Contacts of the strand formed by residues 317 - 322 (chain C) in PDB entry 3NJ4


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 GLU 317 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315C  ALA*     3.0     9.4    -      -       -      +
    316C  VAL*     1.3    84.9    -      -       +      +
    318C  LYS*     1.3    60.6    +      -       -      +
    319C  VAL*     4.1    19.1    -      -       +      +
    327C  ARG      5.7     0.9    -      -       -      +
    328C  TYR*     3.5     2.3    -      -       -      -
    329C  ARG*     2.9    73.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 318 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312C  ASN*     3.5    13.0    -      -       -      +
    315C  ALA*     5.2     0.7    -      -       +      -
    317C  GLU*     1.3    76.6    -      -       -      +
    319C  VAL*     1.3    68.5    +      -       -      +
    320C  ASN*     4.9     5.5    -      -       -      +
    326C  ASP*     3.4    30.0    +      -       -      -
    327C  ARG      4.2     3.6    -      -       -      -
    328C  TYR*     3.3    50.7    -      -       +      +
    341C  GLU*     5.6     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 319 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  LYS*     5.4     8.7    -      -       +      -
    317C  GLU*     4.1    19.7    -      -       +      +
    318C  LYS*     1.3    78.7    -      -       -      +
    320C  ASN*     1.3    63.0    +      -       -      +
    321C  ILE*     4.6     6.3    -      -       +      -
    326C  ASP*     3.5     7.4    -      -       -      +
    327C  ARG*     2.9    60.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 320 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  LYS*     3.1    21.8    +      -       -      +
    318C  LYS*     4.3     5.1    +      -       -      +
    319C  VAL*     1.3    74.4    -      -       -      +
    321C  ILE*     1.3    59.9    +      -       -      +
    322C  LYS*     2.8    36.7    +      -       -      +
    323C  PRO*     4.1     4.4    -      -       -      +
    324C  GLN      4.5     1.4    -      -       -      +
    325C  VAL      3.3     5.2    +      -       -      +
    326C  ASP*     2.8    24.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 321 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  TRP*     3.3    28.0    -      -       +      +
     20A  LYS*     3.4    35.8    +      -       +      +
     21A  ALA*     4.7     4.7    -      -       +      +
     24A  ILE*     3.8    28.0    -      -       +      -
    206C  ALA      6.0     0.4    -      -       -      +
    319C  VAL*     4.3     2.9    -      -       +      +
    320C  ASN*     1.3    74.8    -      -       -      +
    322C  LYS*     1.3    68.5    +      -       +      +
    325C  VAL*     3.0    33.0    +      -       +      +
    326C  ASP      3.8     0.2    -      -       -      -
    327C  ARG*     3.4    39.5    -      -       +      +
    337C  ILE*     5.5     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 322 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  TRP*     4.1    32.8    -      -       +      +
    205C  ARG      3.0    25.6    +      -       -      -
    206C  ALA*     3.5    23.8    +      -       -      +
    208C  ASP*     5.1     4.6    +      -       -      -
    320C  ASN*     2.8    26.6    +      -       -      -
    321C  ILE*     1.3    83.3    -      -       +      +
    323C  PRO*     1.3    81.1    -      -       +      +
    325C  VAL*     3.0    26.2    +      -       +      -
----------------------------------------------------------
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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