Contacts of the strand formed by residues 509 - 512 (chain B) in PDB entry 3U0Z


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 509 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491B  ILE*     4.8     3.4    -      -       +      -
    504B  ILE*     4.7     4.5    -      -       +      -
    508B  VAL*     1.3    77.7    -      -       -      +
    510B  GLY*     1.3    60.4    +      -       -      +
    519B  MET      3.6     0.5    -      -       -      +
    520B  LYS*     3.3     3.7    -      -       -      -
    521B  LEU*     2.8    40.7    +      -       +      +
    527B  PHE*     4.6    14.4    -      -       +      -
    542B  VAL*     4.2    16.4    -      -       +      -
    543B  ARG      3.5    13.5    -      -       -      +
    544B  ALA*     4.7     0.2    -      -       -      -
    545B  ASP*     4.0     4.9    -      -       -      +
    548B  CYS*     4.5    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 510 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509B  ALA*     1.3    72.6    -      -       -      +
    511B  VAL*     1.3    64.6    +      -       -      -
    512B  ILE*     3.9     5.6    +      -       -      +
    518B  GLU*     3.5    20.0    -      -       -      -
    519B  MET      3.4     5.8    -      -       -      -
    520B  LYS*     4.4     1.1    -      -       -      -
    541B  SER      3.7     0.7    -      -       -      +
    542B  VAL*     3.5     6.6    -      -       -      +
    543B  ARG*     3.0    33.9    +      -       -      +
    545B  ASP*     3.6    10.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 511 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509B  ALA      5.1     0.2    -      -       -      +
    510B  GLY*     1.3    73.0    -      -       -      -
    512B  ILE*     1.3    64.6    +      -       -      +
    513B  THR*     5.0     2.9    -      -       -      +
    516B  SER*     4.1     4.1    +      -       -      +
    517B  LYS      3.4    16.5    -      -       -      +
    519B  MET*     2.8    40.9    +      -       +      +
    521B  LEU*     4.0    16.4    -      -       +      -
    540B  ALA*     4.1    15.7    -      -       +      -
    541B  SER      3.6     4.5    -      -       -      +
    542B  VAL*     4.8     9.2    -      -       +      -
    583B  ILE*     5.8     2.2    -      -       +      -
    646B  CMP      3.6    57.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 512 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    490B  TYR*     6.2     2.7    -      -       +      -
    494B  GLU*     4.0     1.2    -      -       -      +
    510B  GLY      4.2     7.6    -      -       -      +
    511B  VAL*     1.3    82.7    -      -       -      +
    513B  THR*     1.3    79.4    +      -       -      +
    516B  SER*     3.9     2.2    -      -       -      +
    517B  LYS      3.7    13.7    -      -       -      +
    518B  GLU*     3.4    34.1    -      -       +      +
    540B  ALA*     3.6     1.7    -      -       -      +
    541B  SER*     2.9    43.7    +      -       -      +
    543B  ARG*     4.7    19.3    -      -       +      +
----------------------------------------------------------
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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