Contacts of the strand formed by residues 33 - 40 (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 LEU 33 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  VAL*     3.9    13.2    -      -       +      -
     12A  GLU      3.9     3.8    -      -       -      +
     13A  TYR*     3.9    21.0    -      -       +      -
     28A  ILE*     5.5     0.2    -      -       -      +
     31A  ASP      3.8     0.8    +      -       -      -
     32A  SER*     1.3    75.3    +      -       -      +
     34A  ARG*     1.3    58.8    +      -       -      +
     53A  HIS*     4.6     1.4    -      -       -      -
     54A  PHE*     3.5    58.0    +      -       +      +
     77A  LEU*     3.8    29.8    -      -       +      -
     81A  ASP*     3.7    24.5    -      -       +      +
     84A  LYS*     4.3    11.7    -      -       +      +
     85A  VAL*     4.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  VAL*     3.9     1.0    -      -       -      +
     12A  GLU*     2.7    61.1    +      -       -      +
     14A  ALA*     3.2    25.0    -      -       -      +
     15A  LYS      3.1    19.8    -      -       -      +
     16A  SER      3.8     1.4    +      -       -      +
     19A  ALA*     4.5     4.7    -      -       -      +
     28A  ILE*     3.8    22.6    -      -       +      +
     32A  SER      4.0     0.9    -      -       -      +
     33A  LEU*     1.3    76.5    -      -       -      +
     35A  MET*     1.3    68.7    +      -       -      +
     51A  TRP*     3.0    56.2    -      -       +      +
     52A  TYR      3.6    14.1    -      -       -      +
     54A  PHE      4.4     0.9    -      -       -      +
     21B    G      2.7    36.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  TYR*     4.9     2.9    -      -       +      -
     10A  ARG      3.3     6.7    -      -       -      +
     11A  VAL*     3.8    16.6    -      -       +      -
     34A  ARG*     1.3    80.1    -      -       -      +
     36A  ALA*     1.3    57.3    +      -       -      +
     51A  TRP*     3.1     6.6    -      -       -      -
     52A  TYR*     2.9    34.7    +      -       -      +
     54A  PHE*     3.8    34.0    -      -       +      +
     57A  PHE*     3.6    48.5    -      -       +      -
     58A  TRP*     4.4    10.8    -      -       +      -
     64A  ILE*     5.5     1.3    -      -       +      -
     71A  VAL*     3.8    35.9    -      -       +      -
     85A  VAL*     4.6     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  TYR*     3.2     6.6    -      -       -      +
     10A  ARG*     2.9    33.2    +      -       +      +
     35A  MET*     1.3    73.4    -      -       -      +
     37A  ILE*     1.3    59.9    +      -       -      +
     38A  MET*     3.6     1.2    +      -       -      +
     49A  PRO*     3.9    10.3    -      -       +      -
     50A  HIS      3.1    16.6    -      -       -      +
     51A  TRP*     2.9    42.6    -      -       +      -
     57A  PHE*     3.9     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  LEU*     3.5    12.8    -      -       +      -
      9A  TYR*     3.4    31.4    -      -       +      +
     36A  ALA*     1.3    73.5    -      -       -      +
     38A  MET*     1.3    70.7    +      -       -      +
     39A  VAL*     3.3    10.3    -      -       +      +
     50A  HIS*     3.4    41.1    +      -       +      +
     52A  TYR*     4.2     2.5    -      -       +      +
     57A  PHE*     4.1     1.0    -      -       -      -
     62A  HIS*     3.2    45.1    -      -       +      +
    144A  VAL*     6.1     0.7    -      -       +      -
    149A  PRO      4.4    15.3    -      -       -      +
    150A  GLN*     6.3     0.4    -      -       -      -
    152A  GLY*     4.4    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  SER*     5.4     8.5    -      -       -      +
      7A  LYS*     3.8    17.0    -      -       +      +
      8A  LEU*     2.6    42.9    +      -       +      +
      9A  TYR      5.0     3.1    -      -       -      +
     10A  ARG*     4.1    37.2    -      -       +      +
     36A  ALA      3.6     3.0    +      -       -      +
     37A  ILE*     1.3    69.1    -      -       -      +
     39A  VAL*     1.3    69.2    +      -       -      +
     47A  LYS*     3.4    52.3    -      -       +      -
     48A  VAL      4.0     4.0    -      -       -      +
     49A  PRO*     4.7    13.5    -      -       -      -
     72A  ASP*     4.7     8.5    -      -       +      +
    149A  PRO*     4.5     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ILE*     3.3     5.2    -      -       +      +
     38A  MET*     1.3    84.6    -      -       -      +
     40A  GLN*     1.3    60.4    +      -       -      +
     41A  SER*     5.9     0.2    -      -       -      -
     47A  LYS*     3.0     5.3    -      -       -      -
     48A  VAL*     2.7    66.6    +      -       +      +
     50A  HIS*     2.9    42.6    -      -       +      +
    149A  PRO*     3.3    40.4    -      -       +      +
     23B    T      5.6     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  VAL*     1.3    74.9    -      -       -      +
     41A  SER*     1.3    71.8    +      -       -      +
     42A  PRO*     3.8     7.3    -      -       -      +
     46A  GLY      4.1    10.3    -      -       -      +
     47A  LYS*     4.3     3.6    -      -       +      +
    146A  PRO*     4.7    23.9    +      -       +      +
    149A  PRO*     4.6    12.4    -      -       -      +
----------------------------------------------------------
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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