Contacts of the strand formed by residues 618 - 622 (chain A) in PDB entry 2XR9


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 618 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    591A  THR*     4.0     9.7    -      -       +      +
    592A  LYS*     2.9    55.1    +      -       -      +
    595A  HIS*     4.6     4.2    -      -       +      +
    596A  LEU*     3.6    19.3    -      -       +      +
    600A  ARG*     4.9     0.2    -      -       -      -
    611A  ILE*     3.6    11.4    -      -       +      +
    612A  LEU      3.4    13.2    -      -       -      +
    613A  TYR*     3.5    21.0    -      -       +      -
    617A  PHE*     1.3    76.9    -      -       -      +
    619A  SER*     1.3    67.1    +      -       -      +
    630A  TRP*     3.4    15.1    -      -       +      -
    631A  THR*     3.4     1.7    -      -       -      +
    632A  SER      2.7    34.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 619 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610A  ASP      3.5     0.7    -      -       -      +
    611A  ILE*     3.4     5.5    -      -       -      +
    612A  LEU*     2.9    54.7    +      -       -      +
    614A  HIS*     4.1     5.9    -      -       -      -
    617A  PHE*     4.6     6.0    -      -       -      -
    618A  GLU*     1.3    78.4    -      -       -      +
    620A  GLY*     1.3    59.5    +      -       -      +
    621A  TYR      4.7     0.7    +      -       -      -
    628A  PRO*     4.4    11.1    -      -       -      +
    630A  TRP*     3.3    22.4    -      -       -      -
    631A  THR*     3.7    15.5    -      -       -      -
    699A  THR      4.9     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 620 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    609A  TYR*     4.0    13.5    -      -       -      -
    610A  ASP      3.5     5.6    -      -       -      -
    611A  ILE*     4.3     1.1    -      -       -      -
    619A  SER*     1.3    71.3    -      -       -      +
    621A  TYR*     1.3    56.8    +      -       -      -
    622A  SER      3.7     0.2    +      -       -      -
    628A  PRO*     3.3     3.0    -      -       -      +
    629A  LEU*     2.7    35.0    +      -       -      +
    630A  TRP*     3.0    36.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 621 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    609A  TYR*     3.2     4.9    -      -       -      -
    610A  ASP*     2.7    50.6    +      -       +      +
    612A  LEU*     3.6    23.3    -      -       +      -
    619A  SER*     3.8     2.4    -      -       -      +
    620A  GLY*     1.3    71.7    -      -       -      +
    622A  SER*     1.3    71.3    +      -       -      +
    623A  GLU*     3.5     3.9    +      -       +      -
    626A  LEU*     3.4    20.5    +      -       -      -
    627A  MET*     3.5    28.5    -      -       -      -
    628A  PRO*     3.9     4.3    -      -       +      -
    658A  VAL*     3.7    19.7    -      -       +      -
    662A  PHE      2.6    29.4    +      -       -      -
    663A  SER*     3.6    10.2    -      -       -      -
    664A  GLN*     4.2     1.2    +      -       -      +
    698A  VAL      5.0     2.2    +      -       -      -
    699A  THR*     3.7    39.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 622 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    607A  THR*     4.4     5.2    +      -       -      -
    608A  SER      3.9     7.7    +      -       -      -
    609A  TYR*     4.0     3.8    -      -       -      +
    620A  GLY      3.7     2.4    +      -       -      -
    621A  TYR*     1.3    74.3    -      -       -      +
    623A  GLU*     1.3    57.5    +      -       -      +
    624A  ILE*     3.1    11.8    +      -       -      +
    625A  PHE*     3.1    25.6    +      -       -      -
    626A  LEU*     3.0    30.1    +      -       -      -
    627A  MET      2.9    21.0    +      -       -      -
    629A  LEU*     3.8    28.7    -      -       -      +
----------------------------------------------------------
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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