Contacts of the strand formed by residues 21 - 27 (chain A) in PDB entry 3U8Z


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 21 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  LYS*     1.4    89.6    +      -       +      +
     22A  PHE*     1.3    59.4    +      -       -      +
     36A  ASN*     4.0    31.8    +      -       +      +
     37A  CYS      3.2     9.4    -      -       -      +
     38A  GLU*     3.9    25.8    -      -       +      +
     39A  MET*     3.4    15.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  THR*     1.3    73.5    -      -       -      +
     23A  THR*     1.3    71.5    +      -       -      +
     24A  VAL*     3.6    19.1    -      -       +      -
     35A  PHE      3.6     0.2    -      -       -      +
     36A  ASN*     3.7     4.7    -      -       -      -
     37A  CYS*     2.8    51.8    +      -       -      +
     38A  GLU      3.6    19.1    -      -       -      -
     39A  MET*     3.7    29.4    -      -       +      -
     81A  VAL*     3.2    35.0    -      -       +      -
     82A  LEU*     4.3    16.8    -      -       +      -
     92A  VAL*     4.5    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  PHE*     1.3    78.8    -      -       -      +
     24A  VAL*     1.3    67.8    +      -       -      +
     25A  ARG      4.3     0.7    -      -       -      +
     34A  GLU*     3.8    37.0    -      -       +      +
     35A  PHE      3.4     8.7    -      -       -      +
     36A  ASN*     3.9    12.5    +      -       -      +
     91A  PRO*     5.3     3.5    -      -       +      +
     92A  VAL*     4.3    14.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  PHE*     3.6    31.9    -      -       +      -
     23A  THR*     1.3    76.1    -      -       -      +
     25A  ARG*     1.3    62.7    +      -       -      +
     26A  ILE*     3.7    17.0    +      -       +      -
     34A  GLU*     3.3     4.2    -      -       -      -
     35A  PHE*     2.9    35.4    +      -       -      +
     37A  CYS*     3.6    17.9    -      -       +      -
     46A  LEU*     3.9    16.6    -      -       +      -
     81A  VAL*     4.7     1.6    -      -       +      -
     92A  VAL*     3.5    14.8    -      -       +      +
     94A  PHE*     3.7    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  THR*     4.3     1.6    -      -       +      +
     24A  VAL*     1.3    69.3    -      -       -      +
     26A  ILE*     1.3    62.9    +      -       -      +
     27A  VAL*     4.1     6.3    -      -       +      -
     32A  GLU*     3.8    36.9    +      -       +      +
     33A  MET      3.3    13.5    -      -       -      +
     34A  GLU*     3.7    24.6    +      -       +      +
     91A  PRO*     4.0    31.3    -      -       +      +
     92A  VAL      2.8     9.8    +      -       -      +
     93A  THR*     3.3    31.9    +      -       +      +
     94A  PHE      3.0    26.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  VAL*     3.7    26.9    +      -       +      -
     25A  ARG*     1.3    73.1    -      -       -      +
     27A  VAL*     1.3    61.8    +      -       -      +
     28A  THR*     3.8     6.8    +      -       +      -
     31A  ALA      3.8     1.2    -      -       -      +
     33A  MET*     2.7    42.5    +      -       +      +
     35A  PHE*     3.6    31.2    -      -       +      -
     46A  LEU*     4.3     8.3    -      -       +      -
     50A  VAL*     3.9    25.4    -      -       +      -
     64A  LEU*     3.7    22.7    -      -       +      -
     94A  PHE*     3.4    13.7    -      -       +      +
     96A  PHE*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ARG*     4.4    11.9    -      -       +      -
     26A  ILE*     1.3    74.6    -      -       -      +
     28A  THR*     1.4    69.4    +      -       -      +
     31A  ALA      3.6     8.3    -      -       -      +
     32A  GLU*     4.5    12.8    -      -       +      -
     93A  THR*     4.2    22.9    -      -       +      -
     94A  PHE      2.9    11.0    +      -       -      +
     95A  HIS*     3.3    33.6    -      -       +      +
     96A  PHE      2.7    30.8    +      -       -      +
     97A  LEU*     5.7     0.5    -      -       -      +
----------------------------------------------------------
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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