Contacts of the strand formed by residues 360 - 366 (chain B) in PDB entry 3EZB


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 VAL 360 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305B  GLU*     4.0    34.1    -      -       +      +
    306B  VAL      3.9     7.9    -      -       -      +
    307B  THR*     3.4    26.7    -      -       +      +
    337B  SER*     5.0     4.2    +      -       -      -
    338B  ASN*     4.8     9.7    +      -       -      +
    358B  GLY      3.3     9.1    +      -       -      +
    359B  THR*     1.3    74.2    -      -       -      +
    361B  VAL*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 361 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305B  GLU*     3.2    23.4    -      -       -      +
    306B  VAL*     3.2    16.3    +      -       +      +
    308B  ILE*     4.2     8.1    -      -       +      -
    335B  VAL*     4.8     7.0    -      -       +      -
    336B  THR      3.8    10.3    -      -       -      +
    337B  SER*     4.2     4.7    -      -       -      -
    355B  LEU*     3.7    31.6    -      -       +      -
    359B  THR*     3.2    20.8    +      -       +      +
    360B  VAL*     1.3    77.1    -      -       -      +
    362B  THR*     1.3    68.3    +      -       -      +
    363B  ILE*     4.8     1.1    -      -       +      -
    381B  MET*     3.4    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 362 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303B  GLN*     4.0    20.9    -      -       +      +
    304B  GLN      3.3    14.4    -      -       -      +
    305B  GLU*     3.3    21.3    +      -       +      +
    335B  VAL*     3.7     4.3    -      -       -      +
    336B  THR*     3.1    44.3    +      -       -      +
    361B  VAL*     1.3    79.5    -      -       -      +
    363B  ILE*     1.3    66.2    +      -       -      +
    364B  SER*     3.7    18.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 363 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303B  GLN*     3.2     3.5    -      -       -      -
    304B  GLN      2.9    29.1    +      -       -      +
    306B  VAL*     4.0    11.9    -      -       +      -
    322B  PHE*     4.4    14.4    -      -       +      -
    333B  ILE*     4.5     9.2    -      -       +      -
    334B  THR      3.9     6.3    -      -       -      +
    335B  VAL*     4.9     4.5    -      -       +      +
    361B  VAL*     4.8     1.8    -      -       +      -
    362B  THR*     1.3    74.3    -      -       -      +
    364B  SER*     1.3    61.1    +      -       -      +
    374B  VAL*     3.8    20.8    -      -       +      +
    377B  LEU*     4.0    50.7    -      -       +      +
    378B  VAL*     4.1     7.2    -      -       +      +
    381B  MET*     3.7    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 364 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  MET*     4.1    21.8    -      -       -      -
    302B  PHE      3.5     4.9    -      -       -      -
    303B  GLN*     3.3    27.0    +      -       -      +
    333B  ILE*     4.2     0.3    -      -       -      +
    334B  THR*     2.8    44.6    +      -       -      -
    336B  THR*     5.0     6.7    +      -       -      -
    362B  THR*     3.7    10.8    +      -       -      +
    363B  ILE*     1.3    73.7    -      -       -      +
    365B  ALA*     1.3    62.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 365 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  MET*     3.8     4.5    -      -       -      +
    302B  PHE*     3.3    22.3    +      -       -      +
    332B  GLU      3.1    17.5    -      -       -      +
    333B  ILE*     3.7    19.5    -      -       +      -
    364B  SER*     1.3    76.9    -      -       -      +
    366B  GLU*     1.3    61.5    +      -       -      +
    370B  GLU*     3.2    33.0    -      -       +      +
    373B  ALA*     4.7     2.0    -      -       +      -
    374B  VAL*     4.2    14.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 366 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  MET*     4.0    36.6    +      -       +      +
    331B  SER*     3.0     7.8    +      -       -      -
    332B  GLU*     3.0    30.7    +      -       +      +
    365B  ALA*     1.3    75.5    -      -       -      +
    367B  GLY*     1.3    61.6    +      -       -      +
    370B  GLU*     3.4    11.4    -      -       -      +
----------------------------------------------------------
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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