Contacts of the strand formed by residues 109 - 116 (chain N) in PDB entry 5A0Q


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 THR 109 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11N  VAL*     5.6     0.2    -      -       -      +
     53N  ALA*     4.0     0.3    -      -       -      -
     54N  SER      3.2    35.4    +      -       -      +
    107N  TRP      4.0     2.8    +      -       -      -
    108N  ASN*     1.3    75.7    +      -       -      +
    110N  MET*     1.4    59.9    +      -       -      +
    124N  TYR*     3.3    42.2    -      -       +      +
    125N  VAL      3.4     7.6    -      -       -      +
    126N  ASP*     4.2     2.9    +      -       -      -
    127N  MET*     3.7    19.2    +      -       -      +
    139N  THR*     3.8    19.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 110 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43N  MET*     4.3     4.9    -      -       -      -
     51N  LEU*     3.8    24.5    -      -       +      -
     52N  GLY      3.2    12.1    -      -       -      +
     53N  ALA*     3.6    28.3    -      -       +      -
     60N  PHE*     4.3    10.8    -      -       -      -
     63N  LEU*     3.6    35.9    -      -       +      -
     92N  LEU*     3.8    24.2    -      -       +      -
     96N  MET*     4.0    11.2    -      -       +      -
    108N  ASN*     4.2    15.9    -      -       +      +
    109N  THR*     1.4    76.7    -      -       -      +
    111N  VAL*     1.4    61.1    +      -       -      +
    112N  ILE*     4.1     3.5    -      -       -      +
    124N  TYR*     3.5     2.4    -      -       -      -
    125N  VAL*     3.0    33.2    +      -       -      +
    139N  THR*     4.8     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11N  VAL*     4.6    15.7    -      -       +      +
     12N  LEU      5.1     0.2    -      -       -      +
     13N  GLY*     4.4     7.2    -      -       -      +
     22N  ILE*     4.4    15.4    -      -       +      +
     50N  MET      4.0     0.5    -      -       -      +
     51N  LEU*     3.3     3.1    -      -       -      -
     52N  GLY      3.1    27.2    +      -       -      -
    110N  MET*     1.4    71.7    -      -       -      +
    112N  ILE*     1.4    64.3    +      -       -      +
    113N  GLY      4.0     0.8    +      -       -      +
    122N  LEU*     4.2    19.1    -      -       +      -
    123N  GLY      3.4    10.3    -      -       -      +
    124N  TYR*     4.7     2.5    -      -       +      -
    137N  LEU*     3.8    36.8    -      -       +      +
    139N  THR*     3.7    26.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 112 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49N  THR*     5.3     2.7    -      -       -      +
     50N  MET      3.4    18.4    -      -       -      +
     51N  LEU*     3.5    36.6    -      -       +      -
     85N  PRO*     4.5    15.3    -      -       +      +
     88N  ILE*     4.1    13.0    -      -       +      -
     89N  HIS*     3.3    45.1    -      -       +      +
     92N  LEU*     4.0     6.3    -      -       +      -
    110N  MET      4.1     2.9    -      -       -      +
    111N  VAL*     1.4    71.7    -      -       -      +
    113N  GLY*     1.3    57.6    +      -       -      +
    114N  GLY      3.7     0.3    +      -       -      -
    121N  PHE*     3.3    10.7    -      -       -      +
    122N  LEU*     4.3     0.9    -      -       -      -
    123N  GLY      3.0    33.9    +      -       -      +
    125N  VAL*     3.7    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 113 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20N  VAL*     4.2     4.9    -      -       -      -
     22N  ILE*     3.7    21.3    -      -       -      +
     49N  THR*     3.4     1.5    -      -       -      -
     50N  MET*     3.0    38.4    +      -       -      +
    111N  VAL*     4.4     0.2    -      -       -      +
    112N  ILE*     1.3    70.8    -      -       -      +
    114N  GLY*     1.3    57.2    +      -       -      -
    121N  PHE      3.5     6.1    -      -       -      -
    122N  LEU*     4.0    11.7    -      -       -      -
    192N  VAL*     3.7     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 114 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20N  VAL*     4.5     4.0    -      -       -      +
     49N  THR*     3.7    24.7    -      -       -      -
     85N  PRO*     3.5    13.5    -      -       -      +
    112N  ILE      3.7     1.4    +      -       -      -
    113N  GLY*     1.3    74.0    -      -       -      -
    115N  TYR*     1.3    62.5    +      -       -      -
    116N  ALA      3.4     1.9    +      -       -      -
    120N  SER*     4.5     1.6    -      -       -      -
    121N  PHE      3.0    32.3    +      -       -      +
    192N  VAL*     4.6     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 115 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18N  GLY*     4.1    20.0    -      -       -      -
     19N  GLY      4.6     5.4    -      -       -      +
     20N  VAL*     4.8     0.4    -      -       +      +
     48N  SER*     3.5    18.2    +      -       -      +
     49N  THR*     4.9     1.8    -      -       -      +
     85N  PRO*     5.2     0.7    -      -       -      -
    114N  GLY*     1.3    69.7    -      -       -      -
    116N  ALA*     1.3    57.1    -      -       -      +
    117N  ASP      4.2     2.0    +      -       -      -
    118N  GLY*     2.8    48.3    +      -       -      -
    119N  GLU      3.3    14.6    -      -       -      -
    120N  SER*     3.6    16.4    -      -       -      +
    192N  VAL*     3.5    28.0    -      -       +      +
    193N  THR      5.1     0.2    -      -       -      +
    194N  GLU*     3.7    44.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 116 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84N  SER*     5.0     6.5    -      -       -      -
     85N  PRO*     3.6    31.4    -      -       +      -
     86N  ARG*     5.3     4.5    -      -       -      +
    114N  GLY      3.4     0.8    +      -       -      -
    115N  TYR*     1.3    73.7    -      -       -      +
    117N  ASP*     1.4    73.9    +      -       +      +
    118N  GLY      3.4     1.3    -      -       -      -
    119N  GLU*     2.7    32.0    +      -       -      +
----------------------------------------------------------
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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