Contacts of the strand formed by residues 318 - 327 (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 ARG 318 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236N  TYR      4.0     5.3    +      -       -      +
    237N  LYS*     4.4    15.3    -      -       -      +
    238N  PRO*     3.8    27.8    -      -       +      +
    313N  MET*     3.9     5.8    -      -       -      -
    316N  GLN      4.4     0.2    +      -       -      -
    317N  VAL*     1.3    73.5    -      -       -      +
    319N  ALA*     1.3    63.2    +      -       -      +
    320N  ALA*     3.9     7.3    +      -       -      +
    337N  LEU*     3.5     2.4    -      -       -      -
    338N  GLU*     2.8    61.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 319 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235N  ALA*     3.4     4.2    -      -       -      +
    236N  TYR*     3.0    49.4    +      -       +      +
    313N  MET*     3.7     5.6    -      -       +      +
    318N  ARG*     1.3    73.4    +      -       -      +
    320N  ALA*     1.3    63.8    +      -       -      +
    321N  GLN      3.4     2.2    -      -       -      +
    322N  VAL*     4.4    13.9    -      -       +      -
    335N  LEU*     4.7     6.1    -      -       +      -
    336N  PHE      3.3     9.4    -      -       -      +
    337N  LEU*     3.8    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 320 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234N  GLU      3.9     0.5    -      -       -      +
    235N  ALA*     3.2    20.1    -      -       -      +
    318N  ARG*     3.9    10.7    +      -       -      +
    319N  ALA*     1.3    72.1    -      -       -      +
    321N  GLN*     1.3    71.3    +      -       +      +
    336N  PHE*     3.0    13.6    +      -       +      +
    338N  GLU*     3.9    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 321 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234N  GLU      3.8     3.6    -      -       -      +
    319N  ALA*     4.7     0.5    -      -       -      +
    320N  ALA*     1.3    91.3    +      -       +      +
    322N  VAL*     1.3    68.4    +      -       -      +
    323N  GLU*     5.5     2.2    -      -       +      +
    335N  LEU*     3.7     0.3    -      -       -      +
    336N  PHE*     2.9    60.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 322 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230N  TRP*     4.4    16.6    -      -       +      -
    233N  LYS      3.8    11.7    -      -       -      +
    234N  GLU*     3.2    27.9    +      -       -      +
    235N  ALA*     4.1     4.7    -      -       -      -
    236N  TYR*     3.5    35.9    -      -       +      -
    319N  ALA*     4.4     5.8    -      -       +      -
    321N  GLN*     1.3    79.2    -      -       -      +
    323N  GLU*     1.3    71.5    +      -       -      +
    324N  ALA*     4.1     0.7    +      -       -      +
    333N  LEU*     4.4     4.7    -      -       +      -
    334N  THR      3.7     2.7    -      -       -      -
    335N  LEU*     3.7    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 323 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220N  ARG*     4.7     5.0    +      -       -      -
    321N  GLN*     5.5     2.5    -      -       +      +
    322N  VAL*     1.3    79.3    -      -       -      +
    324N  ALA*     1.3    60.6    +      -       -      +
    325N  GLU      4.3     0.2    -      -       -      -
    332N  TYR      3.7     0.2    -      -       -      +
    333N  LEU*     3.4     4.7    -      -       -      -
    334N  THR*     2.9    56.8    +      -       -      +
    336N  PHE*     3.8    28.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 324 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230N  TRP*     3.7    32.1    -      -       +      -
    322N  VAL*     4.1     2.2    +      -       +      +
    323N  GLU*     1.3    77.1    -      -       -      +
    325N  GLU*     1.3    61.6    +      -       -      +
    326N  GLU      4.0     1.6    +      -       -      -
    331N  VAL*     3.8    13.0    -      -       +      -
    332N  TYR      3.6     3.1    -      -       -      -
    333N  LEU*     4.0     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 325 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224N  ARG*     4.7     2.9    +      -       -      -
    324N  ALA*     1.3    72.5    -      -       -      +
    326N  GLU*     1.3    67.8    +      -       -      +
    327N  GLU*     3.6     8.4    +      -       +      +
    331N  VAL*     3.4     3.0    -      -       -      +
    332N  TYR*     2.9    58.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 326 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1284D  GLU*     5.6     3.8    -      -       -      +
   1286D  THR*     4.1    32.0    +      -       -      +
    227N  LEU*     3.5    41.8    -      -       +      +
    324N  ALA      4.0     3.0    +      -       -      -
    325N  GLU*     1.3    76.0    -      -       -      +
    327N  GLU*     1.3    61.4    +      -       -      +
    328N  GLY      5.0     5.7    -      -       -      +
    330N  THR      3.8     7.0    -      -       -      +
    331N  VAL*     4.4     3.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 327 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224N  ARG*     3.1    37.0    +      -       -      +
    325N  GLU*     3.6     9.0    +      -       +      +
    326N  GLU*     1.3    74.6    -      -       -      +
    328N  GLY*     1.3    68.5    +      -       -      +
    329N  GLU      3.3     0.2    +      -       -      -
    330N  THR*     2.8    36.6    +      -       -      +
----------------------------------------------------------
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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