Contacts of the strand formed by residues 206 - 212 (chain M) in PDB entry 3INU


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 TYR 206 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126M  PRO*     6.3     0.7    -      -       +      -
    140M  LEU*     3.3    32.8    -      -       +      -
    157M  TRP*     4.5     8.5    -      +       +      -
    162M  ASN*     3.6    13.9    -      -       -      -
    166M  LEU*     3.4    28.7    -      -       +      -
    191M  VAL*     5.7     0.2    -      -       +      -
    193M  VAL*     3.6    27.5    -      -       +      +
    194M  PRO*     4.8     1.9    -      -       -      +
    197M  SER*     2.9    35.0    +      -       -      -
    198M  LEU*     4.9     8.5    -      -       +      -
    203M  GLN*     3.6    39.2    +      -       +      -
    205M  THR*     1.3    80.1    -      -       -      +
    207M  ILE*     1.3    64.6    +      -       -      +
    222M  LYS*     3.8     0.5    -      -       -      +
    225M  VAL*     2.9    39.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 207 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157M  TRP*     3.8     4.6    -      -       -      -
    162M  ASN*     2.9    35.5    +      -       -      +
    205M  THR*     5.1     9.0    -      -       +      -
    206M  TYR*     1.3    82.2    -      -       -      +
    208M  CYS*     1.3    61.0    +      -       -      +
    209M  ASN*     3.4     6.1    -      -       -      +
    220M  ASP*     3.2    34.3    -      -       +      +
    221M  LYS      3.0    17.7    -      -       -      +
    222M  LYS*     3.5    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 208 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121M  VAL*     4.3     0.9    -      -       -      -
    142M  CYS*     2.0    55.0    -      -       -      -
    154M  VAL*     4.2     6.1    -      -       +      -
    156M  SER      3.2     7.0    -      -       -      +
    157M  TRP*     3.5    33.1    -      -       +      -
    207M  ILE*     1.3    72.2    -      -       -      +
    209M  ASN*     1.3    61.8    +      -       -      +
    210M  VAL*     3.5    15.0    +      -       -      +
    219M  VAL      3.6     0.3    -      -       -      +
    220M  ASP*     3.5    18.7    -      -       -      -
    221M  LYS      3.3    10.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 209 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153M  THR      3.5     1.7    -      -       -      +
    154M  VAL*     3.4     5.0    -      -       -      -
    156M  SER*     2.6    47.9    +      -       -      +
    162M  ASN*     4.1     0.3    -      -       -      -
    163M  SER*     3.0    42.0    +      -       -      +
    207M  ILE*     3.4    12.4    -      -       -      +
    208M  CYS*     1.3    68.3    -      -       -      +
    210M  VAL*     1.3    61.9    +      -       -      +
    211M  ASN*     5.1     1.4    -      -       -      +
    219M  VAL      3.5     6.5    -      -       -      +
    220M  ASP*     2.8    23.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 210 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119M  PRO*     4.3    11.0    -      -       +      -
    121M  VAL*     4.0    29.4    -      -       +      -
    144M  VAL*     3.5    46.0    -      -       +      -
    152M  VAL*     4.3     8.1    -      -       +      -
    153M  THR      3.4     6.3    -      -       -      +
    154M  VAL*     4.2     9.4    -      -       +      -
    208M  CYS*     3.5    13.4    +      -       -      +
    209M  ASN*     1.3    77.1    -      -       -      +
    211M  ASN*     1.3    63.5    +      -       -      +
    212M  HIS      4.2     0.4    -      -       -      +
    217M  THR*     3.9     1.0    -      -       +      +
    218M  LYS*     3.5     3.3    -      -       -      +
    219M  VAL*     2.8    38.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 211 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151M  PRO      4.5     0.3    -      -       -      +
    152M  VAL*     3.5     5.1    -      -       -      -
    153M  THR*     2.9    54.4    +      -       -      +
    209M  ASN      5.1     2.0    -      -       -      +
    210M  VAL*     1.3    75.5    -      -       -      +
    212M  HIS*     1.3    60.4    +      -       -      +
    213M  LYS*     3.9    32.1    +      -       -      +
    216M  ASN      5.7     0.2    -      -       -      -
    217M  THR      3.1    13.2    +      -       -      +
    218M  LYS*     3.5    30.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 212 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117M  LYS      3.4    21.8    -      -       -      -
    118M  GLY*     3.7     4.6    -      -       -      -
    119M  PRO*     3.6    22.7    -      -       +      -
    147M  TYR*     3.8     4.9    -      +       +      -
    148M  PHE      3.5    11.9    -      -       -      -
    149M  PRO      2.8    23.4    +      -       -      -
    151M  PRO      3.1    25.6    -      -       -      -
    152M  VAL*     3.6    15.7    -      -       +      -
    210M  VAL      4.2     0.4    -      -       -      -
    211M  ASN*     1.3    72.1    +      -       -      +
    213M  LYS*     1.3    62.6    +      -       -      +
    214M  PRO*     3.8    11.7    -      -       +      +
    215M  SER*     2.7    36.4    +      -       -      +
    216M  ASN      3.2     2.6    +      -       -      -
    217M  THR*     2.9    33.1    +      -       -      +
----------------------------------------------------------
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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