Contacts of the strand formed by residues 45 - 54 (chain B) in PDB entry 6MZL


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 45 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ILE*     3.7    32.5    -      -       +      -
     36B  ASN      4.2     3.4    -      -       -      -
     37B  ASN      4.4     0.9    -      -       -      -
     38B  ILE*     3.7    26.9    -      -       +      -
     44B  SER*     1.3    86.5    +      -       -      +
     46B  VAL*     1.3    71.0    -      -       -      +
    151B  SER*     3.3     2.6    -      -       -      -
    152B  LEU*     2.8    54.5    +      -       +      +
    153B  ASP      4.3     0.4    +      -       -      -
    159B  LEU*     5.3     5.8    -      -       +      -
    161B  PHE*     4.3    14.1    -      -       +      -
    189B  TRP*     5.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ILE*     3.7     4.5    -      -       -      -
     36B  ASN*     2.8    47.8    +      -       +      +
     37B  ASN*     3.6    31.2    +      -       +      +
     44B  SER*     5.0     4.0    -      -       -      +
     45B  VAL*     1.3    84.5    -      -       -      +
     47B  GLY*     1.3    59.8    +      -       -      +
     73B  TYR*     4.7    11.2    -      -       +      +
    149B  ASN*     5.3     2.9    -      -       -      +
    150B  PHE*     3.7     8.1    -      -       -      +
    151B  SER*     3.9    14.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  VAL*     6.3     0.9    -      -       -      -
     34B  CYS      3.2    15.3    -      -       -      -
     35B  ILE*     4.7     0.4    -      -       -      -
     36B  ASN*     4.6     1.8    -      -       -      -
     45B  VAL*     5.7     0.2    -      -       -      -
     46B  VAL*     1.3    78.5    -      -       -      +
     48B  PHE*     1.3    63.0    +      -       -      -
    149B  ASN*     3.4     5.3    +      -       -      +
    150B  PHE*     2.8    51.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  VAL*     3.9    10.0    -      -       +      +
     33B  VAL*     4.0     0.9    -      -       -      +
     34B  CYS*     3.4    55.7    +      -       +      -
     36B  ASN*     3.8    11.9    -      -       -      -
     47B  GLY*     1.3    75.2    -      -       -      +
     49B  VAL*     1.3    59.8    +      -       -      +
     50B  GLU*     4.5    13.0    -      -       +      -
    147B  HIS*     3.4    34.3    -      +       +      +
    148B  ILE      2.9    12.8    -      -       -      +
    149B  ASN*     4.3     6.7    -      -       +      +
    150B  PHE*     3.9     2.7    -      -       -      -
    205B  GLU*     4.5     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  GLN*     3.3    32.3    -      -       +      +
     32B  VAL      3.3    15.3    -      -       -      +
     33B  VAL*     5.0     3.4    -      -       +      -
     48B  PHE*     1.3    74.9    -      -       -      +
     50B  GLU*     1.3    65.9    +      -       -      +
     51B  LEU*     3.7    17.3    -      -       +      -
    146B  ILE      3.2     0.3    -      -       -      +
    147B  HIS*     3.2     4.9    +      -       -      -
    148B  ILE*     2.8    51.8    +      -       +      -
    150B  PHE*     3.5    24.0    -      -       +      -
    190B  PHE*     4.6     8.5    -      -       +      -
    191B  PRO*     5.1     8.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  GLN*     3.3     9.5    -      -       -      +
     32B  VAL*     3.1    43.3    +      -       +      +
     48B  PHE*     4.5    11.8    -      -       +      -
     49B  VAL*     1.3    79.7    -      -       -      +
     51B  LEU*     1.3    62.3    +      -       -      +
     52B  THR*     5.2     1.1    +      -       -      -
     76B  ARG*     4.6     3.8    +      -       -      -
    145B  LYS*     5.9     5.8    -      -       +      +
    146B  ILE      2.6    13.0    -      -       -      +
    147B  HIS*     2.9    35.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  LEU*     5.5    15.5    -      -       +      -
     30B  HIS      3.7     4.3    -      -       -      +
     31B  GLN*     4.2    15.0    -      -       +      +
     49B  VAL*     3.7    33.0    -      -       +      -
     50B  GLU*     1.3    80.3    -      -       -      +
     52B  THR*     1.3    64.8    +      -       -      +
     53B  ILE*     4.0     1.3    -      -       +      -
     65B  LEU*     3.7    37.9    -      -       +      -
    144B  LEU      3.6     0.7    -      -       -      +
    145B  LYS*     3.1    10.6    -      -       -      +
    146B  ILE*     2.8    59.4    +      -       +      +
    148B  ILE*     4.9     0.9    -      -       +      -
    192B  CYS*     6.0     0.2    -      -       -      -
    193B  VAL*     6.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  LEU*     3.6     5.9    -      -       -      +
     29B  THR*     3.0    49.3    +      -       +      +
     30B  HIS*     3.0    33.0    +      -       +      +
     50B  GLU      5.2     0.9    +      -       -      -
     51B  LEU*     1.3    74.3    +      -       -      +
     53B  ILE*     1.3    60.7    +      -       -      +
     54B  PHE*     5.4     9.2    -      -       +      -
    143B  VAL*     5.9     3.1    -      -       +      -
    144B  LEU      3.6     6.5    -      -       -      +
    145B  LYS*     4.9    10.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  TYR*     3.6    28.7    -      -       +      -
     27B  LYS      3.7     4.7    -      -       -      +
     28B  LEU*     3.6    21.1    -      -       +      -
     51B  LEU*     4.7     1.3    -      -       +      +
     52B  THR*     1.3    74.9    -      -       -      +
     54B  PHE*     1.3    71.4    +      -       -      +
     55B  PRO*     3.4    22.0    -      -       +      +
     63B  ILE*     4.9    17.3    -      -       +      -
     65B  LEU*     6.6     0.2    -      -       +      -
    144B  LEU*     2.9    58.0    +      -       +      +
    146B  ILE*     4.1    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  LYS*     2.8    48.0    +      -       +      +
     28B  LEU*     4.8     0.2    -      -       -      +
     29B  THR*     4.3    25.5    -      -       +      +
     52B  THR*     4.3     8.5    +      -       +      -
     53B  ILE*     1.3    80.4    -      -       -      +
     55B  PRO*     1.3    68.1    -      -       -      +
    142B  LYS      3.3     5.2    -      -       -      +
    143B  VAL*     3.5    39.7    -      -       +      -
    488B  PHE*     4.8    12.6    -      +       -      -
    490B  SER*     4.7    15.0    -      -       -      -
----------------------------------------------------------
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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