LYS*     2.9    31.9    +      -       +      +
     18N  ILE*     3.1    29.1    +      -       +      +
     20N  SER*     1.3    86.3    -      -       -      +
     22N  SER*     1.3    62.4    +      -       -      +
     23N  TYR*     3.5    20.6    -      -       -      -
     90N  MET*     3.9    28.3    +      -       +      +
    518N  PRO*     4.7     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 22 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1118M  LYS*     3.3    24.1    +      -       -      +
     18N  ILE      3.2     5.5    +      -       -      -
     19N  ARG      3.3    11.1    +      -       -      +
     21N  TRP*     1.3    79.5    -      -       -      +
     23N  TYR*     1.3    60.0    +      -       -      +
     24N  GLY      2.8    19.3    +      -       -      -
     90N  MET      3.3     8.3    -      -       -      -
     91N  GLY      3.0     3.6    -      -       -      -
     92N  HIS*     2.6    50.9    +      -       -      -
----------------------------------------------------------
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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