Contacts of the strand formed by residues 298 - 301 (chain B) in PDB entry 2ANL


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 THR 298 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194B  GLN*     6.0     0.2    -      -       -      +
    210B  ASN*     3.1    21.3    +      -       -      +
    212B  ILE*     4.5    13.7    -      -       +      -
    222B  ALA*     4.3     0.9    -      -       -      -
    223B  PRO*     3.6    12.5    -      -       -      +
    292B  VAL      4.8     0.2    -      -       -      +
    294B  ILE*     3.8    40.4    -      -       +      +
    295B  ASP*     2.9    37.1    +      -       -      +
    296B  LYS      3.8     1.2    -      -       -      +
    297B  ASN*     1.3    77.5    +      -       -      +
    299B  PHE*     1.3    78.6    +      -       -      +
    300B  ILE*     5.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199B  VAL*     3.2    43.1    -      -       +      -
    201B  PHE*     4.0     7.4    -      +       -      -
    206B  MET*     4.8     7.6    -      -       +      -
    209B  ALA*     4.4    15.5    -      -       +      -
    210B  ASN      2.8     4.8    +      -       -      -
    211B  VAL*     3.7    19.5    -      -       +      -
    212B  ILE*     3.3    25.0    +      -       -      +
    221B  THR*     3.5    14.4    -      -       -      +
    222B  ALA*     3.7     3.1    -      -       +      -
    223B  PRO*     3.0    27.6    -      -       +      -
    226B  PHE*     3.2    34.8    -      +       -      -
    259B  PHE*     4.5     7.2    -      +       -      -
    297B  ASN*     4.8     0.7    -      -       -      -
    298B  THR*     1.3    86.4    -      -       -      +
    300B  ILE*     1.3    74.2    +      -       -      +
    301B  LEU*     5.3     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  ILE*     3.2    15.7    -      -       +      +
    214B  ASP*     3.5    33.9    -      -       +      +
    217B  THR*     5.1     0.9    -      -       -      +
    219B  THR      5.1     2.9    -      -       -      +
    220B  ILE*     3.3     8.0    -      -       -      -
    221B  THR*     3.1    43.0    +      -       +      +
    294B  ILE*     4.0    22.2    -      -       +      -
    298B  THR*     5.2     0.7    -      -       +      -
    299B  PHE*     1.3    84.3    -      -       -      +
    301B  LEU*     1.3    70.7    +      -       -      +
    302B  GLY      4.9     0.9    -      -       -      +
   3152B  JE2      4.0    47.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197B  LEU*     5.8     2.2    -      -       +      -
    211B  VAL*     4.1    20.9    -      -       +      -
    212B  ILE      2.4    15.3    +      -       -      +
    213B  VAL*     3.4    12.0    -      -       +      +
    214B  ASP*     2.8    28.0    +      -       -      -
    220B  ILE*     3.9    20.0    -      -       +      +
    259B  PHE*     3.8    37.7    -      -       +      -
    299B  PHE*     5.3     3.1    -      -       +      -
    300B  ILE*     1.3    82.4    -      -       -      +
    302B  GLY*     1.3    59.6    +      -       -      +
    305B  PHE*     3.7    49.4    -      -       +      -
    306B  MET*     4.3     3.1    -      -       -      +
    322B  PHE*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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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