Contacts of the strand formed by residues 509 - 513 (chain B) in PDB entry 2JGE


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 GLN 509 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427B  ALA*     4.6     0.9    +      -       -      +
    501B  PRO*     3.7    35.6    -      -       +      +
    502B  PRO      4.2     9.6    -      -       -      +
    503B  TYR*     3.3    32.9    +      -       -      +
    504B  THR*     4.6     1.1    +      -       -      +
    507B  ALA*     3.8    22.7    -      -       +      +
    508B  GLN*     1.3    75.4    -      -       -      +
    510B  TYR*     1.3    61.6    +      -       -      +
    520B  VAL*     3.7    19.3    -      -       +      +
    521B  ARG      3.2     6.1    -      -       -      +
    522B  ARG*     3.8    23.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 510 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427B  ALA*     3.4    29.4    -      -       +      +
    428B  TYR      4.3     2.9    -      -       -      +
    429B  ILE*     3.7    29.7    -      -       +      +
    500B  TRP*     4.9     1.8    -      -       -      +
    501B  PRO*     5.4     0.7    -      -       -      -
    503B  TYR*     4.7     2.0    -      +       +      -
    508B  GLN      3.6    12.8    -      -       -      +
    509B  GLN*     1.3    75.3    -      -       -      +
    511B  VAL*     1.3    76.6    +      -       -      +
    520B  VAL*     3.5     4.1    -      -       -      +
    521B  ARG*     2.8    69.0    +      -       +      +
    522B  ARG      4.8     0.3    +      -       -      -
    523B  GLY      3.4    34.0    +      -       -      -
    524B  LEU*     3.8    28.7    -      -       +      +
    525B  ARG      5.2     0.9    +      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    427B  ALA      3.1     3.8    +      -       -      -
    428B  TYR*     3.3     4.2    -      -       +      -
    429B  ILE*     2.9    26.0    +      -       -      +
    500B  TRP*     3.4    60.3    -      -       +      -
    501B  PRO*     4.0    13.2    -      -       +      -
    510B  TYR*     1.3    83.3    -      -       -      +
    512B  SER*     1.3    59.5    +      -       -      +
    513B  LEU*     4.2     3.1    -      -       +      -
    518B  LEU*     3.6    29.8    -      -       +      -
    519B  GLU      3.3     9.9    -      -       -      +
    520B  VAL*     4.3     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 512 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429B  ILE*     3.4     7.8    -      -       -      +
    431B  GLU*     3.7    13.5    -      -       -      -
    475B  ARG*     5.0     1.0    +      -       -      -
    510B  TYR*     4.9     0.2    -      -       -      -
    511B  VAL*     1.3    72.5    -      -       -      +
    513B  LEU*     1.3    61.8    +      -       -      +
    514B  ASN*     3.7    14.9    +      -       -      +
    516B  LYS      5.3     0.2    -      -       -      +
    517B  PRO      4.9     1.2    +      -       -      +
    518B  LEU*     3.6    23.2    -      -       -      +
    519B  GLU*     3.2    30.1    +      -       -      +
    521B  ARG*     3.5    32.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 513 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428B  TYR*     3.7    36.8    -      -       +      -
    429B  ILE      2.7    12.9    +      -       -      +
    430B  PHE*     3.5    16.0    -      -       +      -
    431B  GLU      2.8    31.4    +      -       -      -
    432B  HIS      3.9     1.6    +      -       -      -
    472B  PHE*     3.9     5.7    -      -       -      -
    475B  ARG*     4.6     2.5    -      -       -      +
    476B  LEU*     3.7    23.1    -      -       +      -
    479B  TYR*     3.6    21.8    -      -       +      -
    480B  TRP*     3.8    20.6    -      -       +      -
    500B  TRP*     4.3     3.6    -      -       +      -
    511B  VAL*     4.2     3.8    -      -       +      -
    512B  SER*     1.3    70.1    -      -       -      +
    514B  ASN*     1.3    58.8    +      -       -      +
    518B  LEU*     3.6    28.0    -      -       +      -
----------------------------------------------------------
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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