Contacts of the strand formed by residues 657 - 662 (chain A) in PDB entry 4UIS


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 ARG 657 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  PRO*     5.7     7.9    -      -       +      -
    181A  PHE*     4.5     7.6    -      -       -      -
    218A  PHE*     2.7    76.1    +      -       +      +
    655A  ALA*     4.1    20.0    +      -       -      +
    656A  ILE*     1.3    76.0    -      -       -      +
    658A  ALA*     1.3    68.1    +      -       -      +
    659A  ARG*     5.2    10.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 658 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  PRO*     4.2    10.6    -      -       -      +
     44A  LEU*     4.4    15.5    +      -       +      +
     47A  THR*     6.2     0.6    -      -       +      +
    181A  PHE*     4.1    12.1    -      -       +      -
    215A  MET*     3.9    17.9    -      -       +      -
    216A  GLN      3.2    15.3    -      -       -      +
    217A  LEU*     3.6    24.2    -      -       +      +
    218A  PHE*     5.4     1.1    -      -       -      -
    657A  ARG*     1.3    80.5    -      -       -      +
    659A  ARG*     1.3    65.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 659 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ILE      3.9    11.3    -      -       -      +
     43A  PRO*     4.1    23.2    -      -       +      +
     44A  LEU*     5.1     0.9    -      -       -      +
    215A  MET*     4.0     4.7    -      -       -      -
    216A  GLN*     2.9    60.2    +      -       +      +
    218A  PHE*     4.9    11.3    -      -       +      -
    657A  ARG*     5.2    10.8    -      -       +      +
    658A  ALA*     1.3    76.3    -      -       -      +
    660A  ILE*     1.3    70.9    +      -       -      +
    661A  PHE*     3.8    12.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 660 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ILE*     3.0    61.4    +      -       +      +
     44A  LEU*     5.5     4.4    -      -       +      +
     73A  ILE*     3.5    13.7    -      -       +      -
    192A  ILE*     3.9     9.9    -      -       +      -
    195A  CYS*     4.4     4.5    -      -       -      -
    213A  CYS*     3.4    29.8    -      -       -      -
    214A  ALA      3.1    18.4    -      -       -      +
    215A  MET*     3.6    18.6    -      -       +      +
    659A  ARG*     1.3    78.8    +      -       -      +
    661A  PHE*     1.3    68.8    +      -       -      +
    662A  LEU*     6.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 661 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ILE      5.2     0.7    -      -       -      +
     70A  THR*     3.7    13.7    -      -       -      -
    213A  CYS*     4.0     1.7    -      -       -      -
    214A  ALA*     2.9    53.6    +      -       +      +
    216A  GLN*     3.4    39.7    -      -       +      -
    659A  ARG*     3.8    20.6    -      -       +      +
    660A  ILE*     1.3    86.7    -      -       -      +
    662A  LEU*     1.3    75.9    +      -       -      +
    663A  ILE*     3.5    26.2    -      -       +      -
    664A  ALA      5.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 662 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  CYS*     6.3     3.1    -      -       -      -
    199A  HIS*     5.6    14.6    -      -       +      +
    212A  LEU      3.7     7.9    -      -       -      +
    213A  CYS*     4.8     4.0    -      -       -      +
    660A  ILE*     6.3     1.1    -      -       +      -
    661A  PHE*     1.3    84.0    -      -       -      +
    663A  ILE*     1.3    66.6    +      -       -      +
    664A  ALA*     3.8     1.2    +      -       -      +
----------------------------------------------------------
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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