Contacts of the strand formed by residues 490 - 495 (chain A) in PDB entry 4N41


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 ALA 490 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    477A  PHE*     3.5     1.4    -      -       -      -
    478A  ASP*     2.9    33.6    +      -       -      +
    489A  GLY*     1.3    75.1    -      -       -      +
    491A  ALA*     1.3    63.7    +      -       -      +
    504A  THR      3.6     8.3    -      -       -      +
    505A  LEU*     3.7    10.5    -      -       +      -
    522A  LEU*     3.7    12.3    -      -       -      +
    659A  ALA*     4.3     3.1    -      -       -      +
    662A  LEU*     3.6    26.2    -      -       +      -
    663A  VAL*     3.6    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 491 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    475A  VAL*     4.1    11.9    -      -       +      -
    476A  GLY      3.1    13.0    -      -       -      +
    477A  PHE*     4.0    19.5    -      -       +      -
    490A  ALA*     1.3    77.2    -      -       -      +
    492A  CYS*     1.3    68.7    +      -       -      +
    504A  THR*     2.9    39.7    +      -       -      +
    522A  LEU*     4.0    14.1    -      -       +      +
    526A  THR*     4.6     3.8    -      -       -      +
    659A  ALA*     4.4     1.6    -      -       -      -
    662A  LEU*     3.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 492 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    475A  VAL*     3.2     4.0    -      -       -      +
    476A  GLY      2.9    30.1    +      -       -      -
    491A  ALA*     1.3    80.9    -      -       -      +
    493A  ALA*     1.3    63.9    +      -       -      +
    502A  LEU      3.3     9.2    -      -       -      +
    503A  TRP*     4.0     5.6    -      -       -      -
    504A  THR*     4.8     0.4    -      -       -      +
    526A  THR*     5.8     0.4    -      -       -      -
    655A  PRO*     3.5    18.3    -      -       -      +
    658A  LEU*     3.6    23.1    -      -       +      -
    659A  ALA*     3.6    24.0    -      -       -      +
    662A  LEU*     3.9     9.6    -      -       -      -
    684A  PHE*     3.7    19.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 493 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473A  LEU*     4.0     9.6    -      -       +      -
    474A  ALA      3.1    11.4    -      -       -      +
    475A  VAL*     3.8     4.9    -      -       +      -
    492A  CYS*     1.3    77.1    -      -       -      +
    494A  VAL*     1.3    63.5    +      -       -      +
    500A  HIS      3.5     1.1    -      -       -      +
    501A  LEU*     3.4     9.1    -      -       -      +
    502A  LEU*     2.9    42.6    +      -       +      +
    526A  THR*     3.7    30.5    -      -       +      +
    655A  PRO*     4.7     2.0    -      -       -      +
    658A  LEU*     5.2     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 494 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472A  GLU      3.9     0.7    -      -       -      +
    473A  LEU*     3.2     4.6    -      -       -      +
    474A  ALA*     2.9    34.3    +      -       +      +
    493A  ALA*     1.3    74.1    -      -       -      +
    495A  GLY*     1.3    62.1    +      -       -      +
    496A  GLY      4.3     2.9    -      -       -      +
    498A  GLY      5.1     0.9    -      -       -      +
    499A  GLY*     4.1    17.9    -      -       -      -
    500A  HIS      3.3     3.6    -      -       -      -
    501A  LEU*     3.4    22.4    -      -       +      -
    638A  LEU*     4.0    18.2    -      -       +      -
    641A  LEU*     3.5    26.2    -      -       +      -
    654A  ALA*     4.8     1.3    -      -       +      -
    655A  PRO*     3.7    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 495 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472A  GLU      3.1     5.4    -      -       -      -
    473A  LEU*     3.6    13.0    -      -       -      -
    494A  VAL*     1.3    79.6    -      -       -      +
    496A  GLY*     1.3    61.1    +      -       -      -
    498A  GLY      3.9     5.2    +      -       -      +
    500A  HIS*     3.1    32.4    +      -       -      +
    502A  LEU*     5.5     2.0    -      -       -      +
    530A  PHE*     4.5    11.0    -      -       -      -
----------------------------------------------------------
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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