Contacts of the strand formed by residues 445 - 448 (chain U) in PDB entry 2GLJ


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 GLU 445 (chain U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109U  PRO*     6.5     0.2    -      -       -      -
    260U  MET*     3.1     5.2    -      -       -      -
    261U  GLY      2.9    29.8    +      -       -      +
    263U  GLY*     3.3    10.6    +      -       -      -
    264U  GLN*     2.8    46.5    +      -       +      +
    265U  ASP*     3.0    26.8    +      -       -      +
    437U  LEU*     3.9     7.1    -      -       +      +
    438U  LEU      3.8     4.3    -      -       -      +
    439U  ASN*     3.5    20.2    -      -       -      +
    440U  MSE      3.7     5.0    -      -       -      -
    441U  HIS*     3.1    23.8    +      -       -      -
    442U  ALA      3.5    15.7    -      -       -      +
    444U  TRP*     1.3    74.2    -      -       -      +
    446U  ILE*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 446 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252U  TYR*     3.6    36.8    -      -       +      +
    258U  MET*     3.6    39.5    -      -       +      -
    259U  VAL      3.2     4.7    -      -       -      +
    260U  MET*     4.1    21.1    -      -       +      -
    363U  LEU*     5.1     1.9    -      -       +      +
    437U  LEU*     3.1    19.6    -      -       -      +
    438U  LEU*     3.1    47.2    +      -       +      +
    439U  ASN*     4.5     9.4    -      -       -      +
    445U  GLU*     1.3    81.9    -      -       -      +
    447U  SER*     1.3    66.1    +      -       -      +
    173X  GLY      6.1     0.4    -      -       -      -
    175X  SER*     6.0     2.0    -      -       -      -
    200X  ASN*     4.7     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 447 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33U  ASN*     5.2     0.2    +      -       -      -
    258U  MET*     2.9    11.2    -      -       -      +
    259U  VAL*     2.8    39.0    +      -       -      +
    264U  GLN*     2.8    32.7    +      -       -      -
    268U  ILE*     3.7    16.8    -      -       -      +
    363U  LEU*     4.3     3.1    -      -       -      -
    435U  VAL*     4.9     1.6    -      -       -      -
    436U  ALA      4.4     4.9    -      -       -      -
    437U  LEU*     3.5    11.9    -      -       -      -
    446U  ILE*     1.3    74.1    -      -       -      +
    448U  SER*     1.3    60.9    +      -       -      +
    449U  LYS      3.7     0.4    +      -       -      -
    452U  ILE*     4.0     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 448 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13U  TRP*     4.2     6.1    +      -       -      -
    257U  SER      3.8     7.3    +      -       -      -
    258U  MET*     4.3     0.9    -      -       -      -
    363U  LEU*     3.4    21.7    -      -       -      +
    364U  GLY*     3.8     7.6    -      -       -      -
    435U  VAL*     5.1     0.2    -      -       -      +
    436U  ALA      4.7     2.4    +      -       -      -
    447U  SER*     1.3    75.1    -      -       -      +
    449U  LYS*     1.3    64.8    +      -       -      +
    450U  ALA*     3.5    15.9    +      -       -      +
    451U  ASP*     2.8    43.1    +      -       -      +
    452U  ILE*     2.8    14.8    +      -       -      +
    203X  ILE*     4.5     3.6    -      -       -      +
----------------------------------------------------------
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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