Contacts of the strand formed by residues 107 - 112 (chain E) in PDB entry 4V1M


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 107 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26E  ARG*     5.5     8.3    -      -       -      +
     28E  TYR*     3.2    22.7    +      -       -      +
     77E  SER      3.4     3.4    +      -       -      +
     78E  LEU*     3.4    23.2    -      -       -      +
     79E  TRP*     3.1    20.8    +      -       -      +
    100E  ILE*     5.1     2.9    -      -       -      -
    105E  PHE*     4.1     8.2    -      -       -      +
    106E  GLN*     1.4    88.1    +      -       +      +
    108E  GLY*     1.3    58.9    +      -       -      +
    131E  THR*     3.4    29.6    -      -       -      +
    133E  GLU*     5.8     5.2    -      -       +      +
    191E  LYS*     4.7    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 108 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78E  LEU*     4.4     0.7    -      -       -      -
     79E  TRP      3.2     9.2    -      -       -      -
     96E  PHE*     4.0     4.9    -      -       -      -
    100E  ILE*     4.2    18.8    -      -       -      +
    107E  THR*     1.3    76.9    -      -       -      +
    109E  ILE*     1.3    58.2    +      -       -      -
    131E  THR      2.9    12.0    +      -       -      -
    132E  ILE*     3.3     8.6    -      -       -      +
    133E  GLU*     2.8    32.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 109 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19E  VAL*     5.6     1.8    -      -       +      -
     22E  MET*     3.7    24.7    -      -       +      -
     23E  VAL*     4.6     4.3    -      -       +      -
     26E  ARG*     4.6     3.6    -      -       -      +
     78E  LEU*     3.6    35.0    -      -       +      -
     79E  TRP      2.8     9.1    +      -       -      +
     80E  VAL*     3.5    18.5    -      -       +      +
     81E  GLU      2.8    31.9    +      -       -      +
     96E  PHE*     3.9     4.4    -      -       -      -
    107E  THR*     6.1     0.2    -      -       -      -
    108E  GLY*     1.3    74.4    -      -       -      -
    110E  PHE*     1.3    57.9    +      -       -      +
    111E  VAL*     4.0    19.6    +      -       +      -
    133E  GLU*     3.4    23.1    -      -       +      +
    135E  PHE*     3.7    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 110 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81E  GLU*     3.3    31.9    -      -       +      -
     82E  PHE      4.4     1.6    -      -       -      -
     83E  CYS*     3.7    26.9    -      -       +      -
     88E  VAL*     3.6    39.5    -      -       +      -
     92E  THR*     4.9     7.0    -      -       +      -
     93E  MET*     4.6     8.1    -      -       +      -
     96E  PHE*     3.7    39.7    -      +       +      -
    109E  ILE*     1.3    71.4    -      -       -      +
    111E  VAL*     1.3    70.8    +      -       -      +
    112E  TYR*     3.4     5.2    +      -       +      -
    116E  ILE*     3.7    21.3    -      -       +      -
    132E  ILE*     5.3     0.7    -      -       +      -
    133E  GLU      2.7    15.6    +      -       -      +
    134E  THR*     3.7     6.5    -      -       +      -
    135E  PHE      3.1    21.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15E  ALA*     6.1     0.4    -      -       +      -
     19E  VAL*     4.5     4.0    -      -       +      -
     80E  VAL*     4.5     7.6    -      -       +      -
     81E  GLU      2.9    11.0    +      -       -      +
     82E  PHE*     3.5    58.6    -      -       +      +
     83E  CYS      3.6     7.8    +      -       -      +
    109E  ILE*     4.1    17.9    -      -       +      -
    110E  PHE*     1.3    74.1    -      -       -      +
    112E  TYR*     1.4    58.0    +      -       -      +
    113E  GLN      4.4     0.3    +      -       -      -
    135E  PHE*     3.3     7.6    -      -       +      +
    137E  GLU*     3.8    34.2    -      -       +      +
    140E  LEU*     3.9    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 112 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83E  CYS*     5.4     1.1    -      -       -      -
     88E  VAL*     4.1    14.8    -      -       +      -
    110E  PHE*     3.7     8.1    -      -       +      -
    111E  VAL*     1.4    73.0    -      -       -      +
    113E  GLN*     1.3    62.6    +      -       -      +
    114E  ASN      3.5    10.1    -      -       -      -
    115E  ASN*     3.6    26.9    -      -       -      +
    116E  ILE*     3.6    36.1    -      -       +      -
    121E  MET*     5.3     6.9    -      -       +      +
    134E  THR*     4.1    12.6    +      -       -      -
    135E  PHE      3.2    16.9    +      -       -      -
    136E  ASN*     3.3    49.9    +      -       +      +
    137E  GLU*     3.0    25.3    +      -       -      -
----------------------------------------------------------
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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