Contacts of the strand formed by residues 59 - 64 (chain z) in PDB entry 6FF7


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 THR 59 (chain z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3959  TRP*     5.9     3.1    -      -       -      -
     51N  GLY*     3.4     9.4    +      -       -      -
     55N  GLU      4.1     8.3    -      -       -      -
     56N  THR*     2.3    36.4    +      -       -      +
     58N  GLY      2.3    12.7    -      -       -      +
     59N  THR*     0.5   361.6    -      -       -      +
     49z  ARG      4.4     0.2    -      -       -      +
     55z  GLU      4.2     1.3    -      -       -      -
     56z  THR*     2.9     7.0    -      -       -      +
     58z  GLY      1.3    20.6    -      -       -      -
     60z  ALA*     1.3    14.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 60 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22N  TYR*     3.8     1.4    -      -       -      +
     23N  ILE*     2.9     6.5    +      -       +      +
     26N  LEU*     5.4     5.4    -      -       +      -
     59N  THR*     1.0    58.7    -      -       -      +
     60N  ALA*     0.2   425.2    +      -       +      +
     61N  TYR      2.2     0.2    +      -       -      -
     22z  TYR*     3.8     1.6    -      -       -      -
     23z  ILE*     4.2     8.3    -      -       +      -
     49z  ARG      3.4     3.1    -      -       -      -
     59z  THR      1.3    10.3    -      -       -      -
     61z  TYR*     1.3    24.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 61 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48N  ILE*     3.6     0.9    -      -       -      +
     49N  ARG*     2.8    16.8    -      -       +      +
     60N  ALA*     2.3     6.9    -      -       -      +
     61N  TYR*     0.6   407.4    +      -       +      +
     22z  TYR*     4.9     0.4    -      -       -      +
     48z  ILE*     3.5     1.4    -      -       -      +
     49z  ARG*     2.9    29.7    +      -       +      +
     60z  ALA*     1.3    32.6    -      -       -      +
     62z  VAL*     1.3     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20N  ILE*     3.2     1.7    -      -       -      -
     21N  LEU      2.9     3.1    +      -       -      -
     23N  ILE*     6.3     0.2    -      -       +      -
     39N  PHE*     5.5     0.9    -      -       +      -
     48N  ILE*     4.1     7.0    -      -       +      +
     60N  ALA*     6.1     0.2    -      -       +      -
     61N  TYR*     0.8    92.1    -      -       -      +
     62N  VAL*     0.3   323.9    +      -       +      +
     63N  VAL*     1.3    25.6    +      -       -      +
     21z  LEU      3.0     0.2    +      -       -      -
     39z  PHE*     5.5     1.8    -      -       +      -
     47z  GLN      3.6     9.0    -      -       -      +
     48z  ILE*     4.7     0.2    -      -       +      -
     61z  TYR      1.3     5.2    -      -       -      -
     63z  VAL*     1.3    20.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 63 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19N  ARG      2.9    12.3    -      -       -      +
     20N  ILE*     4.4     5.4    -      -       +      -
     47N  GLN*     2.8    18.4    +      -       +      +
     48N  ILE*     4.5     0.2    -      -       -      +
     63N  VAL*     0.7   381.4    +      -       +      +
     19z  ARG*     3.5     4.5    -      -       +      +
     46z  ARG*     2.9    19.8    +      -       +      -
     47z  GLN      2.9     5.7    +      -       -      +
     62z  VAL*     1.3    32.3    -      -       -      +
     64z  TYR*     1.3    11.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 64 (chain z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19N  ARG      2.7     3.5    +      -       -      +
     44N  PRO      3.9     5.6    -      -       -      +
     46N  ARG*     3.4     1.6    -      -       -      +
     63N  VAL*     0.9    64.5    -      -       -      +
     64N  TYR*     0.3   421.7    +      -       +      +
     65N  GLU*     1.6     2.2    +      -       -      -
     19z  ARG*     4.7     0.2    -      -       -      +
     46z  ARG*     3.4    19.9    -      -       -      +
     63z  VAL*     1.3     8.4    -      -       -      +
     65z  GLU*     1.3    12.3    -      -       -      -
     70z  ALA*     5.2     3.1    -      -       +      -
----------------------------------------------------------
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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