Contacts of the strand formed by residues 106 - 114 (chain A) in PDB entry 3MIB


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 106 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ALA*     4.1     6.3    -      -       +      -
    102A  SER      3.2    19.5    +      -       -      +
    103A  MET      4.7     1.6    -      -       -      +
    105A  THR*     1.3    83.4    -      -       +      +
    107A  HIS*     1.3    62.4    +      -       -      +
    108A  HIS      3.7     9.6    -      -       -      +
    109A  MET*     3.7    29.6    -      -       +      -
    141A  TRP*     3.7    21.1    -      -       +      -
    143A  ARG*     3.2    18.7    +      -       -      +
    171A  VAL*     3.9    12.3    -      -       +      -
    172A  HIS      3.7     3.1    -      -       -      +
    173A  TYR*     4.1     3.8    -      -       +      +
    187A  SER*     3.5    32.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  ASP*     6.1     0.2    -      -       -      -
    105A  THR      3.5     2.0    +      -       -      -
    106A  VAL*     1.3    72.3    -      -       -      +
    108A  HIS*     1.3    60.0    +      -       +      +
    141A  TRP*     4.3     0.6    -      -       -      -
    142A  ALA*     4.1     0.5    -      -       -      -
    143A  ARG*     3.2    52.9    +      -       +      +
    144A  ASN*     5.9     3.3    +      -       -      -
    172A  HIS*     2.7    34.7    +      +       +      +
    174A  GLY*     4.2    11.4    -      -       -      +
    271A  PRO*     5.9     8.3    -      -       +      -
    357A   CU      2.0    29.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  TYR*     3.5    16.4    -      +       -      -
    106A  VAL*     3.7     1.6    -      -       -      +
    107A  HIS*     1.3    83.1    -      -       +      +
    109A  MET*     1.3    72.3    +      -       -      +
    110A  LEU*     3.8    27.7    -      -       +      +
    141A  TRP*     3.1    16.8    -      -       -      +
    142A  ALA*     4.4     6.1    -      -       +      -
    170A  GLN*     3.8    18.9    +      -       -      -
    172A  HIS*     2.9    50.0    +      -       +      +
    240A  ARG*     5.3     4.3    +      -       -      -
    272A  GLN      6.1     2.2    -      -       -      +
    357A   CU      2.0    29.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  PRO*     4.0    10.1    -      -       +      -
    101A  ALA*     3.7    28.5    -      -       +      -
    106A  VAL*     3.7    12.8    -      -       +      -
    108A  HIS*     1.3    78.1    -      -       -      +
    110A  LEU*     1.3    67.0    +      -       -      +
    139A  TYR*     4.0     1.7    -      -       +      +
    140A  ALA*     3.4     3.8    -      -       -      -
    141A  TRP*     2.8    63.8    +      -       +      +
    169A  LEU*     4.5     5.6    -      -       +      -
    170A  GLN      3.2     7.6    -      -       -      +
    171A  VAL*     4.1    15.9    -      -       +      -
    187A  SER*     4.6     0.9    -      -       -      -
    188A  GLY*     3.5    42.4    -      -       -      +
    189A  VAL*     4.3     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  HIS*     3.8    16.6    -      -       +      +
    109A  MET*     1.3    84.5    -      -       -      +
    111A  LEU*     1.3    61.5    +      -       -      +
    112A  PHE*     3.7    30.2    -      -       +      -
    137A  ILE*     4.0     7.4    -      -       +      -
    139A  TYR*     3.4     3.6    -      -       -      +
    140A  ALA*     3.5    24.0    -      -       +      -
    168A  VAL      3.7     0.7    -      -       -      +
    169A  LEU*     3.5     6.7    -      -       -      +
    170A  GLN*     2.8    60.1    +      -       +      +
    240A  ARG*     3.7    35.4    -      -       -      +
    272A  GLN      4.9     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  ILE*     3.8    22.4    -      -       +      -
     97A  PHE*     3.7    22.9    -      -       +      -
    110A  LEU*     1.3    74.1    -      -       -      +
    112A  PHE*     1.3    60.5    +      -       -      +
    137A  ILE*     3.7     4.5    -      -       -      +
    138A  LEU*     2.8    33.3    +      -       +      -
    139A  TYR*     2.9    25.5    +      -       +      +
    167A  PHE*     4.0    17.3    -      -       +      -
    168A  VAL      3.4    19.5    -      -       -      +
    169A  LEU*     4.1    14.8    -      -       +      -
    189A  VAL*     4.7     9.6    -      -       +      -
    191A  VAL*     3.7    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  LEU*     3.7    41.7    -      -       +      -
    111A  LEU*     1.3    72.8    -      -       -      +
    113A  GLY*     1.3    61.8    +      -       -      +
    130A  THR*     3.6    30.3    -      -       +      -
    131A  CYS*     4.8     0.9    -      -       -      -
    135A  ALA*     3.6    30.1    -      -       +      -
    136A  ASN      3.2     5.6    -      -       -      +
    137A  ILE*     3.7    34.8    -      -       +      -
    138A  LEU*     4.1     5.2    -      -       -      -
    167A  PHE*     3.3    10.4    -      -       -      +
    168A  VAL*     2.8    47.4    +      -       +      +
    170A  GLN*     4.3    11.4    -      -       +      -
    318A  TYR*     5.5     6.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  PHE*     1.3    74.1    -      -       -      +
    114A  CYS*     1.3    61.7    +      -       -      +
    136A  ASN*     2.7    45.2    +      -       -      +
    138A  LEU*     3.9     9.1    -      -       -      +
    164A  SER*     3.1    18.4    -      -       -      -
    166A  TYR      3.4     8.7    -      -       -      -
    167A  PHE*     4.7     1.6    -      -       -      -
    361A  GOL      3.8     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  GLY*     1.3    74.6    -      -       -      +
    115A  ASN*     1.3    65.4    +      -       -      +
    117A  PRO*     4.0    12.1    -      -       -      -
    131A  CYS*     2.0    48.5    -      -       -      -
    133A  ASP*     3.5    12.3    -      -       -      +
    134A  LYS      3.6    12.3    -      -       -      +
    136A  ASN*     4.9     1.6    -      -       -      +
    164A  SER*     3.3     6.2    +      -       -      -
    165A  LYS      3.4     1.8    +      -       -      -
    166A  TYR*     3.0    35.8    +      -       -      +
    168A  VAL*     3.8    14.6    -      -       -      -
----------------------------------------------------------
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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