Contacts of the strand formed by residues 120 - 124 (chain B) in PDB entry 5T0I


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 HIS 120 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  SER      5.9     2.5    -      -       -      -
     92A  PRO      6.0     0.2    -      -       -      -
     93A  LEU*     3.5    31.9    -      -       +      +
    115B  ILE*     5.3     0.2    -      -       -      -
    116B  ILE*     3.0    40.3    +      -       +      +
    118B  ASP*     3.2    28.1    +      -       +      +
    119B  ASN*     1.3    76.3    -      -       -      +
    121B  ALA*     1.3    59.7    +      -       -      +
    122B  ILE      4.0     0.2    -      -       -      -
    132B  TYR*     3.8    36.8    +      +       +      +
    133B  VAL      3.3     1.6    -      -       -      -
    134B  SER*     2.5    26.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112B  LEU*     4.7     7.9    -      -       +      -
    114B  GLU      3.8     4.0    -      -       -      +
    115B  ILE*     4.3    23.3    -      -       +      +
    119B  ASN      4.5     2.5    -      -       -      +
    120B  HIS*     1.3    71.4    -      -       -      +
    122B  ILE*     1.3    64.2    +      -       -      +
    123B  VAL*     3.4     6.5    +      -       +      +
    133B  VAL*     2.5    45.8    +      -       +      +
    135B  ILE*     6.1     1.8    -      -       +      -
    159B  VAL*     5.6     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  THR*     5.5     3.8    -      -       +      -
    153A  LEU*     5.2    10.3    -      -       +      -
    155A  PRO*     5.2     4.3    -      -       +      -
    112B  LEU*     3.4     4.5    -      -       -      +
    113B  GLU*     3.1    35.8    +      -       -      +
    114B  GLU*     2.7    65.6    +      -       +      +
    116B  ILE*     3.8    24.0    -      -       +      -
    120B  HIS      3.9     0.4    +      -       -      -
    121B  ALA*     1.3    69.9    -      -       -      +
    123B  VAL*     1.3    63.0    +      -       -      +
    130B  GLU*     4.2    11.4    -      -       +      -
    131B  HIS      3.2    17.0    -      -       -      +
    132B  TYR*     3.8    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  THR      3.4    12.3    -      -       -      +
    112B  LEU*     3.7    20.0    -      -       +      -
    113B  GLU*     4.0     1.3    -      -       -      +
    121B  ALA*     3.4     9.8    +      -       +      +
    122B  ILE*     1.3    77.2    -      -       -      +
    124B  SER*     1.3    64.2    +      -       -      +
    129B  SER      3.5     0.5    -      -       -      +
    130B  GLU*     3.3    24.9    -      -       -      +
    131B  HIS*     3.7     9.3    +      -       +      -
    133B  VAL*     3.7    24.9    -      -       +      -
    150B  VAL*     4.8     5.8    -      -       +      -
    152B  LEU*     3.7    38.6    -      -       +      -
    159B  VAL*     5.1     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  THR*     2.2    51.9    +      -       -      -
    112B  LEU      5.4     0.7    -      -       -      -
    113B  GLU*     2.4    39.0    +      -       -      +
    123B  VAL*     1.3    72.5    +      -       -      +
    125B  THR*     1.3    59.7    +      -       -      +
    128B  GLY*     6.4     0.2    -      -       -      -
    129B  SER      3.3     9.9    -      -       -      -
    130B  GLU*     3.9     7.0    +      -       -      +
----------------------------------------------------------
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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