Contacts of the strand formed by residues 370 - 374 (chain D) in PDB entry 4O9U


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 VAL 370 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288D  MET*     3.6    46.0    -      -       +      +
    289D  LEU*     4.8     4.3    -      -       +      -
    292D  ALA*     3.6     9.9    -      -       +      -
    294D  LYS      3.2     2.6    +      -       -      -
    295D  VAL*     3.2    11.7    -      -       +      +
    296D  VAL      3.0    22.2    +      -       -      -
    368D  VAL*     3.4     4.2    -      -       -      +
    369D  ASP*     1.3    86.2    -      -       +      +
    371D  ALA*     1.3    60.7    +      -       -      +
    372D  VAL*     3.6    18.1    +      -       +      +
    404D  ASN*     3.2    10.3    -      -       +      +
    406D  ILE*     3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 371 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296D  VAL*     3.3     9.9    -      -       +      +
    298D  VAL*     5.3     0.9    -      -       +      -
    365D  PHE*     4.3    13.2    -      -       +      -
    368D  VAL*     4.0     4.0    -      -       +      +
    369D  ASP      4.4     0.2    -      -       -      -
    370D  VAL*     1.3    70.1    -      -       -      +
    372D  VAL*     1.3    63.7    +      -       -      +
    373D  VAL*     3.4     2.0    +      -       +      +
    399D  VAL*     3.8    24.2    -      -       +      -
    402D  ALA*     3.9    19.9    -      -       +      +
    404D  ASN      2.7    10.9    +      -       -      +
    405D  VAL*     3.3    11.0    -      -       +      +
    406D  ILE      3.3    18.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 372 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289D  LEU*     3.9    23.6    -      -       +      -
    295D  VAL*     4.4     5.2    -      -       +      -
    296D  VAL      2.8     8.6    +      -       -      +
    297D  PHE*     3.2    32.3    -      -       +      -
    298D  VAL*     2.7    31.5    +      -       -      +
    370D  VAL*     3.6    21.7    +      -       +      -
    371D  ALA*     1.3    68.8    -      -       -      +
    373D  VAL*     1.3    58.0    +      -       -      +
    374D  ILE*     4.2     1.5    +      -       +      +
    406D  ILE*     3.4    22.0    -      -       +      +
    408D  ILE*     4.1    22.9    -      -       +      -
    440D  LEU*     5.5     0.7    -      -       +      -
    443D  LEU*     5.1     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 373 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298D  VAL*     3.4    28.0    -      -       +      +
    371D  ALA      3.7    10.8    -      -       -      +
    372D  VAL*     1.3    77.0    -      -       -      +
    374D  ILE*     1.3    58.7    +      -       -      +
    376D  ALA*     3.7    32.5    -      -       +      +
    380D  VAL*     4.3    10.8    -      -       +      -
    399D  VAL*     3.9    20.6    -      -       +      -
    405D  VAL*     4.2     7.6    -      -       +      -
    406D  ILE      2.5    14.9    +      -       -      +
    407D  VAL*     4.3    13.2    -      -       +      -
    408D  ILE*     2.7    35.4    +      -       -      +
    423D  LEU*     5.0     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 374 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297D  PHE*     5.2     2.9    -      -       +      -
    298D  VAL      2.9    10.8    +      -       -      +
    299D  PRO*     3.5    23.9    -      -       +      +
    300D  GLY      2.9    27.4    +      -       -      -
    303D  MET*     3.9    19.6    +      -       +      -
    308D  ALA*     4.5     0.9    -      -       +      -
    312D  LEU*     4.1    23.3    -      -       +      -
    372D  VAL*     5.0     2.0    -      -       +      +
    373D  VAL*     1.3    74.2    -      -       -      +
    375D  GLY*     1.3    61.5    +      -       -      +
    376D  ALA      3.2     1.5    +      -       -      -
    408D  ILE*     3.7    33.0    -      -       +      -
    436D  ALA*     3.6    32.1    -      -       +      -
    440D  LEU*     4.2    15.7    -      -       +      -
----------------------------------------------------------
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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