Contacts of the strand formed by residues 45 - 54 (chain G) in PDB entry 3ZWG


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 TRP 45 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37G  ILE*     3.4    27.4    -      -       +      -
     38G  ASP      3.8     0.2    -      -       -      -
     39G  ASN*     3.0    44.9    -      -       +      -
     41G  SER*     2.8    18.0    +      -       -      -
     43G  LYS      3.5     3.8    -      -       -      -
     44G  THR*     1.3    75.9    -      -       -      +
     46G  THR*     1.3    66.3    +      -       -      +
     63G  HIS      3.7     0.3    -      -       -      +
     64G  LYS*     3.6     6.1    -      -       -      +
     65G  VAL*     2.8    48.8    +      -       +      +
     71G  LEU*     4.5    11.2    -      -       +      -
     92G  TYR*     3.9    19.1    -      +       +      -
     93G  SER      3.3     5.2    -      -       -      +
     94G  MET*     3.8    25.2    -      -       +      +
    100G  LEU*     3.4    30.5    -      -       +      -
    176G  VAL*     3.6    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 46 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44G  THR*     4.3     5.2    +      -       -      +
     45G  TRP*     1.3    76.0    -      -       -      +
     47G  ALA*     1.3    66.4    +      -       -      +
     63G  HIS*     3.2    32.3    -      -       +      +
     64G  LYS*     3.1    33.1    +      -       -      +
     92G  TYR*     3.3     4.2    -      -       -      -
     93G  SER*     2.7    54.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 47 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46G  THR*     1.3    75.4    -      -       -      +
     48G  MET*     1.3    62.3    +      -       -      +
     61G  LEU*     3.6    27.8    -      -       +      +
     62G  PRO      3.5    11.7    -      -       -      +
     63G  HIS*     2.9    31.3    +      -       -      +
     92G  TYR*     3.2    27.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 48 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46G  THR      3.6     0.2    +      -       -      -
     47G  ALA*     1.3    79.6    -      -       -      +
     49G  ASN*     1.3    71.7    +      -       -      +
     61G  LEU*     4.5     2.1    -      -       -      +
     91G  ALA*     2.9    15.3    +      -       +      +
     92G  TYR      3.6     5.8    -      -       -      -
     93G  SER*     3.5    37.5    -      -       -      +
     99G  THR*     3.6    18.4    -      -       +      +
    125G  GLN*     4.3    17.0    -      -       -      +
    126G  LYS      3.4    32.8    -      -       -      +
    127G  ARG*     3.7    28.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 49 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48G  MET*     1.3    84.9    -      -       -      +
     50G  THR*     1.3    79.6    +      -       -      +
     51G  TYR*     3.9     1.4    -      -       -      +
     61G  LEU*     3.7    11.9    -      -       -      +
     89G  VAL      3.8     0.7    -      -       -      +
     90G  ILE*     3.6     1.4    -      -       -      -
     91G  ALA*     2.9    30.3    +      -       -      +
    127G  ARG*     3.5    32.0    -      -       -      +
    128G  ALA*     3.0    44.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 50 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49G  ASN*     1.3    85.7    +      -       -      +
     51G  TYR*     1.3    66.9    +      -       -      +
     52G  PHE*     3.4    39.9    +      -       +      -
     61G  LEU*     3.9    11.1    -      -       -      +
     73G  TYR*     3.0    31.5    +      -       +      +
     89G  VAL      3.2    17.0    -      -       -      +
     90G  ILE*     4.0     9.1    -      -       +      +
    104G  PHE*     4.5     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 51 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49G  ASN*     3.9     3.4    -      -       -      +
     50G  THR*     1.3    73.8    -      -       -      +
     52G  PHE*     1.3    68.5    +      -       -      +
     53G  ARG*     4.0    22.6    -      -       +      -
     88G  GLY*     3.1     5.5    -      -       -      -
     89G  VAL*     2.8    38.0    +      -       +      +
    128G  ALA*     3.6    27.1    -      -       +      +
    129G  ASP*     3.7    20.0    -      -       -      -
    130G  GLN*     2.7    52.5    +      -       +      +
    133G  TYR*     4.1    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 52 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50G  THR*     3.4    32.6    +      -       +      -
     51G  TYR*     1.3    83.7    -      -       -      +
     53G  ARG*     1.3    63.4    +      -       -      +
     54G  SER      3.7    13.5    -      -       -      +
     55G  GLY      3.2    28.4    -      -       -      +
     56G  THR*     3.8    13.5    -      -       -      -
     57G  SER*     3.7    31.4    -      -       -      -
     73G  TYR*     3.9    14.4    -      +       -      -
     75G  GLY*     4.6     3.1    -      -       -      -
     86G  VAL*     4.1    10.5    -      -       +      -
     87G  VAL      3.7     5.2    -      -       -      -
    104G  PHE*     3.9    20.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 53 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51G  TYR*     3.6    21.2    +      -       +      -
     52G  PHE*     1.3    73.3    -      -       -      +
     54G  SER*     1.3    72.9    +      -       -      +
     87G  VAL*     2.8    25.2    +      -       +      +
     88G  GLY      5.0     0.2    -      -       -      +
    130G  GLN*     3.5    31.0    +      -       -      +
    133G  TYR*     3.8    33.1    +      -       +      +
    138G  TYR*     5.5     3.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 54 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52G  PHE*     3.7     5.7    -      -       -      -
     53G  ARG*     1.3    94.2    +      -       -      +
     55G  GLY*     1.3    63.6    +      -       -      +
     78G  ASN*     4.5     1.8    -      -       -      -
     84G  THR*     4.4    17.6    -      -       -      +
     85G  GLY      3.4    22.8    +      -       -      -
     86G  VAL*     3.2     2.4    -      -       -      -
     87G  VAL*     2.8    37.1    +      -       -      +
----------------------------------------------------------
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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