Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 2N8A


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 47 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     5.0     7.3    -      -       -      +
      4A  SER      5.5     0.2    +      -       -      -
      5A  SER*     3.9    34.3    +      -       -      +
     38A  MET*     3.4    48.2    -      -       +      -
     39A  VAL      3.0    15.9    -      -       -      +
     40A  GLN*     4.3     2.2    -      -       +      +
     44A  PHE*     5.3     1.0    -      -       -      -
     46A  GLY*     1.3    77.6    -      -       -      -
     48A  VAL*     1.3    63.8    +      -       -      +
     49A  PRO*     3.8     5.9    -      -       -      +
     22B    C      5.3     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  MET*     4.8     0.7    -      -       -      -
     39A  VAL*     2.7    52.2    +      -       +      +
     41A  SER*     3.7    13.9    -      -       -      +
     44A  PHE*     3.4    33.7    -      -       +      -
     47A  LYS*     1.3    73.9    -      -       -      +
     49A  PRO*     1.3    75.4    -      -       +      +
     50A  HIS*     3.8     6.3    +      -       +      -
     22B    C      4.0    25.8    -      -       +      +
     23B    T      3.3    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  ALA*     3.9     7.9    -      -       +      -
     37A  ILE      4.2     4.5    -      -       -      +
     38A  MET*     4.7    13.7    -      -       -      -
     47A  LYS      3.8     5.8    -      -       -      +
     48A  VAL*     1.3    93.2    -      -       +      +
     50A  HIS*     1.3    63.8    +      -       -      +
     51A  TRP*     3.2    48.5    +      -       +      +
     21B    G      6.3     1.6    -      -       +      -
     22B    C      4.3    23.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  LYS*     4.3    21.4    +      -       +      -
     36A  ALA*     3.1    13.0    -      -       -      +
     37A  ILE*     3.4    25.2    +      -       +      -
     39A  VAL*     2.9    51.4    -      -       +      +
     48A  VAL*     4.5    10.9    -      -       +      +
     49A  PRO*     1.3    73.1    +      -       -      +
     51A  TRP*     1.3    59.2    +      -       -      +
     52A  TYR*     2.8    36.2    -      -       +      +
    149A  PRO*     5.1     2.8    -      -       -      +
    150A  GLN*     5.1    14.1    -      -       +      +
     22B    C      6.1     1.4    -      -       +      +
     23B    T      4.7    28.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with TRP 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  ARG*     3.3    34.5    -      -       +      -
     12A  GLU*     3.6    18.8    -      -       +      -
     19A  ALA*     4.6     7.6    -      -       +      -
     20A  SER      3.7     3.9    +      -       -      +
     21A  CYS*     3.5     2.1    -      -       -      -
     22A  LYS*     3.0    26.8    +      -       -      +
     28A  ILE*     3.7    18.8    -      -       +      -
     34A  ARG*     3.0    51.6    -      -       +      +
     35A  MET*     3.1    20.9    -      -       -      -
     36A  ALA*     2.9    35.4    -      -       +      -
     49A  PRO*     3.2    40.6    +      -       +      +
     50A  HIS*     1.3    70.4    -      -       -      +
     52A  TYR*     1.3    67.4    +      -       -      +
     21B    G      5.0     6.8    +      -       +      -
     22B    C      4.0    17.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  CYS*     3.7     7.0    -      -       -      -
     22A  LYS*     3.0    38.3    -      -       +      +
     23A  LYS*     3.6    26.5    -      -       +      -
     28A  ILE*     4.0     7.6    -      -       -      -
     34A  ARG*     3.6     4.3    -      -       -      +
     35A  MET      2.9    31.7    +      -       -      +
     37A  ILE*     4.2     4.5    -      -       +      +
     50A  HIS*     2.8    44.5    -      -       +      +
     51A  TRP*     1.3    78.4    -      -       -      +
     53A  HIS*     1.3    71.6    +      -       -      +
     54A  PHE      3.5     0.2    +      -       -      -
     56A  CYS      4.7     0.7    -      -       -      -
     57A  PHE*     3.7    30.3    -      +       -      +
     60A  VAL*     4.8    12.5    -      -       +      +
     62A  HIS*     3.8    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  CYS*     3.2    20.7    -      -       +      +
     24A  CYS*     3.5     6.9    -      -       -      -
     26A  GLU*     3.3    16.8    -      -       +      -
     27A  SER      2.8    25.7    +      -       -      -
     28A  ILE*     3.4    20.6    -      -       +      -
     29A  PRO*     4.1     7.8    -      -       +      +
     32A  SER*     5.5     0.9    -      -       -      -
     33A  LEU      4.6     3.1    -      -       -      -
     34A  ARG*     4.8     1.6    -      -       -      +
     52A  TYR*     1.3    76.9    -      -       -      +
     54A  PHE*     1.3    68.6    +      -       -      +
     55A  SER*     3.1     5.6    +      -       -      +
     56A  CYS*     3.2    16.7    +      -       -      +
     57A  PHE*     3.2     6.6    +      -       -      +
   1000A   ZN      2.0    38.1    -      -       -      -
----------------------------------------------------------
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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