Contacts of the strand formed by residues 19 - 26 (chain B) in PDB entry 5T4S


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 19 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  THR      3.3     2.6    -      -       -      +
     14B  ASN*     3.7     1.7    -      -       -      +
     15B  TYR*     2.8    59.7    +      -       +      +
     18B  THR*     1.3    90.3    +      -       -      +
     20B  TYR*     1.3    62.3    +      -       -      +
     21B  TYR*     3.9    14.3    -      -       +      -
    121B  LEU*     3.0    24.1    +      -       -      +
    123B  GLU*     2.8    31.0    +      -       -      +
    124B  PHE*     3.3    23.1    -      -       +      -
    402B  77O      3.8    23.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  LEU*     4.5     6.4    -      -       +      +
     13B  THR      3.3     4.7    -      -       -      -
     14B  ASN*     3.1    30.1    +      -       +      -
     17B  ASP*     3.3    17.6    +      -       -      -
     19B  GLN*     1.3    76.0    -      -       -      +
     21B  TYR*     1.3    63.4    +      -       -      +
     36B  VAL*     3.7    10.9    -      -       -      +
     37B  PHE      4.5     1.9    +      -       -      -
    162B  TYR*     3.5    57.0    +      +       +      -
    163B  ASN      2.7    21.7    +      -       -      -
    173B  GLY      3.3    28.3    -      -       -      -
    174B  GLY*     5.0     1.3    -      -       -      -
    317B  ALA*     3.7    23.6    -      -       +      -
    321B  ARG*     3.1    18.2    +      -       -      -
    402B  77O      3.2    23.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263A  PRO*     4.6     8.3    +      -       -      +
     12B  LEU*     3.9     7.3    -      -       -      +
     13B  THR*     2.8    65.2    +      -       +      +
     15B  TYR*     3.7    27.6    -      -       +      +
     19B  GLN*     3.9    16.6    -      -       +      -
     20B  TYR*     1.3    77.7    -      -       -      +
     22B  GLY*     1.3    57.4    +      -       -      +
     34B  LYS*     3.8    38.4    +      -       +      +
     35B  VAL      3.1    24.9    -      -       -      +
     36B  VAL*     4.1     0.9    -      -       +      +
     37B  PHE*     5.2     0.4    -      -       -      -
    123B  GLU*     3.5    29.6    +      -       +      +
    124B  PHE*     3.8    18.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLY 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  VAL*     4.0     0.7    -      -       -      -
     11B  ILE      3.6    17.9    -      -       -      -
     12B  LEU*     3.7    12.6    -      -       -      +
     21B  TYR*     1.3    75.2    -      -       -      +
     23B  GLU*     1.3    64.3    +      -       -      -
     34B  LYS*     3.3     4.8    -      -       -      -
     35B  VAL*     2.6    41.3    +      -       -      +
     37B  PHE*     3.9     7.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  THR*     3.6    26.4    +      -       +      +
    283A  ASP*     3.7    12.0    -      -       -      +
    322A  LYS*     2.5    38.8    +      -       -      -
     10B  VAL*     3.8    22.0    -      -       +      +
     11B  ILE      4.6     4.8    +      -       -      +
     22B  GLY*     1.3    78.5    -      -       -      +
     24B  ILE*     1.3    66.9    +      -       -      +
     32B  THR*     3.7    22.2    -      -       +      +
     33B  PHE      3.3     6.7    -      -       -      +
     34B  LYS*     5.0     4.7    -      -       +      -
     37B  PHE*     5.0     0.2    -      -       -      -
     98B  THR      4.3     2.6    -      -       -      +
     99B  VAL*     4.9     1.6    -      -       -      -
    100B  GLY      4.9     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  GLY      4.2     0.2    +      -       -      -
     23B  GLU*     1.3    79.9    -      -       -      +
     25B  GLY*     1.3    57.9    +      -       -      +
     26B  ILE*     4.0    26.2    -      -       +      -
     31B  GLN      3.6     0.7    -      -       -      +
     32B  THR*     3.4     5.1    -      -       -      -
     33B  PHE*     2.9    32.7    +      -       +      +
     35B  VAL*     3.8    34.1    -      -       +      -
     37B  PHE*     3.9    13.0    -      -       +      -
     44B  VAL*     4.5     7.4    -      -       +      -
     46B  VAL*     4.7     1.1    -      -       +      -
     97B  ILE*     4.0    15.3    -      -       +      -
     98B  THR      3.2    13.5    -      -       -      +
     99B  VAL*     3.9    19.7    -      -       +      -
    128B  VAL*     3.8    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  ILE*     1.3    73.1    -      -       -      +
     26B  ILE*     1.3    61.2    +      -       -      -
     27B  GLY      4.3     0.4    -      -       -      -
     30B  PRO*     4.2    16.6    -      -       -      -
     31B  GLN      3.3    10.1    -      -       -      -
     32B  THR*     4.5     4.0    -      -       -      -
     96B  ILE      4.3     0.7    -      -       -      -
     97B  ILE*     3.1    11.1    -      -       -      +
     98B  THR*     2.8    40.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  ILE*     4.0    13.2    -      -       +      -
     25B  GLY*     1.3    79.0    -      -       -      +
     27B  GLY*     1.3    62.9    +      -       -      +
     29B  PRO      3.9     1.4    -      -       -      +
     31B  GLN*     2.9    36.8    +      -       -      +
     33B  PHE*     3.7    16.4    -      -       +      -
     44B  VAL*     5.3     0.7    -      -       +      -
     46B  VAL*     3.7    40.4    -      -       +      -
     64B  PHE*     3.5    27.8    -      -       +      -
     95B  ASP*     3.8     8.1    -      -       +      -
     96B  ILE      3.5     1.6    -      -       -      -
     97B  ILE*     3.8    20.0    -      -       +      -
    108B  PHE*     3.7    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