Contacts of the strand formed by residues 39 - 48 (chain E) in PDB entry 2Z7F


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 GLY 39 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34E  GLN*     3.2     4.8    -      -       -      +
     35E  LEU*     2.9    34.2    +      -       -      +
     36E  ARG      3.2     2.5    +      -       -      -
     38E  GLY*     1.3    78.6    -      -       -      +
     40E  HIS*     1.3    67.5    +      -       -      -
     41E  PHE*     3.4     2.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 40 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  MET*     5.6     0.2    -      -       +      -
     32E  SER*     2.8    22.3    +      -       -      +
     33E  LEU      3.5     6.1    -      -       -      -
     34E  GLN*     3.9     9.0    -      -       -      +
     39E  GLY*     1.3    73.0    -      -       -      -
     41E  PHE*     1.3    62.0    +      -       -      +
     42E  CYS      3.2    30.1    +      -       -      -
     43E  GLY*     3.8     4.3    -      -       -      -
     73E  LEU*     3.5    25.6    -      -       +      +
    141E  TRP*     3.9    37.9    -      +       +      +
    151E  ILE*     4.8    10.6    -      -       +      +
    193E  GLY*     2.9    30.6    +      -       -      -
     74I  LEU*     4.2    12.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 41 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33E  LEU*     2.9    52.5    +      -       +      -
     34E  GLN      3.6     4.3    -      -       -      -
     35E  LEU*     3.6    45.3    -      -       +      -
     39E  GLY      4.4     1.8    -      -       -      +
     40E  HIS*     1.3    81.1    -      -       -      +
     42E  CYS*     1.3    83.9    +      -       +      +
     58E  CYS*     3.3    27.1    -      -       +      -
     59E  VAL*     4.5     1.8    -      -       +      -
     62E  VAL*     4.4     3.6    -      -       +      -
     65E  VAL*     4.0    22.0    -      -       +      -
    193E  GLY*     4.6    10.0    -      -       -      -
     73I  MET*     3.9    24.6    -      -       +      +
     74I  LEU*     5.0     6.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 42 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33E  LEU*     2.8    35.8    +      -       +      +
     40E  HIS*     3.2    15.7    +      -       -      -
     41E  PHE*     1.3   100.9    -      -       +      +
     43E  GLY*     1.3    60.5    +      -       -      +
     58E  CYS*     2.1    56.8    -      -       +      -
    193E  GLY      4.3     1.8    -      -       -      -
    195E  SER*     3.5    15.5    -      -       -      +
     73I  MET*     4.1     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 43 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  MET*     4.1     4.9    -      -       -      -
     31E  VAL      3.3    10.3    -      -       -      -
     33E  LEU*     4.0     0.7    -      -       -      +
     40E  HIS*     3.8     6.8    +      -       -      -
     42E  CYS*     1.3    76.9    -      -       -      +
     44E  ALA*     1.3    57.3    +      -       -      +
     54E  SER*     2.8    27.2    +      -       -      -
    193E  GLY      4.3     0.6    +      -       -      -
    195E  SER      2.8    10.3    +      -       -      -
    196E  GLY*     3.2    10.6    -      -       -      +
    197E  SER*     3.6    19.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 44 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29E  PHE      3.9     0.7    -      -       -      +
     30E  MET*     4.0     0.2    -      -       -      +
     31E  VAL*     3.0    48.0    +      -       +      -
     33E  LEU*     4.0    12.8    -      -       +      -
     43E  GLY*     1.3    76.3    -      -       -      +
     45E  THR*     1.3    65.8    +      -       -      +
     52E  VAL*     4.3     8.3    -      -       +      -
     53E  MET      3.3    15.7    -      -       -      +
     54E  SER*     3.9     8.7    -      -       -      -
    196E  GLY      3.4     6.8    +      -       -      -
    197E  SER*     4.4     0.8    -      -       -      +
    198E  PRO*     3.9     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 45 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29E  PHE*     3.4    15.9    -      -       +      -
     31E  VAL*     4.0     3.1    -      -       -      -
     44E  ALA*     1.3    74.7    -      -       -      +
     46E  LEU*     1.3    65.2    +      -       -      +
     47E  ILE*     3.4     8.9    +      -       +      +
     52E  VAL*     3.2     4.1    -      -       -      -
     53E  MET*     2.9    47.9    +      -       +      +
    121E  ALA*     3.5    31.2    -      -       +      -
    196E  GLY      4.7     1.2    +      -       -      -
    198E  PRO*     3.2    28.1    -      -       -      +
    209E  ILE*     4.1    11.0    -      -       +      +
    212E  ILE*     5.7     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 46 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28E  PRO      4.9     1.1    -      -       -      +
     29E  PHE*     2.9    19.4    +      -       -      +
     31E  VAL*     3.6     7.4    -      -       +      +
     45E  THR*     1.3    69.4    -      -       -      +
     47E  ILE*     1.3    59.5    +      -       -      +
     48E  ALA      3.1    26.0    -      -       -      +
     49E  PRO      4.2     7.4    -      -       -      +
     51E  PHE      3.6     8.7    -      -       -      +
     52E  VAL*     3.8    14.4    -      -       +      -
     68E  LEU*     4.1    19.1    -      -       +      -
    108E  LEU*     4.4     2.9    -      -       +      -
    112E  ALA*     4.5     5.4    -      -       +      -
    114E  ILE*     4.6     2.2    -      -       +      -
    118E  VAL*     3.6    31.4    -      -       +      -
    119E  GLN      3.6    22.9    -      -       -      +
    120E  VAL*     3.6     6.0    -      -       +      +
    121E  ALA*     2.8    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 47 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45E  THR*     3.4     9.2    +      -       +      +
     46E  LEU*     1.3    78.4    -      -       -      +
     48E  ALA*     1.3    60.3    +      -       -      +
     51E  PHE*     3.0    28.1    +      -       +      +
     52E  VAL      4.3     3.1    -      -       -      -
     53E  MET*     3.7    50.0    -      -       +      +
    105E  ILE*     4.4     8.3    -      -       +      -
    120E  VAL*     3.2    19.8    -      -       -      +
    121E  ALA*     4.5     4.5    -      -       +      +
    123E  LEU*     4.3    16.8    -      -       +      +
    238E  ILE*     3.7    27.8    -      -       +      -
    242E  ILE*     3.7    28.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 48 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46E  LEU*     3.1    19.8    -      -       -      +
     47E  ILE*     1.3    77.1    -      -       -      +
     49E  PRO*     1.4    76.7    -      -       +      +
     50E  ASN*     3.0     4.7    +      -       -      +
     51E  PHE*     3.2    34.2    +      -       +      +
    120E  VAL*     3.7    11.9    -      -       -      +
    242E  ILE*     4.6    13.9    -      -       +      +
----------------------------------------------------------
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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