Contacts of the strand formed by residues 46 - 55 (chain B) in PDB entry 6D6Q


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 LYS 46 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  TYR*     3.0    30.7    -      -       +      +
     40B  ILE      3.4     6.5    -      -       -      -
     41B  GLU*     3.8    17.0    +      -       +      -
     43B  GLY      5.1     0.6    +      -       -      -
     44B  ASN*     3.3    13.4    +      -       -      +
     45B  THR*     1.3    89.5    -      -       -      +
     47B  ALA*     1.3    62.9    +      -       -      +
    126B  VAL*     3.8     1.0    -      -       -      -
    127B  LEU*     2.9    44.2    +      -       +      +
    128B  GLN*     2.6    40.0    +      -       +      +
     41E  VAL*     4.5    22.3    +      -       +      -
     42E  VAL*     5.0     7.9    -      -       +      +
     43E  SER*     5.1     4.8    +      -       -      -
    289E  PHE*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  TYR*     3.3    23.0    -      -       -      -
     40B  ILE*     3.1    32.7    +      -       +      +
     45B  THR*     4.2     2.3    -      -       +      +
     46B  LYS*     1.3    73.8    -      -       -      +
     48B  LEU*     1.3    61.5    +      -       -      +
    124B  VAL*     5.1     0.4    -      -       +      -
    125B  GLN      3.7     5.2    -      -       -      -
    126B  VAL*     4.5     3.8    -      -       +      +
    136B  ALA*     3.8    26.0    -      -       +      +
    137B  CYS*     4.1    19.3    -      -       -      +
    140B  ALA*     4.1     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  VAL*     5.2     1.8    -      -       +      -
     31B  PHE*     3.7    34.5    -      -       +      -
     38B  ALA      3.9    12.3    -      -       -      +
     39B  TYR*     4.2     9.2    -      -       +      +
     47B  ALA*     1.3    78.8    -      -       -      +
     49B  ALA*     1.3    70.3    +      -       -      +
     50B  VAL*     4.1     9.0    -      -       +      -
    123B  TYR      3.9     0.2    -      -       -      +
    124B  VAL*     3.4     4.1    -      -       -      +
    125B  GLN*     2.9    43.4    +      -       +      +
    127B  LEU*     4.5    11.7    -      -       +      -
    140B  ALA*     4.8     1.6    -      -       -      -
     88E  SER*     5.0     4.5    +      -       -      +
    142E  LEU*     4.7    16.8    -      -       +      -
    289E  PHE*     4.0    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  SER*     3.8     1.0    -      -       -      -
     38B  ALA*     3.4    27.2    +      -       +      +
     48B  LEU*     1.3    75.6    -      -       -      +
     50B  VAL*     1.3    74.8    +      -       -      +
    122B  ILE*     5.8     0.2    -      -       +      -
    123B  TYR      3.3     8.5    -      -       -      +
    124B  VAL*     4.6     4.7    -      -       +      +
    140B  ALA*     3.4    39.1    -      -       +      +
    141B  ALA*     3.5    14.6    -      -       +      +
    144B  ALA*     4.0     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  PHE*     4.5    13.7    -      -       +      -
     34B  ALA*     4.0     9.6    -      -       +      -
     36B  GLY      3.5    13.2    -      -       -      +
     37B  SER*     4.6     1.8    -      -       -      +
     48B  LEU*     4.1    11.7    -      -       +      -
     49B  ALA*     1.3    87.5    -      -       -      +
     51B  VAL*     1.3    72.0    +      -       -      +
     52B  TYR*     3.3    38.4    -      -       +      +
    121B  ASP      3.7     0.6    -      -       -      +
    122B  ILE*     3.4     1.0    -      -       -      +
    123B  TYR*     2.9    35.4    +      -       +      +
    144B  ALA*     4.7     0.2    -      -       -      -
     88E  SER*     3.9    28.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ASP*     3.7     4.0    -      -       -      +
     36B  GLY*     3.0    41.1    +      -       -      +
     50B  VAL*     1.3    81.5    -      -       -      +
     52B  TYR*     1.3    65.8    +      -       -      +
     53B  GLY*     3.4     3.5    +      -       -      -
    120B  ILE*     5.5     1.6    -      -       +      -
    121B  ASP      3.2     5.8    -      -       -      +
    122B  ILE*     3.9    26.5    -      -       +      -
    141B  ALA*     4.5     1.3    -      -       -      +
    144B  ALA*     3.6    31.2    -      -       +      +
    145B  VAL*     4.0    14.4    -      -       +      +
    148B  ALA*     3.6    12.1    -      -       +      +
    150B  ILE*     4.9     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  GLN*     4.3     9.1    +      -       -      +
     34B  ALA*     3.9    26.9    -      -       +      +
     35B  ASP*     4.5     6.5    -      -       -      +
     50B  VAL*     3.3    25.4    -      -       +      +
     51B  VAL*     1.3    69.8    -      -       -      +
     53B  GLY*     1.3    70.4    +      -       -      +
     55B  HIS*     3.9    10.0    +      -       +      +
    120B  ILE*     3.9     1.2    -      -       -      +
    121B  ASP*     2.9    39.5    +      -       +      +
    123B  TYR*     3.7    27.8    -      +       -      -
     87E  ALA      4.3     4.7    -      -       -      -
     88E  SER      2.6    27.5    +      -       -      -
     89E  ALA      3.2    13.9    +      -       -      -
     91E  PRO*     4.2    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ASP*     3.3    25.1    +      -       -      -
     51B  VAL      3.4     6.2    +      -       -      -
     52B  TYR*     1.3    78.9    -      -       -      +
     54B  PRO*     1.3    65.3    -      -       -      -
     55B  HIS*     2.6    17.7    +      -       -      -
    119B  GLN      2.6    20.6    -      -       -      +
    120B  ILE*     4.4     2.7    -      -       -      -
    148B  ALA*     5.6     1.1    -      -       -      -
    150B  ILE*     4.5     9.0    -      -       -      -
     75H  ARG*     4.4     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  GLY*     1.3    81.2    -      -       -      +
     55B  HIS*     1.3    58.2    +      -       -      +
    115B  HIS*     4.2    35.2    -      -       +      +
    118B  SER*     4.2    11.2    -      -       -      -
    119B  GLN      3.0    10.8    -      -       -      +
    120B  ILE*     4.0    13.4    -      -       +      -
    148B  ALA      5.7     1.3    -      -       -      +
    150B  ILE*     4.1    22.7    -      -       +      -
     75H  ARG*     3.7    18.2    +      -       +      -
    103H  ARG*     3.0    32.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  TYR*     3.9    14.6    +      -       +      +
     53B  GLY      2.6    28.1    +      -       -      +
     54B  PRO*     1.3    74.8    -      -       -      +
     56B  GLU*     1.3    81.5    +      -       -      +
     58B  ARG*     3.4    23.1    +      -       -      -
    118B  SER*     3.3     8.0    -      -       -      -
    119B  GLN*     3.0    44.9    +      -       -      -
    121B  ASP*     3.0    29.8    +      -       +      -
     91E  PRO*     5.1     6.4    -      -       +      +
     75H  ARG*     4.1    20.4    -      -       -      +
    102H  SER      4.6     1.8    -      -       -      +
    103H  ARG      3.9    11.0    -      -       -      -
----------------------------------------------------------
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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