Contacts of the strand formed by residues 374 - 378 (chain E) in PDB entry 4R2G


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 HIS 374 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256E  SER*     4.6     1.3    -      -       -      -
    257E  THR*     3.5     3.6    -      -       -      -
    258E  GLN*     3.6    19.5    +      -       +      +
    259E  LEU*     3.7    52.3    +      -       +      +
    261E  LEU*     4.3    11.7    -      -       +      +
    294E  ILE*     4.2    22.8    -      -       +      +
    331E  CYS*     5.4     0.2    -      -       -      -
    373E  MET*     1.3    66.7    -      -       -      +
    375E  SER*     1.3    63.0    +      -       -      +
    376E  PHE*     3.4    47.1    -      +       +      -
    383E  PHE      3.9     0.2    -      -       -      +
    385E  CYS*     2.9    44.7    +      -       +      +
    387E  SER*     4.1     9.8    +      -       -      +
    416E  LEU*     5.4     4.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 375 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256E  SER*     3.5     1.9    -      -       -      -
    257E  THR*     2.5    58.2    +      -       -      +
    370E  GLU*     2.9    31.0    +      -       -      +
    373E  MET      2.9     0.8    +      -       -      -
    374E  HIS*     1.3    72.3    +      -       -      +
    376E  PHE*     1.3    63.8    +      -       -      +
    383E  PHE      3.3    11.4    -      -       -      -
    384E  TYR*     4.1    11.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 376 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254E  VAL*     5.6     0.2    -      -       +      -
    255E  VAL      4.2     7.0    -      -       -      +
    256E  SER*     4.4    10.1    -      -       -      -
    261E  LEU*     4.4    13.5    -      -       +      -
    296E  CYS*     3.4    30.3    -      -       +      -
    374E  HIS*     3.4    42.0    -      +       +      -
    375E  SER*     1.3    74.0    -      -       -      +
    377E  ASN*     1.3    72.2    +      -       -      +
    378E  CYS*     3.7    16.2    -      -       +      -
    381E  GLU      3.7     0.5    -      -       -      +
    382E  PHE*     3.8     6.5    -      -       -      -
    383E  PHE*     2.9    61.8    +      +       +      +
    385E  CYS*     3.4    22.7    -      -       -      -
    445E  CYS*     4.7     3.6    -      -       -      -
    511E  NAG      5.1     2.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 377 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112E  TRP*     4.3    11.5    -      -       +      -
    116E  LEU*     4.2    10.5    -      -       -      +
    210E  PHE*     3.9    23.0    -      -       +      +
    254E  VAL*     5.8     1.5    -      -       +      +
    255E  VAL      4.3    10.3    +      -       -      +
    376E  PHE*     1.3    79.5    -      -       -      +
    378E  CYS*     1.3    62.8    +      -       -      +
    379E  GLY      4.1     0.5    +      -       -      -
    380E  GLY*     3.4    25.7    +      -       -      -
    381E  GLU      3.4     9.5    +      -       -      -
    382E  PHE*     3.6    31.8    -      -       +      -
    511E  NAG      3.8    26.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 378 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296E  CYS      4.4     4.5    -      -       -      -
    376E  PHE*     3.7    10.8    -      -       +      -
    377E  ASN*     1.3    73.9    -      -       -      +
    379E  GLY*     1.3    65.9    +      -       -      +
    380E  GLY      3.3     0.4    -      -       -      -
    381E  GLU*     3.1    21.4    +      -       -      +
    383E  PHE*     3.5    17.2    -      -       +      -
    443E  ILE*     3.2    30.2    -      -       -      +
    445E  CYS*     2.0    58.6    -      -       -      -
    511E  NAG      5.4     1.6    -      -       -      -
----------------------------------------------------------
 Back to top of page


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